{"gene":"FAM111A","run_date":"2026-06-09T23:54:43","timeline":{"discoveries":[{"year":2012,"finding":"FAM111A was identified as a host restriction factor for SV40 replication. Affinity purification followed by mass spectrometry revealed a specific interaction between the SV40 large T antigen (LT) C-terminal region and FAM111A. Depletion of FAM111A recapitulated the effects of heterologous expression of the LT C-terminal region, rescuing viral gene expression and lytic infection of SV40 host range mutants in restrictive cells.","method":"Affinity purification/mass spectrometry, siRNA depletion, viral replication assays","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal interaction confirmed by AP-MS, functional rescue with depletion, replicated in subsequent studies","pmids":["23093934"],"is_preprint":false},{"year":2013,"finding":"FAM111A encodes a 611 amino acid protein with homology to trypsin-like peptidases. Disease-causing mutations in Kenny-Caffey syndrome (KCS) and osteocraniostenosis (OCS) map to a surface-exposed segment clustered away from the predicted active site, suggesting pathogenesis involves disruption of protein-protein interactions rather than impaired catalysis.","method":"Exome sequencing, molecular modeling of protein structure","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — molecular modeling with mutational mapping, replicated across multiple unrelated patients but no in vitro functional assay","pmids":["23684011"],"is_preprint":false},{"year":2017,"finding":"FAM111A functions as a host restriction factor for orthopoxvirus SPI-1 deletion mutants. Genome-wide siRNA screen and secondary confirmation assays showed that depletion of FAM111A (along with RFC3 and IRF2) increased replication of the SPI-1 deletion mutant. IRF2 was further shown to regulate basal FAM111A expression levels by microarray, qRT-PCR, and immunoblotting, making the IRF2 effect on viral replication indirect (through FAM111A).","method":"Genome-wide siRNA screen, secondary confirmation assays, microarray, qRT-PCR, immunoblotting","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — genome-wide screen with secondary validation, multiple orthogonal methods confirming IRF2→FAM111A regulatory axis","pmids":["28320935"],"is_preprint":false},{"year":2018,"finding":"FAM111A localizes to nucleoli in uninfected cells in a cell cycle-dependent manner, and relocalizes to SV40 viral replication centers upon infection with wild-type or host range (HR) mutant SV40. FAM111A restricts HR virus replication center formation, and this restriction is dependent on viral DNA replication, as inhibition of viral DNA replication with aphidicolin or replication-defective SV40 mutants diminished the effect of FAM111A depletion on viral gene expression.","method":"Immunofluorescence localization, aphidicolin inhibition, FAM111A depletion, replication-defective mutant SV40","journal":"Journal of virology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — direct localization experiments tied to functional consequence, multiple genetic/pharmacological perturbations in a single study","pmids":["30333173"],"is_preprint":false},{"year":2020,"finding":"FAM111A is a PCNA-interacting serine protease that protects replication forks from protein obstacles (DNA-protein crosslinks, DPCs) via its trypsin-like protease domain. FAM111A protects forks specifically from PARP1-DNA complexes trapped by PARP inhibitors, a function not shared by SPRTN. The PCNA interaction motif (PIP box) and a DNA-binding domain necessary for protease activity in vivo are required for this function.","method":"PCNA interaction assays, domain mutagenesis, PARP inhibitor treatment, replication fork protection assays, cell survival assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple domain mutants tested, PARP inhibitor DPC model with orthogonal assays, complementation experiments, replicated concept in subsequent papers","pmids":["32165630"],"is_preprint":false},{"year":2021,"finding":"IRF2 inhibits ZIKV replication by upregulating FAM111A expression, which in turn enhances the host restriction effect of RFC3. Knockdown of IRF2 reduced FAM111A expression; overexpression of IRF2 increased it. This regulatory axis was shown to operate independently of type I IFN signaling.","method":"siRNA knockdown, plasmid overexpression, RT-qPCR, western blot, viral replication assays","journal":"Virology journal","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab, multiple methods but mechanistic link between FAM111A and RFC3 downstream not fully resolved","pmids":["34930359"],"is_preprint":false},{"year":2022,"finding":"FAM111A knockout (Fam111a-/-) mice exhibit normal electrolyte homeostasis, normal serum PTH, calcium, magnesium, and phosphate, and unaffected bone morphology and density on a standard diet. This indicates FAM111A loss alone is not sufficient to recapitulate the electrolyte/skeletal phenotype of Kenny-Caffey syndrome in mice.","method":"Fam111a knockout mouse model (C57BL/6N), serum/urine electrolyte measurement, gene expression analysis, histology","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — clean KO mouse with defined phenotypic readouts, multiple electrolyte and histological endpoints, single lab","pmids":["35715480"],"is_preprint":false},{"year":2023,"finding":"FAM111A facilitates efficient activation of DNA replication origins under normal conditions. FAM111A-depleted cells show reduced single-stranded DNA (ssDNA) formation and better survival under hydroxyurea treatment. Unrestrained FAM111A expression causes DNA damage and cell death dependent on intact peptidase activity and S-phase entry, but not on PCNA binding.","method":"siRNA depletion, overexpression of WT and patient mutants, ssDNA formation assays, cell survival assays, DNA damage markers","journal":"Life science alliance","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal assays (ssDNA, survival, damage markers), domain dissection with PCNA-binding mutant, multiple mutant constructs","pmids":["37793778"],"is_preprint":false},{"year":2023,"finding":"FAM111A directly degrades vaccinia virus (VACV) DNA-binding protein I3 through autophagy. Upon VACV infection, FAM111A translocates from nucleus to cytoplasm by degrading the nuclear pore complex via its protease activity, then interacts with and promotes I3 degradation. This antiviral function requires the trypsin-like protease domain and DNA-binding domain but not the PCNA-interacting motif. The poxvirus virulence factor SPI-1 antagonizes FAM111A by preventing its nuclear export.","method":"FAM111A deletion/overexpression, co-immunoprecipitation, viral replication assays, viral DNA quantification, nuclear pore complex degradation assays, autophagy assays, confocal microscopy","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (CoIP, domain mutants, localization, viral replication), mechanistic pathway experimentally confirmed in a single rigorous study","pmids":["37607234"],"is_preprint":false},{"year":2024,"finding":"FAM111A is a dