{"gene":"COL4A5","run_date":"2026-06-09T22:57:19","timeline":{"discoveries":[{"year":1990,"finding":"Mutations (intragenic deletion, Pst I site variant, uncharacterized abnormality) in COL4A5 were identified as causative for X-linked Alport syndrome, establishing that the alpha5(IV) collagen chain encoded by COL4A5 is a structural component of the glomerular basement membrane whose disruption causes nephritis and deafness.","method":"Southern blotting, restriction fragment analysis, direct genomic analysis in Alport syndrome kindreds","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct mutation identification in multiple kindreds, replicated by many subsequent studies across multiple labs","pmids":["2349482"],"is_preprint":false},{"year":1992,"finding":"Deletions in the 5' end of COL4A5 extending beyond its 5' end are associated with Alport syndrome plus diffuse leiomyomatosis (DL), suggesting a contiguous gene deletion syndrome involving COL4A5 and an adjacent gene (later identified as COL4A6) responsible for smooth muscle proliferation.","method":"Southern blotting with cDNA probes spanning COL4A5 and 5' end genomic probe in patients with DL-AS association","journal":"Kidney international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Southern blot in three patients, single lab, consistent with later work on COL4A5/COL4A6 deletions","pmids":["1453602"],"is_preprint":false},{"year":1994,"finding":"COL4A5 and COL4A6 genes are arranged head-to-head on chromosome Xq22 and share a bidirectional promoter region; COL4A6 is transcribed from two alternative promoters in a tissue-specific manner, with transcription start sites 442 bp and 1,492 bp from the COL4A5 transcription start site.","method":"Genomic sequencing, RT-PCR of tissue-specific transcripts, characterization of 5' flanking sequences","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct sequencing and RT-PCR in multiple tissues, replicated by subsequent promoter studies","pmids":["7972123"],"is_preprint":false},{"year":1994,"finding":"The COL4A5 gene contains 51 exons spanning ~140 kb of DNA, with exon size and distribution pattern highly homologous to COL4A1; the complete exon structure was determined from genomic lambda phage clones.","method":"Genomic cloning and sequencing of 17 lambda phage clones covering the COL4A5 gene","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct genomic sequencing of entire gene structure, foundational reference","pmids":["8120014"],"is_preprint":false},{"year":1994,"finding":"COL4A5 gene deletion in an Alport patient leads to absence of alpha5(IV) chain in the glomerular basement membrane and production of post-transplant alloantibodies directed against the alpha3(IV) chain (not alpha5(IV)), establishing that COL4A5 mutations cause defective assembly of the alpha3(IV) chain into the GBM network.","method":"Circulating antibody binding assay to GBM constituents, recombinant NC1 domains of human type IV collagen chains, COL4A5 gene deletion analysis","journal":"Kidney international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding experiments with recombinant proteins, single lab, single patient","pmids":["8196274"],"is_preprint":false},{"year":1994,"finding":"Splice site mutations in COL4A5 cause aberrant mRNA splicing including use of cryptic splice sites within exons, exon skipping, and incorporation of frameshift mutations leading to premature stop codons; female carriers show variable stability of mutated mRNA relative to normal transcript.","method":"RT-PCR and mRNA analysis of COL4A5 splice site mutations in patients and carriers","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct mRNA analysis in patients, single lab, multiple mutations analyzed","pmids":["8004101"],"is_preprint":false},{"year":1993,"finding":"COL4A5 mRNA undergoes differential tissue-specific splicing: an 18 bp sequence (encoding two Gly-X-Y triplets) is present between exons 10 and 11 in kidney mRNA but absent in white blood cell mRNA, indicating a kidney-specific additional exon. A complex mutation deleting part of the triple helical domain and the entire NC1 domain was identified in an Alport patient.","method":"RT-PCR of COL4A5 cDNA from lymphoblasts and kidney tissue, direct sequencing","journal":"Kidney international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct comparison of tissue-specific mRNA, single lab","pmids":["8301933"],"is_preprint":false},{"year":1995,"finding":"The alpha5(IV) and alpha6(IV) chains encoded by COL4A5 and COL4A6 show distinct tissue-specific distribution: alpha5(IV) is present in glomerular basement membrane but alpha6(IV) is absent there, whereas both are co-localized in skin, smooth muscle cells, and adipocyte basement membranes. In Bowman's capsule and distal tubules, alpha6(IV) is present but its pattern differs from alpha5(IV).","method":"Immunofluorescence with peptide-specific rat monoclonal antibodies against NC1 domains of alpha5(IV) and alpha6(IV); Western blotting","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal antibody-based localization in multiple tissues, Western blot validation, replicated by subsequent studies","pmids":["7657706"],"is_preprint":false},{"year":1996,"finding":"The type and severity of COL4A5 mutation determines the immunohistochemical expression pattern of alpha3(IV)-alpha5(IV) collagen chains in the glomerular basement membrane: deletional and splice site mutations cause complete absence of alpha3(IV)-alpha5(IV) chains, while glycine missense substitutions generally permit residual antigenicity of these chains, demonstrating that alpha5(IV) chain integrity is required for the assembly of the alpha3/alpha4/alpha5 network.","method":"Immunohistochemistry with monoclonal antibody series recognizing alpha1(IV)-alpha6(IV) chains in kidney biopsies from patients with identified COL4A5 mutations","journal":"Kidney international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct correlation of mutation type with protein expression in tissues, single center, 9 patients","pmids":["8807602"],"is_preprint":false},{"year":1998,"finding":"Deletions at the 5' end of COL4A5 extending into COL4A6 in diffuse leiomyomatosis/Alport syndrome involve breakpoints with topoisomerase I and II consensus sequences; immunohistochemical analysis confirms absence of alpha5(IV) and alpha6(IV) chains in most basement membranes of the smooth muscle tumor, with mosaic staining in one patient indicating somatic mosaicism.","method":"Characterization of deletion breakpoints by sequencing; immunohistochemistry with alpha-chain-specific monoclonal antibodies","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct breakpoint sequencing and immunostaining, single lab","pmids":["9463311"],"is_preprint":false},{"year":2000,"finding":"The proximal bidirectional promoter between COL4A5 and COL4A6 contains minimal promoters within 100 bp of each transcription start site that are functionally distinct; a bidirectional positive regulatory element functions in multiple cell types but not in glomerular visceral epithelial cells (which selectively transcribe COL4A5). The intergenic region is 292 bp.","method":"RNase protection assays for transcription start site mapping; transient transfections with reporter gene constructs; gel shift and footprinting assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — multiple orthogonal methods (reporter assay, footprinting, gel shift) in defined cell types, single lab","pmids":["11096082"],"is_preprint":false},{"year":2005,"finding":"The bifunctional promoter between COL4A5 and COL4A6 regulates their expression in a cell-specific manner: in glomerular endothelial and mesangial cells, TGF-beta, EGF, VEGF, and PDGF enhance alpha5(IV) expression but not alpha6(IV); in tubular epithelial cells, the same growth factors enhance alpha6(IV) but not alpha5(IV) expression.","method":"Reporter gene constructs with bidirectional promoter, transient transfection in cell-type-specific lines, growth factor stimulation assays","journal":"The Biochemical journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reporter assay in multiple relevant cell types, single lab","pmids":["15598179"],"is_preprint":false},{"year":2004,"finding":"A large tandem duplication of 35 COL4A5 exons (~65% increase in collagenous domain length) causes Alport syndrome with a founder effect in French Polynesia; the duplicated alpha5(IV) chain can still assemble into the type IV collagen network as demonstrated by immunofluorescence, yet uniformly produces thin GBM in males and variable severity of renal disease.","method":"Linkage analysis, mutation screening, immunofluorescence analysis of type IV collagen assembly","journal":"Kidney international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct immunofluorescence demonstrating assembly of duplicated chain, single population study","pmids":["15149316"],"is_preprint":false},{"year":2006,"finding":"Chromosomal translocation t(X;6)(q13-14;q22) in subungual exostosis rearranges both COL4A5 (at Xq22) and COL12A1 (at 6q13-14), with FISH showing these two collagen genes consistently co-localizing on derivative chromosomes, suggesting formation of a chimeric fusion gene or regulatory sequence exchange.","method":"Interphase and metaphase FISH on tumor cells from five subungual exostoses","journal":"International journal of cancer","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — FISH in five cases showing consistent gene rearrangement, single lab, functional consequence not yet determined","pmids":["16284948"],"is_preprint":false},{"year":2017,"finding":"Contiguous deletions at the 5' ends of COL4A5 and COL4A6 that cause Alport syndrome-diffuse leiomyomatosis involve the bidirectional promoter region shared by both genes; eight of nine deletion alleles involve sequences homologous between COL4A5 and COL4A6, with breakpoints in transposed elements (LINEs, SINEs, DNA transposons, LTR retrotransposons), indicating homologous recombination as the mutational mechanism. Leiomyomatosis requires inactivation of both genes.","method":"Breakpoint characterization by sequencing in five AS-DL patients; analysis of repetitive element content at breakpoints","journal":"Journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct breakpoint sequencing in five patients, single lab, consistent mechanistic model","pmids":["28275241"],"is_preprint":false},{"year":2020,"finding":"Exon skipping using antisense oligonucleotides (ASO) targeting exon 21 of COL4A5 in truncating variant Alport syndrome enables formation of the type IV collagen alpha3/alpha4/alpha5 heterotrimer (demonstrated by triple helix formation assay), restores alpha5 chain expression on glomerular and tubular basement membranes in vivo, and prolongs survival in treated mice.","method":"Type IV collagen alpha3/alpha4/alpha5 chain triple helix formation assay; in vitro and in vivo ASO treatment; immunostaining; survival analysis in mouse model","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — biochemical trimer formation assay combined with in vivo functional rescue, multiple orthogonal readouts","pmids":["32488001"],"is_preprint":false},{"year":2020,"finding":"A cell-based split nanoluciferase assay measuring alpha345(IV) heterotrimer formation showed that COL4A5 glycine missense mutations associated with early proteinuria and renal failure significantly reduce secreted trimer, either by reducing intracellular trimer formation or blocking secretion; mutations without early proteinuria showed trimer formation and secretion patterns similar to wild-type.","method":"Split nanoluciferase-fused alpha3/alpha5 mutant and alpha4 co-transfection assay measuring intracellular and secreted heterotrimer by luminescence","journal":"Kidney international reports","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — biochemical reconstitution-type cell assay with multiple mutants, single lab, correlates with clinical data","pmids":["32405592"],"is_preprint":false},{"year":2021,"finding":"Col4a5-deficient rats generated by CRISPR/rGONAD show disruption of both alpha3/alpha4/alpha5(IV) and alpha5/alpha5/alpha6(IV) type IV collagen networks in the kidney, demonstrating that Col4a5 is required for assembly of both collagen IV heterotrimeric networks in vivo.","method":"CRISPR-mediated Col4a5 knockout in rats; immunostaining for collagen IV alpha chain distribution; histological and ultrastructural analysis","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic loss-of-function with specific protein network readout, single lab","pmids":["34675305"],"is_preprint":false},{"year":2018,"finding":"A Col4a5 R471X nonsense mutation introduced into mice by CRISPR/Cas9 abolishes Col4a5 mRNA and protein expression in kidney, producing proteinuria, hematuria, glomerulosclerosis, interstitial fibrosis, and GBM irregular thickening with lamination consistent with Alport syndrome.","method":"CRISPR/Cas9 knock-in mouse model; RT-PCR and Western blot for Col4a5 expression; pathological and electron microscopy analysis","journal":"Biochemistry and biophysics reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct genetic loss-of-function with defined molecular and pathological phenotype, single lab","pmids":["30582011"],"is_preprint":false},{"year":2010,"finding":"A COL4A5 missense mutation (p.F222C) in a non-collagenous interruption of the collagenous domain causes severe glomerular disease with global/segmental glomerulosclerosis and rapid progression to ESRD in males despite normal alpha5(IV) immunostaining, demonstrating that non-collagenous interruption residues are functionally critical for COL4A5 function beyond its structural role in basement membrane network assembly.","method":"Exon sequencing of COL4A5 in affected family; immunostaining for alpha5(IV) collagen in renal biopsies; segregation analysis in family","journal":"Kidney international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mutation with defined renal phenotype and normal protein expression, functional significance of non-collagenous domain established, single lab","pmids":["20881942"],"is_preprint":false},{"year":2021,"finding":"Single-base substitutions at the last nucleotide position of COL4A5 exons cause aberrant splicing (confirmed in 85% of 20 variants tested), resulting in exon skipping or cryptic splice site activation, as determined by hybrid minigene functional splicing assay; in vivo transcript analyses confirmed minigene results in all three cases tested.","method":"Hybrid minigene splicing assay; in vivo transcript analysis by RT-PCR of patient samples","journal":"Kidney international reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — functional splicing assay with multiple variants, validated by in vivo analysis, single lab","pmids":["35005319"],"is_preprint":false},{"year":2019,"finding":"In vitro splicing assays using hybrid minigenes for seven COL4A5 intronic mutations revealed exon skipping in four variants, combined exon skipping and insertion in one, and no change (likely non-pathogenic) in one, providing mechanistic determination of pathogenicity for intronic COL4A5 variants.","method":"Hybrid minigene in vitro splicing assay; comparison to patient transcript data where available","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — functional assay, single lab, validated against patient transcripts in three cases","pmids":["31481700"],"is_preprint":false},{"year":2008,"finding":"Somatic mosaicism for a COL4A5 splice acceptor mutation (c.3998-2 a>t) causes mosaic alpha5(IV) staining in glomeruli and a mild phenotype; mRNA analysis from urinary sediments demonstrated both normal transcript and transcript with exon 44 skipping in the same patient, establishing that the ratio of normal to abnormal transcript determines disease severity.","method":"Direct sequencing showing two allele peaks; restriction enzyme analysis confirming mosaicism; RT-PCR of urinary sediment mRNA; immunohistochemistry","journal":"Nephrology, dialysis, transplantation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple methods confirming mosaicism and its molecular consequence, single patient/lab","pmids":["18332068"],"is_preprint":false}],"current_model":"COL4A5 encodes the alpha5(IV) collagen chain, which heterotrimes with alpha3(IV) and alpha4(IV) to form the type IV collagen network essential for glomerular basement membrane integrity; the COL4A5/COL4A6 gene pair is regulated by a bifunctional bidirectional promoter with cell-type-specific activity, the alpha5(IV) chain is required for proper assembly and secretion of the alpha345(IV) heterotrimer, and mutations disrupting the chain (deletions, truncations, glycine substitutions, splice defects) cause X-linked Alport syndrome through failure of this network, with mutation type and resulting trimer assembly capacity predicting disease severity."},"narrative":{"mechanistic_narrative":"COL4A5 encodes the alpha5(IV) collagen chain, a structural component of basement membranes whose disruption causes X-linked Alport syndrome with nephritis and deafness [PMID:2349482]. The alpha5(IV) chain is required for assembly of the alpha3/alpha4/alpha5(IV) type IV collagen network of the glomerular basement membrane: loss of COL4A5 abolishes incorporation of the alpha3(IV) chain into the GBM [PMID:8196274], and Col4a5 deficiency in vivo disrupts both the alpha3/alpha4/alpha5(IV) and alpha5/alpha5/alpha6(IV) networks [PMID:34675305]. Heterotrimer assembly capacity links genotype to phenotype: deletional and splice-site mutations cause complete absence of alpha3-alpha5(IV) chains while glycine missense substitutions permit residual antigenicity [PMID:8807602], and glycine missense mutations associated with early renal failure measurably reduce intracellular trimer formation or block secretion in a split-nanoluciferase trimer assay [PMID:32405592]. A large proportion of pathogenic variants act through aberrant splicing — cryptic splice site use, exon skipping, and frameshift-driven premature stop codons [PMID:8004101, PMID:35005319]. COL4A5 is arranged head-to-head with COL4A6 on Xq22 and shares a bidirectional, cell-type-specific bifunctional promoter, such that growth factors selectively enhance alpha5(IV) expression in glomerular cells while enhancing alpha6(IV) in tubular cells [PMID:7972123, PMID:15598179]; contiguous deletions at this shared 5' region cause Alport syndrome with diffuse leiomyomatosis [PMID:1453602, PMID:28275241]. Antisense-oligonucleotide exon skipping restores alpha345(IV) heterotrimer formation, GBM alpha5 expression, and survival in a truncating-variant Alport model, providing therapeutic proof of the assembly mechanism [PMID:32488001].","teleology":[{"year":1990,"claim":"Established the disease gene: mutations in COL4A5 cause X-linked Alport syndrome, defining alpha5(IV) as a structural GBM component whose loss produces nephritis and deafness.","evidence":"Southern blotting and restriction/genomic analysis in Alport kindreds","pmids":["2349482"],"confidence":"High","gaps":["Did not resolve how alpha5(IV) integrates into a multi-chain network","Mechanism linking chain loss to GBM failure not yet defined"]},{"year":1994,"claim":"Defined the genomic architecture and regulatory context: the 51-exon COL4A5 gene sits head-to-head with COL4A6 sharing a bidirectional, tissue-specific promoter, framing both single-gene and contiguous-gene-deletion disease.","evidence":"Genomic cloning/sequencing of the gene and RT-PCR of tissue-specific transcripts","pmids":["8120014","7972123"],"confidence":"High","gaps":["Cell-type selectivity of the promoter not yet functionally dissected","Regulatory elements driving glomerulus-specific COL4A5 expression unmapped"]},{"year":1994,"claim":"Connected COL4A5 loss to network assembly failure: gene deletion abolishes alpha5(IV) and prevents alpha3(IV) incorporation into the GBM, showing alpha5 is needed for the alpha3-containing network.","evidence":"Alloantibody binding to recombinant NC1 domains in a deletion patient","pmids":["8196274"],"confidence":"Medium","gaps":["Single patient","Did not directly measure trimer assembly biochemistry"]},{"year":1992,"claim":"Explained the Alport-diffuse leiomyomatosis association as a contiguous-gene phenomenon involving 5' COL4A5 deletions extending into an adjacent gene.","evidence":"Southern blotting with COL4A5 cDNA and 5' genomic probes in DL-AS patients","pmids":["1453602"],"confidence":"Medium","gaps":["Adjacent gene (COL4A6) not yet directly implicated mechanistically","Three patients only"]},{"year":1995,"claim":"Mapped reciprocal tissue distribution of alpha5(IV) and alpha6(IV), showing alpha5 but not alpha6 in GBM and co-localization in skin/smooth muscle, explaining tissue-restricted disease consequences.","evidence":"Immunofluorescence and Western blot with NC1-specific monoclonal antibodies across tissues","pmids":["7657706"],"confidence":"High","gaps":["Did not define which heterotrimers form in each tissue","Chain stoichiometry within networks not resolved"]},{"year":1996,"claim":"Established a genotype-protein correlation: mutation class predicts whether alpha3-alpha5(IV) chains are absent versus retained, linking chain integrity to network assembly.","evidence":"Immunohistochemistry with chain-specific antibodies in biopsies from genotyped patients","pmids":["8807602"],"confidence":"Medium","gaps":["Nine patients, single center","Did not measure trimer assembly directly"]},{"year":2000,"claim":"Functionally dissected the bidirectional promoter, identifying minimal promoters and a positive regulatory element active in most cell types but not glomerular visceral epithelium, explaining selective COL4A5 transcription.","evidence":"RNase protection, reporter transfections, gel shift and footprinting in defined cell lines","pmids":["11096082"],"confidence":"High","gaps":["Transcription factors conferring glomerular selectivity not identified","In vivo relevance of element not tested"]},{"year":2005,"claim":"Showed the bifunctional promoter responds to growth factors in a cell-type-directional manner (alpha5 in glomerular cells, alpha6 in tubular cells), establishing context-dependent regulation.","evidence":"Bidirectional reporter constructs with growth-factor stimulation in cell-type-specific lines","pmids":["15598179"],"confidence":"Medium","gaps":["Signalling intermediates downstream of TGF-beta/EGF/VEGF/PDGF not defined","Reporter assay, single lab"]},{"year":2008,"claim":"Demonstrated that the ratio of normal to aberrant transcript governs disease severity, using somatic mosaicism for a splice mutation producing mosaic alpha5 staining and mild phenotype.","evidence":"Sequencing/restriction mosaicism detection, urinary-sediment RT-PCR, immunohistochemistry","pmids":["18332068"],"confidence":"Medium","gaps":["Single patient","Quantitative threshold of transcript ratio not established"]},{"year":2010,"claim":"Revealed that non-collagenous interruption residues are functionally critical: an interruption-domain missense caused severe disease despite normal alpha5(IV) staining, expanding function beyond bulk network assembly.","evidence":"Exon sequencing, alpha5 immunostaining, and family segregation","pmids":["20881942"],"confidence":"Medium","gaps":["Molecular basis of interruption-residue function unresolved","Single family"]},{"year":2017,"claim":"Defined the mutational mechanism of AS-DL contiguous deletions as homologous recombination between COL4A5/COL4A6 repetitive elements across the shared promoter, with leiomyomatosis requiring inactivation of both genes.","evidence":"Breakpoint sequencing and repetitive-element analysis in AS-DL patients","pmids":["28275241"],"confidence":"Medium","gaps":["Five patients","How biallelic-region loss drives smooth muscle proliferation not mechanistically shown"]},{"year":2020,"claim":"Provided direct biochemical proof of the assembly mechanism: glycine missense mutations tied to early renal failure reduce secreted alpha345(IV) trimer, while benign-course mutations assemble normally.","evidence":"Split-nanoluciferase alpha3/alpha4/alpha5 co-transfection trimer assay across mutants","pmids":["32405592"],"confidence":"Medium","gaps":["Single lab cell-based assay","Does not capture in vivo GBM incorporation kinetics"]},{"year":2020,"claim":"Delivered therapeutic validation of the assembly model: ASO exon-21 skipping restores trimer formation, GBM alpha5 expression, and survival in truncating-variant Alport mice.","evidence":"Triple-helix formation assay plus in vitro/in vivo ASO treatment with immunostaining and survival readouts","pmids":["32488001"],"confidence":"High","gaps":["Limited to specific truncating-variant context","Long-term durability and human translation untested"]},{"year":2021,"claim":"Confirmed in vivo that Col4a5 is required for assembly of both the alpha3/alpha4/alpha5 and alpha5/alpha5/alpha6 networks via a genetic knockout.","evidence":"CRISPR/rGONAD Col4a5-knockout rat with chain-specific immunostaining and ultrastructural analysis","pmids":["34675305"],"confidence":"Medium","gaps":["Single lab","Did not isolate tissue-specific contributions of each network to pathology"]},{"year":2021,"claim":"Systematically established splicing disruption as a major pathogenic mechanism, showing last-nucleotide and intronic variants cause exon skipping or cryptic splice activation.","evidence":"Hybrid minigene splicing assays with in vivo transcript confirmation","pmids":["35005319","31481700"],"confidence":"High","gaps":["Minigene context may not fully recapitulate native splicing","Quantitative effect on residual protein not measured for all variants"]},{"year":null,"claim":"How cell-type-specific transcription factors select COL4A5 versus COL4A6 from the shared promoter, and the molecular basis by which non-collagenous interruption residues contribute to chain function, remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No transcription factor mediating glomerular COL4A5 selectivity identified","Structural basis of interruption-residue requirement unknown","Mechanism linking COL4A5/COL4A6 biallelic loss to leiomyomatosis undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,4,17]}],"localization":[{"term_id":"GO:0031012","term_label":"extracellular matrix","supporting_discovery_ids":[4,7,8]},{"term_id":"GO:0005576","term_label":"extracellular region","supporting_discovery_ids":[7]}],"pathway":[{"term_id":"R-HSA-1474244","term_label":"Extracellular matrix organization","supporting_discovery_ids":[4,8,15,17]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[0,1,18]}],"complexes":["alpha3/alpha4/alpha5(IV) collagen heterotrimer","alpha5/alpha5/alpha6(IV) collagen heterotrimer"],"partners":["COL4A3","COL4A4","COL4A6"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P29400","full_name":"Collagen alpha-5(IV) chain","aliases":[],"length_aa":1685,"mass_kda":161.0,"function":"Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a 'chicken-wire' meshwork together with laminins, proteoglycans and entactin/nidogen","subcellular_location":"Secreted, extracellular space, extracellular matrix, basement membrane","url":"https://www.uniprot.org/uniprotkb/P29400/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/COL4A5","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/COL4A5","total_profiled":1310},"omim":[{"mim_id":"620536","title":"ALPORT SYNDROME 3B, AUTOSOMAL RECESSIVE; ATS3B","url":"https://www.omim.org/entry/620536"},{"mim_id":"609057","title":"EPIDERMOLYSIS BULLOSA SIMPLEX 7, WITH NEPHROPATHY AND DEAFNESS; EBS7","url":"https://www.omim.org/entry/609057"},{"mim_id":"603742","title":"SLIT GUIDANCE LIGAND 1; SLIT1","url":"https://www.omim.org/entry/603742"},{"mim_id":"602431","title":"ROUNDABOUT GUIDANCE RECEPTOR 2; ROBO2","url":"https://www.omim.org/entry/602431"},{"mim_id":"314200","title":"THYROXINE-BINDING GLOBULIN OF SERUM; TBG","url":"https://www.omim.org/entry/314200"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Plasma membrane","reliability":"Approved"},{"location":"Vesicles","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/COL4A5"},"hgnc":{"alias_symbol":[],"prev_symbol":["ASLN","ATS"]},"alphafold":{"accession":"P29400","domains":[{"cath_id":"2.170.240.10","chopping":"1463-1657_1671-1684","consensus_level":"medium","plddt":87.9152,"start":1463,"end":1684}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P29400","model_url":"https://alphafold.ebi.ac.uk/files/AF-P29400-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P29400-F1-predicted_aligned_error_v6.png","plddt_mean":48.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=COL4A5","jax_strain_url":"https://www.jax.org/strain/search?query=COL4A5"},"sequence":{"accession":"P29400","fasta_url":"https://rest.uniprot.org/uniprotkb/P29400.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P29400/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P29400"}},"corpus_meta":[{"pmid":"12682500","id":"PMC_12682500","title":"2001 SCCM/ESICM/ACCP/ATS/SIS International Sepsis Definitions Conference.","date":"2003","source":"Critical care medicine","url":"https://pubmed.ncbi.nlm.nih.gov/12682500","citation_count":4335,"is_preprint":false},{"pmid":"12664219","id":"PMC_12664219","title":"2001 SCCM/ESICM/ACCP/ATS/SIS International Sepsis Definitions Conference.","date":"2003","source":"Intensive care medicine","url":"https://pubmed.ncbi.nlm.nih.gov/12664219","citation_count":1678,"is_preprint":false},{"pmid":"2349482","id":"PMC_2349482","title":"Identification of mutations in the COL4A5 collagen gene in Alport syndrome.","date":"1990","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/2349482","citation_count":710,"is_preprint":false},{"pmid":"20208042","id":"PMC_20208042","title":"An official ATS clinical policy statement: Congenital central hypoventilation syndrome: genetic basis, diagnosis, and management.","date":"2010","source":"American journal of respiratory and critical care medicine","url":"https://pubmed.ncbi.nlm.nih.gov/20208042","citation_count":340,"is_preprint":false},{"pmid":"9214638","id":"PMC_9214638","title":"Mammalian homologues of the Polycomb-group gene Enhancer of zeste mediate gene silencing in Drosophila heterochromatin and at S. cerevisiae telomeres.","date":"1997","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/9214638","citation_count":249,"is_preprint":false},{"pmid":"7657706","id":"PMC_7657706","title":"Differential expression of two basement membrane collagen genes, COL4A6 and COL4A5, demonstrated by immunofluorescence staining using peptide-specific monoclonal antibodies.","date":"1995","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/7657706","citation_count":239,"is_preprint":false},{"pmid":"8622692","id":"PMC_8622692","title":"Casein kinase II phosphorylates I kappa B alpha at S-283, S-289, S-293, and T-291 and is required for its degradation.","date":"1996","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/8622692","citation_count":175,"is_preprint":false},{"pmid":"22493002","id":"PMC_22493002","title":"Ube3a-ATS is an atypical RNA polymerase II transcript that represses the paternal expression of Ube3a.","date":"2012","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/22493002","citation_count":160,"is_preprint":false},{"pmid":"33087932","id":"PMC_33087932","title":"Cas9 gene therapy for Angelman syndrome traps Ube3a-ATS long non-coding RNA.","date":"2020","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/33087932","citation_count":135,"is_preprint":false},{"pmid":"24385930","id":"PMC_24385930","title":"Truncation of Ube3a-ATS unsilences paternal Ube3a and ameliorates behavioral defects in the Angelman syndrome mouse model.","date":"2013","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/24385930","citation_count":134,"is_preprint":false},{"pmid":"8940267","id":"PMC_8940267","title":"Spectrum of mutations in the COL4A5 collagen gene in X-linked Alport syndrome.","date":"1996","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/8940267","citation_count":133,"is_preprint":false},{"pmid":"8651296","id":"PMC_8651296","title":"X-linked Alport syndrome: an SSCP-based mutation survey over all 51 exons of the COL4A5 gene.","date":"1996","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/8651296","citation_count":119,"is_preprint":false},{"pmid":"20174550","id":"PMC_20174550","title":"Anaplasma phagocytophilum Ats-1 is imported into host cell mitochondria and interferes with apoptosis induction.","date":"2010","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/20174550","citation_count":116,"is_preprint":false},{"pmid":"9848783","id":"PMC_9848783","title":"High mutation detection rate in the COL4A5 collagen gene in suspected Alport syndrome using PCR and direct DNA sequencing.","date":"1998","source":"Journal of the American Society of Nephrology : JASN","url":"https://pubmed.ncbi.nlm.nih.gov/9848783","citation_count":104,"is_preprint":false},{"pmid":"23486266","id":"PMC_23486266","title":"Correlation of mutation status and survival with predominant histologic subtype according to the new IASLC/ATS/ERS lung adenocarcinoma classification in stage III (N2) patients.","date":"2013","source":"Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/23486266","citation_count":104,"is_preprint":false},{"pmid":"1453602","id":"PMC_1453602","title":"Alport syndrome and diffuse leiomyomatosis: deletions in the 5' end of the COL4A5 collagen gene.","date":"1992","source":"Kidney international","url":"https://pubmed.ncbi.nlm.nih.gov/1453602","citation_count":96,"is_preprint":false},{"pmid":"9370943","id":"PMC_9370943","title":"Collagen-binding heat shock protein (HSP) 47 expression in anti-thymocyte serum (ATS)-induced glomerulonephritis.","date":"1997","source":"The Journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/9370943","citation_count":81,"is_preprint":false},{"pmid":"29301918","id":"PMC_29301918","title":"ERS/ATS workshop report on respiratory health effects of household air pollution.","date":"2018","source":"The European respiratory journal","url":"https://pubmed.ncbi.nlm.nih.gov/29301918","citation_count":79,"is_preprint":false},{"pmid":"17432928","id":"PMC_17432928","title":"Cell size at S phase initiation: an emergent property of the G1/S network.","date":"2007","source":"PLoS computational biology","url":"https://pubmed.ncbi.nlm.nih.gov/17432928","citation_count":79,"is_preprint":false},{"pmid":"10094548","id":"PMC_10094548","title":"Detection of mutations in COL4A5 in patients with Alport syndrome.","date":"1999","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/10094548","citation_count":78,"is_preprint":false},{"pmid":"8120014","id":"PMC_8120014","title":"Structure of the human type IV collagen COL4A5 gene.","date":"1994","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8120014","citation_count":76,"is_preprint":false},{"pmid":"27137345","id":"PMC_27137345","title":"Lung Adenocarcinoma Staging Using the 2011 IASLC/ATS/ERS Classification: A Pooled Analysis of Adenocarcinoma In Situ and Minimally Invasive Adenocarcinoma.","date":"2016","source":"Clinical lung cancer","url":"https://pubmed.ncbi.nlm.nih.gov/27137345","citation_count":73,"is_preprint":false},{"pmid":"17395133","id":"PMC_17395133","title":"Management and treatment of Andersen-Tawil syndrome (ATS).","date":"2007","source":"Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics","url":"https://pubmed.ncbi.nlm.nih.gov/17395133","citation_count":72,"is_preprint":false},{"pmid":"32488001","id":"PMC_32488001","title":"Development of an exon skipping therapy for X-linked Alport syndrome with truncating variants in COL4A5.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/32488001","citation_count":71,"is_preprint":false},{"pmid":"7972123","id":"PMC_7972123","title":"The genes COL4A5 and COL4A6, coding for basement membrane collagen chains alpha 5(IV) and alpha 6(IV), are located head-to-head in close proximity on human chromosome Xq22 and COL4A6 is transcribed from two alternative promoters.","date":"1994","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/7972123","citation_count":69,"is_preprint":false},{"pmid":"8807602","id":"PMC_8807602","title":"Relationship between COL4A5 gene mutation and distribution of type IV collagen in male X-linked Alport syndrome. Japanese Alport Network.","date":"1996","source":"Kidney international","url":"https://pubmed.ncbi.nlm.nih.gov/8807602","citation_count":68,"is_preprint":false},{"pmid":"17396119","id":"PMC_17396119","title":"Sixteen novel mutations identified in COL4A3, COL4A4, and COL4A5 genes in Slovenian families with Alport syndrome and benign familial hematuria.","date":"2007","source":"Kidney international","url":"https://pubmed.ncbi.nlm.nih.gov/17396119","citation_count":58,"is_preprint":false},{"pmid":"9621285","id":"PMC_9621285","title":"Ultrastructural and immunohistochemical findings in Alport's syndrome: a study of 108 patients from 97 Italian families with particular emphasis on COL4A5 gene mutation correlations.","date":"1998","source":"Journal of the American Society of Nephrology : JASN","url":"https://pubmed.ncbi.nlm.nih.gov/9621285","citation_count":53,"is_preprint":false},{"pmid":"15782134","id":"PMC_15782134","title":"Distinct roles for p53 transactivation and repression in preventing UCN-01-mediated abrogation of DNA damage-induced arrest at S and G2 cell cycle checkpoints.","date":"2005","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/15782134","citation_count":51,"is_preprint":false},{"pmid":"25349703","id":"PMC_25349703","title":"The new IASLC/ATS/ERS lung adenocarcinoma classification from a clinical perspective: current concepts and future prospects.","date":"2014","source":"Journal of thoracic disease","url":"https://pubmed.ncbi.nlm.nih.gov/25349703","citation_count":50,"is_preprint":false},{"pmid":"28928900","id":"PMC_28928900","title":"Dihydroorotate dehydrogenase Inhibitors Target c-Myc and Arrest Melanoma, Myeloma and Lymphoma cells at S-phase.","date":"2017","source":"Journal of Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/28928900","citation_count":50,"is_preprint":false},{"pmid":"10200983","id":"PMC_10200983","title":"Identification of COL4A5 defects in Alport's syndrome by immunohistochemistry of skin.","date":"1999","source":"Kidney international","url":"https://pubmed.ncbi.nlm.nih.gov/10200983","citation_count":48,"is_preprint":false},{"pmid":"35602506","id":"PMC_35602506","title":"Genotype-Phenotype Correlations for Pathogenic COL4A3-COL4A5 Variants in X-Linked, Autosomal Recessive, and Autosomal Dominant Alport Syndrome.","date":"2022","source":"Frontiers in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35602506","citation_count":46,"is_preprint":false},{"pmid":"8196274","id":"PMC_8196274","title":"COL4A5 gene deletion and production of post-transplant anti-alpha 3(IV) collagen alloantibodies in Alport syndrome.","date":"1994","source":"Kidney international","url":"https://pubmed.ncbi.nlm.nih.gov/8196274","citation_count":44,"is_preprint":false},{"pmid":"32339580","id":"PMC_32339580","title":"Isolation and structural characterization of a novel polysaccharide from Hericium erinaceus fruiting bodies and its arrest of cell cycle at S-phage in colon cancer cells.","date":"2020","source":"International journal of biological macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/32339580","citation_count":44,"is_preprint":false},{"pmid":"16027444","id":"PMC_16027444","title":"Maternal disruption of Ube3a leads to increased expression of Ube3a-ATS in trans.","date":"2005","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/16027444","citation_count":43,"is_preprint":false},{"pmid":"1474765","id":"PMC_1474765","title":"Deletions of the COL4A5 gene in patients with Alport syndrome.","date":"1992","source":"Kidney international","url":"https://pubmed.ncbi.nlm.nih.gov/1474765","citation_count":42,"is_preprint":false},{"pmid":"22806311","id":"PMC_22806311","title":"miR-21 induces cell cycle at S phase and modulates cell proliferation by down-regulating hMSH2 in lung cancer.","date":"2012","source":"Journal of cancer research and clinical oncology","url":"https://pubmed.ncbi.nlm.nih.gov/22806311","citation_count":42,"is_preprint":false},{"pmid":"8738805","id":"PMC_8738805","title":"Identification of 17 mutations in ten exons in the COL4A5 collagen gene, but no mutations found in four exons in COL4A6: a study of 250 patients with hematuria and suspected of having Alport syndrome.","date":"1996","source":"Journal of the American Society of Nephrology : JASN","url":"https://pubmed.ncbi.nlm.nih.gov/8738805","citation_count":42,"is_preprint":false},{"pmid":"15954103","id":"PMC_15954103","title":"Novel COL4A5, COL4A4, and COL4A3 mutations in Alport syndrome.","date":"2005","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/15954103","citation_count":42,"is_preprint":false},{"pmid":"31754267","id":"PMC_31754267","title":"New frontiers to cure Alport syndrome: COL4A3 and COL4A5 gene editing in podocyte-lineage cells.","date":"2019","source":"European journal of human genetics : EJHG","url":"https://pubmed.ncbi.nlm.nih.gov/31754267","citation_count":41,"is_preprint":false},{"pmid":"22306658","id":"PMC_22306658","title":"Snf1/AMPK regulates Gcn5 occupancy, H3 acetylation and chromatin remodelling at S. cerevisiae ADY2 promoter.","date":"2012","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/22306658","citation_count":41,"is_preprint":false},{"pmid":"16284948","id":"PMC_16284948","title":"Rearrangement of the COL12A1 and COL4A5 genes in subungual exostosis: molecular cytogenetic delineation of the tumor-specific translocation t(X;6)(q13-14;q22).","date":"2006","source":"International journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/16284948","citation_count":41,"is_preprint":false},{"pmid":"9463311","id":"PMC_9463311","title":"Topoisomerase I and II consensus sequences in a 17-kb deletion junction of the COL4A5 and COL4A6 genes and immunohistochemical analysis of esophageal leiomyomatosis associated with Alport syndrome.","date":"1998","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/9463311","citation_count":40,"is_preprint":false},{"pmid":"10561141","id":"PMC_10561141","title":"Detection of mutations in the COL4A5 gene in over 90% of male patients with X-linked Alport's syndrome by RT-PCR and direct sequencing.","date":"1999","source":"American journal of kidney diseases : the official journal of the National Kidney Foundation","url":"https://pubmed.ncbi.nlm.nih.gov/10561141","citation_count":39,"is_preprint":false},{"pmid":"23927885","id":"PMC_23927885","title":"Adequacy of CT-guided biopsies with histomolecular subtyping of pulmonary adenocarcinomas: influence of ATS/ERS/IASLC guidelines.","date":"2013","source":"Lung cancer (Amsterdam, Netherlands)","url":"https://pubmed.ncbi.nlm.nih.gov/23927885","citation_count":39,"is_preprint":false},{"pmid":"24470729","id":"PMC_24470729","title":"X-linked, COL4A5 hypomorphic Alport mutations such as G624D and P628L may only exhibit thin basement membrane nephropathy with microhematuria and late onset kidney failure.","date":"2013","source":"Hippokratia","url":"https://pubmed.ncbi.nlm.nih.gov/24470729","citation_count":37,"is_preprint":false},{"pmid":"25739341","id":"PMC_25739341","title":"Coinheritance of COL4A5 and MYO1E mutations accentuate the severity of kidney disease.","date":"2015","source":"Pediatric nephrology (Berlin, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/25739341","citation_count":37,"is_preprint":false},{"pmid":"29764427","id":"PMC_29764427","title":"COL4A5 and LAMA5 variants co-inherited in familial hematuria: digenic inheritance or genetic modifier effect?","date":"2018","source":"BMC nephrology","url":"https://pubmed.ncbi.nlm.nih.gov/29764427","citation_count":37,"is_preprint":false},{"pmid":"24095767","id":"PMC_24095767","title":"Transmissible gastroenteritis virus infection induces cell cycle arrest at S and G2/M phases via p53-dependent pathway.","date":"2013","source":"Virus research","url":"https://pubmed.ncbi.nlm.nih.gov/24095767","citation_count":37,"is_preprint":false},{"pmid":"20574986","id":"PMC_20574986","title":"The Alport syndrome COL4A5 variant database.","date":"2010","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/20574986","citation_count":37,"is_preprint":false},{"pmid":"8004101","id":"PMC_8004101","title":"Aberrant splicing of the COL4A5 gene in patients with Alport syndrome.","date":"1994","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/8004101","citation_count":36,"is_preprint":false},{"pmid":"27794102","id":"PMC_27794102","title":"Gibberellins Regulate Ovule Integument Development by Interfering with the Transcription Factor ATS.","date":"2016","source":"Plant physiology","url":"https://pubmed.ncbi.nlm.nih.gov/27794102","citation_count":35,"is_preprint":false},{"pmid":"27073516","id":"PMC_27073516","title":"Association between the histological subtype of lung adenocarcinoma, EGFR/KRAS mutation status and the ALK rearrangement according to the novel IASLC/ATS/ERS classification.","date":"2016","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/27073516","citation_count":35,"is_preprint":false},{"pmid":"25183659","id":"PMC_25183659","title":"X-linked Alport syndrome caused by splicing mutations in COL4A5.","date":"2014","source":"Clinical journal of the American Society of Nephrology : CJASN","url":"https://pubmed.ncbi.nlm.nih.gov/25183659","citation_count":34,"is_preprint":false},{"pmid":"25550848","id":"PMC_25550848","title":"Correlation of EGFR mutation and histological subtype according to the IASLC/ATS/ERS classification of lung adenocarcinoma.","date":"2014","source":"International journal of clinical and experimental pathology","url":"https://pubmed.ncbi.nlm.nih.gov/25550848","citation_count":34,"is_preprint":false},{"pmid":"19965530","id":"PMC_19965530","title":"Alport retinopathy results from \"severe\" COL4A5 mutations and predicts early renal failure.","date":"2009","source":"Clinical journal of the American Society of Nephrology : CJASN","url":"https://pubmed.ncbi.nlm.nih.gov/19965530","citation_count":34,"is_preprint":false},{"pmid":"15780079","id":"PMC_15780079","title":"Detection of mutations in the COL4A5 gene by analyzing cDNA of skin fibroblasts.","date":"2005","source":"Kidney international","url":"https://pubmed.ncbi.nlm.nih.gov/15780079","citation_count":34,"is_preprint":false},{"pmid":"11462238","id":"PMC_11462238","title":"Detection of mutations in the COL4A5 gene by SSCP in X-linked Alport syndrome.","date":"2001","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/11462238","citation_count":33,"is_preprint":false},{"pmid":"35005319","id":"PMC_35005319","title":"Last Nucleotide Substitutions of COL4A5 Exons Cause Aberrant Splicing.","date":"2021","source":"Kidney international reports","url":"https://pubmed.ncbi.nlm.nih.gov/35005319","citation_count":32,"is_preprint":false},{"pmid":"26435150","id":"PMC_26435150","title":"Porcine epidemic diarrhea virus M protein blocks cell cycle progression at S-phase and its subcellular localization in the porcine intestinal epithelial cells.","date":"2015","source":"Acta virologica","url":"https://pubmed.ncbi.nlm.nih.gov/26435150","citation_count":31,"is_preprint":false},{"pmid":"24842107","id":"PMC_24842107","title":"Disialoganglioside GD3-synthase over expression inhibits survival and angiogenesis of pancreatic cancer cells through cell cycle arrest at S-phase and disruption of integrin-β1-mediated anchorage.","date":"2014","source":"The international journal of biochemistry & cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/24842107","citation_count":31,"is_preprint":false},{"pmid":"30968591","id":"PMC_30968591","title":"Novel mutations of COL4A3, COL4A4, and COL4A5 genes in Chinese patients with Alport Syndrome using next generation sequence technique.","date":"2019","source":"Molecular genetics & genomic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/30968591","citation_count":30,"is_preprint":false},{"pmid":"8301933","id":"PMC_8301933","title":"Differential splicing of COL4A5 mRNA in kidney and white blood cells: a complex mutation in the COL4A5 gene of an Alport patient deletes the NC1 domain.","date":"1993","source":"Kidney international","url":"https://pubmed.ncbi.nlm.nih.gov/8301933","citation_count":27,"is_preprint":false},{"pmid":"20064240","id":"PMC_20064240","title":"Classic swine fever virus NS2 protein leads to the induction of cell cycle arrest at S-phase and endoplasmic reticulum stress.","date":"2010","source":"Virology journal","url":"https://pubmed.ncbi.nlm.nih.gov/20064240","citation_count":27,"is_preprint":false},{"pmid":"15149316","id":"PMC_15149316","title":"A large tandem duplication within the COL4A5 gene is responsible for the high prevalence of Alport syndrome in French Polynesia.","date":"2004","source":"Kidney international","url":"https://pubmed.ncbi.nlm.nih.gov/15149316","citation_count":27,"is_preprint":false},{"pmid":"18332068","id":"PMC_18332068","title":"Somatic mosaicism for a mutation of the COL4A5 gene is a cause of mild phenotype male Alport syndrome.","date":"2008","source":"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association","url":"https://pubmed.ncbi.nlm.nih.gov/18332068","citation_count":25,"is_preprint":false},{"pmid":"35211492","id":"PMC_35211492","title":"The Contribution of COL4A5 Splicing Variants to the Pathogenesis of X-Linked Alport Syndrome.","date":"2022","source":"Frontiers in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35211492","citation_count":23,"is_preprint":false},{"pmid":"27626431","id":"PMC_27626431","title":"R-Phycoerythrin Induces SGC-7901 Apoptosis by Arresting Cell Cycle at S Phase.","date":"2016","source":"Marine drugs","url":"https://pubmed.ncbi.nlm.nih.gov/27626431","citation_count":23,"is_preprint":false},{"pmid":"25938491","id":"PMC_25938491","title":"Novel Pactamycin Analogs Induce p53 Dependent Cell-Cycle Arrest at S-Phase in Human Head and Neck Squamous Cell Carcinoma (HNSCC) Cells.","date":"2015","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/25938491","citation_count":23,"is_preprint":false},{"pmid":"29142404","id":"PMC_29142404","title":"Chalepin: A Compound from Ruta angustifolia L. Pers Exhibits Cell Cycle Arrest at S phase, Suppresses Nuclear Factor-Kappa B (NF-κB) Pathway, Signal Transducer and Activation of Transcription 3 (STAT3) Phosphorylation and Extrinsic Apoptotic Pathway in Non-small Cell Lung Cancer Carcinoma (A549).","date":"2017","source":"Pharmacognosy magazine","url":"https://pubmed.ncbi.nlm.nih.gov/29142404","citation_count":22,"is_preprint":false},{"pmid":"32405592","id":"PMC_32405592","title":"Trimerization and Genotype-Phenotype Correlation of COL4A5 Mutants in Alport Syndrome.","date":"2020","source":"Kidney international reports","url":"https://pubmed.ncbi.nlm.nih.gov/32405592","citation_count":21,"is_preprint":false},{"pmid":"8599366","id":"PMC_8599366","title":"Major COL4A5 gene rearrangements in patients with juvenile type Alport syndrome.","date":"1995","source":"American journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/8599366","citation_count":21,"is_preprint":false},{"pmid":"30582011","id":"PMC_30582011","title":"Establishment of X-linked Alport syndrome model mice with a Col4a5 R471X mutation.","date":"2018","source":"Biochemistry and biophysics reports","url":"https://pubmed.ncbi.nlm.nih.gov/30582011","citation_count":21,"is_preprint":false},{"pmid":"28275241","id":"PMC_28275241","title":"Characterization of contiguous gene deletions in COL4A6 and COL4A5 in Alport syndrome-diffuse leiomyomatosis.","date":"2017","source":"Journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28275241","citation_count":20,"is_preprint":false},{"pmid":"28542346","id":"PMC_28542346","title":"Novel mutations in COL4A3, COL4A4, and COL4A5 in Chinese patients with Alport Syndrome.","date":"2017","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/28542346","citation_count":20,"is_preprint":false},{"pmid":"15598179","id":"PMC_15598179","title":"Bifunctional promoter of type IV collagen COL4A5 and COL4A6 genes regulates the expression of alpha5 and alpha6 chains in a distinct cell-specific fashion.","date":"2005","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/15598179","citation_count":20,"is_preprint":false},{"pmid":"30352093","id":"PMC_30352093","title":"Molecular signatures in IASLC/ATS/ERS classified growth patterns of lung adenocarcinoma.","date":"2018","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/30352093","citation_count":19,"is_preprint":false},{"pmid":"25110662","id":"PMC_25110662","title":"A novel COL4A5 mutation identified in a Chinese Han family using exome sequencing.","date":"2014","source":"BioMed research international","url":"https://pubmed.ncbi.nlm.nih.gov/25110662","citation_count":19,"is_preprint":false},{"pmid":"31481700","id":"PMC_31481700","title":"Determination of the pathogenicity of known COL4A5 intronic variants by in vitro splicing assay.","date":"2019","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/31481700","citation_count":19,"is_preprint":false},{"pmid":"15890955","id":"PMC_15890955","title":"Inhibition of the herpes simplex virus type 1 DNA polymerase induces hyperphosphorylation of replication protein A and its accumulation at S-phase-specific sites of DNA damage during infection.","date":"2005","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/15890955","citation_count":18,"is_preprint":false},{"pmid":"25991552","id":"PMC_25991552","title":"Transition from two to one integument in Prunus species: expression pattern of INNER NO OUTER (INO), ABERRANT TESTA SHAPE (ATS) and ETTIN (ETT).","date":"2015","source":"The New phytologist","url":"https://pubmed.ncbi.nlm.nih.gov/25991552","citation_count":18,"is_preprint":false},{"pmid":"10684360","id":"PMC_10684360","title":"Mutational analysis of COL4A5 gene in Korean Alport syndrome.","date":"2000","source":"Pediatric nephrology (Berlin, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/10684360","citation_count":17,"is_preprint":false},{"pmid":"16941480","id":"PMC_16941480","title":"A two-tier approach to mutation detection in the COL4A5 gene for Alport syndrome.","date":"2006","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/16941480","citation_count":16,"is_preprint":false},{"pmid":"31209800","id":"PMC_31209800","title":"Identification of a novel COL4A5 mutation in the proband initially diagnosed as IgAN from a Chinese family with X-linked Alport syndrome.","date":"2019","source":"Science China. Life sciences","url":"https://pubmed.ncbi.nlm.nih.gov/31209800","citation_count":16,"is_preprint":false},{"pmid":"35020912","id":"PMC_35020912","title":"Dissecting the genotype-phenotype correlation of COL4A5 gene mutation and its response to renin-angiotensin-aldosterone system blockers in Chinese male patients with Alport syndrome.","date":"2022","source":"Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association","url":"https://pubmed.ncbi.nlm.nih.gov/35020912","citation_count":15,"is_preprint":false},{"pmid":"7853788","id":"PMC_7853788","title":"Mutations in the COL4A5 gene in Alport syndrome: a possible mutation in primordial germ cells.","date":"1994","source":"Kidney international","url":"https://pubmed.ncbi.nlm.nih.gov/7853788","citation_count":15,"is_preprint":false},{"pmid":"23564952","id":"PMC_23564952","title":"Clinical relevance of the new IASLC/ERS/ATS adenocarcinoma classification.","date":"2013","source":"Journal of clinical pathology","url":"https://pubmed.ncbi.nlm.nih.gov/23564952","citation_count":15,"is_preprint":false},{"pmid":"40646322","id":"PMC_40646322","title":"The UBE3A-ATS antisense oligonucleotide rugonersen in children with Angelman syndrome: a phase 1 trial.","date":"2025","source":"Nature medicine","url":"https://pubmed.ncbi.nlm.nih.gov/40646322","citation_count":14,"is_preprint":false},{"pmid":"18616531","id":"PMC_18616531","title":"MLPA and cDNA analysis improves COL4A5 mutation detection in X-linked Alport syndrome.","date":"2008","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/18616531","citation_count":14,"is_preprint":false},{"pmid":"34675305","id":"PMC_34675305","title":"Creation of X-linked Alport syndrome rat model with Col4a5 deficiency.","date":"2021","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/34675305","citation_count":14,"is_preprint":false},{"pmid":"28940943","id":"PMC_28940943","title":"Associations between epidermal growth factor receptor mutations and histological subtypes of lung adenocarcinoma according to the IASLC/ATS/ERS classification in Chinese patients.","date":"2017","source":"Thoracic cancer","url":"https://pubmed.ncbi.nlm.nih.gov/28940943","citation_count":14,"is_preprint":false},{"pmid":"20881942","id":"PMC_20881942","title":"Novel X-linked glomerulopathy is associated with a COL4A5 missense mutation in a non-collagenous interruption.","date":"2010","source":"Kidney international","url":"https://pubmed.ncbi.nlm.nih.gov/20881942","citation_count":14,"is_preprint":false},{"pmid":"26613025","id":"PMC_26613025","title":"A COL4A5 mutation with glomerular disease and signs of chronic thrombotic microangiopathy.","date":"2015","source":"Clinical kidney journal","url":"https://pubmed.ncbi.nlm.nih.gov/26613025","citation_count":13,"is_preprint":false},{"pmid":"27020204","id":"PMC_27020204","title":"Associations between the IASLC/ATS/ERS lung adenocarcinoma classification and EGFR and KRAS mutations.","date":"2015","source":"Pathology","url":"https://pubmed.ncbi.nlm.nih.gov/27020204","citation_count":13,"is_preprint":false},{"pmid":"9246035","id":"PMC_9246035","title":"Ammonia inhibits proliferation and cell cycle progression at S-phase in human gastric cells.","date":"1997","source":"Digestive diseases and sciences","url":"https://pubmed.ncbi.nlm.nih.gov/9246035","citation_count":13,"is_preprint":false},{"pmid":"11096082","id":"PMC_11096082","title":"Regulation of the paired type IV collagen genes COL4A5 and COL4A6. Role of the proximal promoter region.","date":"2000","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11096082","citation_count":13,"is_preprint":false},{"pmid":"1427889","id":"PMC_1427889","title":"Construction of a yeast artificial chromosome contig encompassing the human alpha 5(IV) collagen gene (COL4A5).","date":"1992","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/1427889","citation_count":13,"is_preprint":false},{"pmid":"7731166","id":"PMC_7731166","title":"A nonsense mutation in the COL4A5 collagen gene in a family with X-linked juvenile Alport syndrome.","date":"1995","source":"Kidney international","url":"https://pubmed.ncbi.nlm.nih.gov/7731166","citation_count":12,"is_preprint":false},{"pmid":"25349702","id":"PMC_25349702","title":"Pulmonary adenocarcinoma: implications of the recent advances in molecular biology, treatment and the IASLC/ATS/ERS classification.","date":"2014","source":"Journal of thoracic disease","url":"https://pubmed.ncbi.nlm.nih.gov/25349702","citation_count":12,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":51284,"output_tokens":5383,"usd":0.117298,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":13909,"output_tokens":4324,"usd":0.088822,"stage2_stop_reason":"end_turn"},"total_usd":0.20612,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1990,\n      \"finding\": \"Mutations (intragenic deletion, Pst I site variant, uncharacterized abnormality) in COL4A5 were identified as causative for X-linked Alport syndrome, establishing that the alpha5(IV) collagen chain encoded by COL4A5 is a structural component of the glomerular basement membrane whose disruption causes nephritis and deafness.\",\n      \"method\": \"Southern blotting, restriction fragment analysis, direct genomic analysis in Alport syndrome kindreds\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct mutation identification in multiple kindreds, replicated by many subsequent studies across multiple labs\",\n      \"pmids\": [\"2349482\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"Deletions in the 5' end of COL4A5 extending beyond its 5' end are associated with Alport syndrome plus diffuse leiomyomatosis (DL), suggesting a contiguous gene deletion syndrome involving COL4A5 and an adjacent gene (later identified as COL4A6) responsible for smooth muscle proliferation.\",\n      \"method\": \"Southern blotting with cDNA probes spanning COL4A5 and 5' end genomic probe in patients with DL-AS association\",\n      \"journal\": \"Kidney international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Southern blot in three patients, single lab, consistent with later work on COL4A5/COL4A6 deletions\",\n      \"pmids\": [\"1453602\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"COL4A5 and COL4A6 genes are arranged head-to-head on chromosome Xq22 and share a bidirectional promoter region; COL4A6 is transcribed from two alternative promoters in a tissue-specific manner, with transcription start sites 442 bp and 1,492 bp from the COL4A5 transcription start site.\",\n      \"method\": \"Genomic sequencing, RT-PCR of tissue-specific transcripts, characterization of 5' flanking sequences\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct sequencing and RT-PCR in multiple tissues, replicated by subsequent promoter studies\",\n      \"pmids\": [\"7972123\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"The COL4A5 gene contains 51 exons spanning ~140 kb of DNA, with exon size and distribution pattern highly homologous to COL4A1; the complete exon structure was determined from genomic lambda phage clones.\",\n      \"method\": \"Genomic cloning and sequencing of 17 lambda phage clones covering the COL4A5 gene\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct genomic sequencing of entire gene structure, foundational reference\",\n      \"pmids\": [\"8120014\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"COL4A5 gene deletion in an Alport patient leads to absence of alpha5(IV) chain in the glomerular basement membrane and production of post-transplant alloantibodies directed against the alpha3(IV) chain (not alpha5(IV)), establishing that COL4A5 mutations cause defective assembly of the alpha3(IV) chain into the GBM network.\",\n      \"method\": \"Circulating antibody binding assay to GBM constituents, recombinant NC1 domains of human type IV collagen chains, COL4A5 gene deletion analysis\",\n      \"journal\": \"Kidney international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding experiments with recombinant proteins, single lab, single patient\",\n      \"pmids\": [\"8196274\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"Splice site mutations in COL4A5 cause aberrant mRNA splicing including use of cryptic splice sites within exons, exon skipping, and incorporation of frameshift mutations leading to premature stop codons; female carriers show variable stability of mutated mRNA relative to normal transcript.\",\n      \"method\": \"RT-PCR and mRNA analysis of COL4A5 splice site mutations in patients and carriers\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct mRNA analysis in patients, single lab, multiple mutations analyzed\",\n      \"pmids\": [\"8004101\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"COL4A5 mRNA undergoes differential tissue-specific splicing: an 18 bp sequence (encoding two Gly-X-Y triplets) is present between exons 10 and 11 in kidney mRNA but absent in white blood cell mRNA, indicating a kidney-specific additional exon. A complex mutation deleting part of the triple helical domain and the entire NC1 domain was identified in an Alport patient.\",\n      \"method\": \"RT-PCR of COL4A5 cDNA from lymphoblasts and kidney tissue, direct sequencing\",\n      \"journal\": \"Kidney international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct comparison of tissue-specific mRNA, single lab\",\n      \"pmids\": [\"8301933\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"The alpha5(IV) and alpha6(IV) chains encoded by COL4A5 and COL4A6 show distinct tissue-specific distribution: alpha5(IV) is present in glomerular basement membrane but alpha6(IV) is absent there, whereas both are co-localized in skin, smooth muscle cells, and adipocyte basement membranes. In Bowman's capsule and distal tubules, alpha6(IV) is present but its pattern differs from alpha5(IV).\",\n      \"method\": \"Immunofluorescence with peptide-specific rat monoclonal antibodies against NC1 domains of alpha5(IV) and alpha6(IV); Western blotting\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal antibody-based localization in multiple tissues, Western blot validation, replicated by subsequent studies\",\n      \"pmids\": [\"7657706\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"The type and severity of COL4A5 mutation determines the immunohistochemical expression pattern of alpha3(IV)-alpha5(IV) collagen chains in the glomerular basement membrane: deletional and splice site mutations cause complete absence of alpha3(IV)-alpha5(IV) chains, while glycine missense substitutions generally permit residual antigenicity of these chains, demonstrating that alpha5(IV) chain integrity is required for the assembly of the alpha3/alpha4/alpha5 network.\",\n      \"method\": \"Immunohistochemistry with monoclonal antibody series recognizing alpha1(IV)-alpha6(IV) chains in kidney biopsies from patients with identified COL4A5 mutations\",\n      \"journal\": \"Kidney international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct correlation of mutation type with protein expression in tissues, single center, 9 patients\",\n      \"pmids\": [\"8807602\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"Deletions at the 5' end of COL4A5 extending into COL4A6 in diffuse leiomyomatosis/Alport syndrome involve breakpoints with topoisomerase I and II consensus sequences; immunohistochemical analysis confirms absence of alpha5(IV) and alpha6(IV) chains in most basement membranes of the smooth muscle tumor, with mosaic staining in one patient indicating somatic mosaicism.\",\n      \"method\": \"Characterization of deletion breakpoints by sequencing; immunohistochemistry with alpha-chain-specific monoclonal antibodies\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct breakpoint sequencing and immunostaining, single lab\",\n      \"pmids\": [\"9463311\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"The proximal bidirectional promoter between COL4A5 and COL4A6 contains minimal promoters within 100 bp of each transcription start site that are functionally distinct; a bidirectional positive regulatory element functions in multiple cell types but not in glomerular visceral epithelial cells (which selectively transcribe COL4A5). The intergenic region is 292 bp.\",\n      \"method\": \"RNase protection assays for transcription start site mapping; transient transfections with reporter gene constructs; gel shift and footprinting assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — multiple orthogonal methods (reporter assay, footprinting, gel shift) in defined cell types, single lab\",\n      \"pmids\": [\"11096082\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"The bifunctional promoter between COL4A5 and COL4A6 regulates their expression in a cell-specific manner: in glomerular endothelial and mesangial cells, TGF-beta, EGF, VEGF, and PDGF enhance alpha5(IV) expression but not alpha6(IV); in tubular epithelial cells, the same growth factors enhance alpha6(IV) but not alpha5(IV) expression.\",\n      \"method\": \"Reporter gene constructs with bidirectional promoter, transient transfection in cell-type-specific lines, growth factor stimulation assays\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reporter assay in multiple relevant cell types, single lab\",\n      \"pmids\": [\"15598179\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"A large tandem duplication of 35 COL4A5 exons (~65% increase in collagenous domain length) causes Alport syndrome with a founder effect in French Polynesia; the duplicated alpha5(IV) chain can still assemble into the type IV collagen network as demonstrated by immunofluorescence, yet uniformly produces thin GBM in males and variable severity of renal disease.\",\n      \"method\": \"Linkage analysis, mutation screening, immunofluorescence analysis of type IV collagen assembly\",\n      \"journal\": \"Kidney international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct immunofluorescence demonstrating assembly of duplicated chain, single population study\",\n      \"pmids\": [\"15149316\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Chromosomal translocation t(X;6)(q13-14;q22) in subungual exostosis rearranges both COL4A5 (at Xq22) and COL12A1 (at 6q13-14), with FISH showing these two collagen genes consistently co-localizing on derivative chromosomes, suggesting formation of a chimeric fusion gene or regulatory sequence exchange.\",\n      \"method\": \"Interphase and metaphase FISH on tumor cells from five subungual exostoses\",\n      \"journal\": \"International journal of cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — FISH in five cases showing consistent gene rearrangement, single lab, functional consequence not yet determined\",\n      \"pmids\": [\"16284948\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Contiguous deletions at the 5' ends of COL4A5 and COL4A6 that cause Alport syndrome-diffuse leiomyomatosis involve the bidirectional promoter region shared by both genes; eight of nine deletion alleles involve sequences homologous between COL4A5 and COL4A6, with breakpoints in transposed elements (LINEs, SINEs, DNA transposons, LTR retrotransposons), indicating homologous recombination as the mutational mechanism. Leiomyomatosis requires inactivation of both genes.\",\n      \"method\": \"Breakpoint characterization by sequencing in five AS-DL patients; analysis of repetitive element content at breakpoints\",\n      \"journal\": \"Journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct breakpoint sequencing in five patients, single lab, consistent mechanistic model\",\n      \"pmids\": [\"28275241\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Exon skipping using antisense oligonucleotides (ASO) targeting exon 21 of COL4A5 in truncating variant Alport syndrome enables formation of the type IV collagen alpha3/alpha4/alpha5 heterotrimer (demonstrated by triple helix formation assay), restores alpha5 chain expression on glomerular and tubular basement membranes in vivo, and prolongs survival in treated mice.\",\n      \"method\": \"Type IV collagen alpha3/alpha4/alpha5 chain triple helix formation assay; in vitro and in vivo ASO treatment; immunostaining; survival analysis in mouse model\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — biochemical trimer formation assay combined with in vivo functional rescue, multiple orthogonal readouts\",\n      \"pmids\": [\"32488001\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"A cell-based split nanoluciferase assay measuring alpha345(IV) heterotrimer formation showed that COL4A5 glycine missense mutations associated with early proteinuria and renal failure significantly reduce secreted trimer, either by reducing intracellular trimer formation or blocking secretion; mutations without early proteinuria showed trimer formation and secretion patterns similar to wild-type.\",\n      \"method\": \"Split nanoluciferase-fused alpha3/alpha5 mutant and alpha4 co-transfection assay measuring intracellular and secreted heterotrimer by luminescence\",\n      \"journal\": \"Kidney international reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — biochemical reconstitution-type cell assay with multiple mutants, single lab, correlates with clinical data\",\n      \"pmids\": [\"32405592\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Col4a5-deficient rats generated by CRISPR/rGONAD show disruption of both alpha3/alpha4/alpha5(IV) and alpha5/alpha5/alpha6(IV) type IV collagen networks in the kidney, demonstrating that Col4a5 is required for assembly of both collagen IV heterotrimeric networks in vivo.\",\n      \"method\": \"CRISPR-mediated Col4a5 knockout in rats; immunostaining for collagen IV alpha chain distribution; histological and ultrastructural analysis\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic loss-of-function with specific protein network readout, single lab\",\n      \"pmids\": [\"34675305\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"A Col4a5 R471X nonsense mutation introduced into mice by CRISPR/Cas9 abolishes Col4a5 mRNA and protein expression in kidney, producing proteinuria, hematuria, glomerulosclerosis, interstitial fibrosis, and GBM irregular thickening with lamination consistent with Alport syndrome.\",\n      \"method\": \"CRISPR/Cas9 knock-in mouse model; RT-PCR and Western blot for Col4a5 expression; pathological and electron microscopy analysis\",\n      \"journal\": \"Biochemistry and biophysics reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct genetic loss-of-function with defined molecular and pathological phenotype, single lab\",\n      \"pmids\": [\"30582011\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"A COL4A5 missense mutation (p.F222C) in a non-collagenous interruption of the collagenous domain causes severe glomerular disease with global/segmental glomerulosclerosis and rapid progression to ESRD in males despite normal alpha5(IV) immunostaining, demonstrating that non-collagenous interruption residues are functionally critical for COL4A5 function beyond its structural role in basement membrane network assembly.\",\n      \"method\": \"Exon sequencing of COL4A5 in affected family; immunostaining for alpha5(IV) collagen in renal biopsies; segregation analysis in family\",\n      \"journal\": \"Kidney international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mutation with defined renal phenotype and normal protein expression, functional significance of non-collagenous domain established, single lab\",\n      \"pmids\": [\"20881942\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Single-base substitutions at the last nucleotide position of COL4A5 exons cause aberrant splicing (confirmed in 85% of 20 variants tested), resulting in exon skipping or cryptic splice site activation, as determined by hybrid minigene functional splicing assay; in vivo transcript analyses confirmed minigene results in all three cases tested.\",\n      \"method\": \"Hybrid minigene splicing assay; in vivo transcript analysis by RT-PCR of patient samples\",\n      \"journal\": \"Kidney international reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — functional splicing assay with multiple variants, validated by in vivo analysis, single lab\",\n      \"pmids\": [\"35005319\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In vitro splicing assays using hybrid minigenes for seven COL4A5 intronic mutations revealed exon skipping in four variants, combined exon skipping and insertion in one, and no change (likely non-pathogenic) in one, providing mechanistic determination of pathogenicity for intronic COL4A5 variants.\",\n      \"method\": \"Hybrid minigene in vitro splicing assay; comparison to patient transcript data where available\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — functional assay, single lab, validated against patient transcripts in three cases\",\n      \"pmids\": [\"31481700\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Somatic mosaicism for a COL4A5 splice acceptor mutation (c.3998-2 a>t) causes mosaic alpha5(IV) staining in glomeruli and a mild phenotype; mRNA analysis from urinary sediments demonstrated both normal transcript and transcript with exon 44 skipping in the same patient, establishing that the ratio of normal to abnormal transcript determines disease severity.\",\n      \"method\": \"Direct sequencing showing two allele peaks; restriction enzyme analysis confirming mosaicism; RT-PCR of urinary sediment mRNA; immunohistochemistry\",\n      \"journal\": \"Nephrology, dialysis, transplantation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple methods confirming mosaicism and its molecular consequence, single patient/lab\",\n      \"pmids\": [\"18332068\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"COL4A5 encodes the alpha5(IV) collagen chain, which heterotrimes with alpha3(IV) and alpha4(IV) to form the type IV collagen network essential for glomerular basement membrane integrity; the COL4A5/COL4A6 gene pair is regulated by a bifunctional bidirectional promoter with cell-type-specific activity, the alpha5(IV) chain is required for proper assembly and secretion of the alpha345(IV) heterotrimer, and mutations disrupting the chain (deletions, truncations, glycine substitutions, splice defects) cause X-linked Alport syndrome through failure of this network, with mutation type and resulting trimer assembly capacity predicting disease severity.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"COL4A5 encodes the alpha5(IV) collagen chain, a structural component of basement membranes whose disruption causes X-linked Alport syndrome with nephritis and deafness [#0]. The alpha5(IV) chain is required for assembly of the alpha3/alpha4/alpha5(IV) type IV collagen network of the glomerular basement membrane: loss of COL4A5 abolishes incorporation of the alpha3(IV) chain into the GBM [#4], and Col4a5 deficiency in vivo disrupts both the alpha3/alpha4/alpha5(IV) and alpha5/alpha5/alpha6(IV) networks [#17]. Heterotrimer assembly capacity links genotype to phenotype: deletional and splice-site mutations cause complete absence of alpha3-alpha5(IV) chains while glycine missense substitutions permit residual antigenicity [#8], and glycine missense mutations associated with early renal failure measurably reduce intracellular trimer formation or block secretion in a split-nanoluciferase trimer assay [#16]. A large proportion of pathogenic variants act through aberrant splicing — cryptic splice site use, exon skipping, and frameshift-driven premature stop codons [#5, #20]. COL4A5 is arranged head-to-head with COL4A6 on Xq22 and shares a bidirectional, cell-type-specific bifunctional promoter, such that growth factors selectively enhance alpha5(IV) expression in glomerular cells while enhancing alpha6(IV) in tubular cells [#2, #11]; contiguous deletions at this shared 5' region cause Alport syndrome with diffuse leiomyomatosis [#1, #14]. Antisense-oligonucleotide exon skipping restores alpha345(IV) heterotrimer formation, GBM alpha5 expression, and survival in a truncating-variant Alport model, providing therapeutic proof of the assembly mechanism [#15].\",\n  \"teleology\": [\n    {\n      \"year\": 1990,\n      \"claim\": \"Established the disease gene: mutations in COL4A5 cause X-linked Alport syndrome, defining alpha5(IV) as a structural GBM component whose loss produces nephritis and deafness.\",\n      \"evidence\": \"Southern blotting and restriction/genomic analysis in Alport kindreds\",\n      \"pmids\": [\"2349482\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve how alpha5(IV) integrates into a multi-chain network\", \"Mechanism linking chain loss to GBM failure not yet defined\"]\n    },\n    {\n      \"year\": 1994,\n      \"claim\": \"Defined the genomic architecture and regulatory context: the 51-exon COL4A5 gene sits head-to-head with COL4A6 sharing a bidirectional, tissue-specific promoter, framing both single-gene and contiguous-gene-deletion disease.\",\n      \"evidence\": \"Genomic cloning/sequencing of the gene and RT-PCR of tissue-specific transcripts\",\n      \"pmids\": [\"8120014\", \"7972123\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cell-type selectivity of the promoter not yet functionally dissected\", \"Regulatory elements driving glomerulus-specific COL4A5 expression unmapped\"]\n    },\n    {\n      \"year\": 1994,\n      \"claim\": \"Connected COL4A5 loss to network assembly failure: gene deletion abolishes alpha5(IV) and prevents alpha3(IV) incorporation into the GBM, showing alpha5 is needed for the alpha3-containing network.\",\n      \"evidence\": \"Alloantibody binding to recombinant NC1 domains in a deletion patient\",\n      \"pmids\": [\"8196274\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single patient\", \"Did not directly measure trimer assembly biochemistry\"]\n    },\n    {\n      \"year\": 1992,\n      \"claim\": \"Explained the Alport-diffuse leiomyomatosis association as a contiguous-gene phenomenon involving 5' COL4A5 deletions extending into an adjacent gene.\",\n      \"evidence\": \"Southern blotting with COL4A5 cDNA and 5' genomic probes in DL-AS patients\",\n      \"pmids\": [\"1453602\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Adjacent gene (COL4A6) not yet directly implicated mechanistically\", \"Three patients only\"]\n    },\n    {\n      \"year\": 1995,\n      \"claim\": \"Mapped reciprocal tissue distribution of alpha5(IV) and alpha6(IV), showing alpha5 but not alpha6 in GBM and co-localization in skin/smooth muscle, explaining tissue-restricted disease consequences.\",\n      \"evidence\": \"Immunofluorescence and Western blot with NC1-specific monoclonal antibodies across tissues\",\n      \"pmids\": [\"7657706\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define which heterotrimers form in each tissue\", \"Chain stoichiometry within networks not resolved\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Established a genotype-protein correlation: mutation class predicts whether alpha3-alpha5(IV) chains are absent versus retained, linking chain integrity to network assembly.\",\n      \"evidence\": \"Immunohistochemistry with chain-specific antibodies in biopsies from genotyped patients\",\n      \"pmids\": [\"8807602\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Nine patients, single center\", \"Did not measure trimer assembly directly\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Functionally dissected the bidirectional promoter, identifying minimal promoters and a positive regulatory element active in most cell types but not glomerular visceral epithelium, explaining selective COL4A5 transcription.\",\n      \"evidence\": \"RNase protection, reporter transfections, gel shift and footprinting in defined cell lines\",\n      \"pmids\": [\"11096082\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Transcription factors conferring glomerular selectivity not identified\", \"In vivo relevance of element not tested\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Showed the bifunctional promoter responds to growth factors in a cell-type-directional manner (alpha5 in glomerular cells, alpha6 in tubular cells), establishing context-dependent regulation.\",\n      \"evidence\": \"Bidirectional reporter constructs with growth-factor stimulation in cell-type-specific lines\",\n      \"pmids\": [\"15598179\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Signalling intermediates downstream of TGF-beta/EGF/VEGF/PDGF not defined\", \"Reporter assay, single lab\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Demonstrated that the ratio of normal to aberrant transcript governs disease severity, using somatic mosaicism for a splice mutation producing mosaic alpha5 staining and mild phenotype.\",\n      \"evidence\": \"Sequencing/restriction mosaicism detection, urinary-sediment RT-PCR, immunohistochemistry\",\n      \"pmids\": [\"18332068\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single patient\", \"Quantitative threshold of transcript ratio not established\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Revealed that non-collagenous interruption residues are functionally critical: an interruption-domain missense caused severe disease despite normal alpha5(IV) staining, expanding function beyond bulk network assembly.\",\n      \"evidence\": \"Exon sequencing, alpha5 immunostaining, and family segregation\",\n      \"pmids\": [\"20881942\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular basis of interruption-residue function unresolved\", \"Single family\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defined the mutational mechanism of AS-DL contiguous deletions as homologous recombination between COL4A5/COL4A6 repetitive elements across the shared promoter, with leiomyomatosis requiring inactivation of both genes.\",\n      \"evidence\": \"Breakpoint sequencing and repetitive-element analysis in AS-DL patients\",\n      \"pmids\": [\"28275241\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Five patients\", \"How biallelic-region loss drives smooth muscle proliferation not mechanistically shown\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Provided direct biochemical proof of the assembly mechanism: glycine missense mutations tied to early renal failure reduce secreted alpha345(IV) trimer, while benign-course mutations assemble normally.\",\n      \"evidence\": \"Split-nanoluciferase alpha3/alpha4/alpha5 co-transfection trimer assay across mutants\",\n      \"pmids\": [\"32405592\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab cell-based assay\", \"Does not capture in vivo GBM incorporation kinetics\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Delivered therapeutic validation of the assembly model: ASO exon-21 skipping restores trimer formation, GBM alpha5 expression, and survival in truncating-variant Alport mice.\",\n      \"evidence\": \"Triple-helix formation assay plus in vitro/in vivo ASO treatment with immunostaining and survival readouts\",\n      \"pmids\": [\"32488001\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Limited to specific truncating-variant context\", \"Long-term durability and human translation untested\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Confirmed in vivo that Col4a5 is required for assembly of both the alpha3/alpha4/alpha5 and alpha5/alpha5/alpha6 networks via a genetic knockout.\",\n      \"evidence\": \"CRISPR/rGONAD Col4a5-knockout rat with chain-specific immunostaining and ultrastructural analysis\",\n      \"pmids\": [\"34675305\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Did not isolate tissue-specific contributions of each network to pathology\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Systematically established splicing disruption as a major pathogenic mechanism, showing last-nucleotide and intronic variants cause exon skipping or cryptic splice activation.\",\n      \"evidence\": \"Hybrid minigene splicing assays with in vivo transcript confirmation\",\n      \"pmids\": [\"35005319\", \"31481700\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Minigene context may not fully recapitulate native splicing\", \"Quantitative effect on residual protein not measured for all variants\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How cell-type-specific transcription factors select COL4A5 versus COL4A6 from the shared promoter, and the molecular basis by which non-collagenous interruption residues contribute to chain function, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No transcription factor mediating glomerular COL4A5 selectivity identified\", \"Structural basis of interruption-residue requirement unknown\", \"Mechanism linking COL4A5/COL4A6 biallelic loss to leiomyomatosis undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 4, 17]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0031012\", \"supporting_discovery_ids\": [4, 7, 8]},\n      {\"term_id\": \"GO:0005576\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1474244\", \"supporting_discovery_ids\": [4, 8, 15, 17]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [0, 1, 18]}\n    ],\n    \"complexes\": [\"alpha3/alpha4/alpha5(IV) collagen heterotrimer\", \"alpha5/alpha5/alpha6(IV) collagen heterotrimer\"],\n    \"partners\": [\"COL4A3\", \"COL4A4\", \"COL4A6\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}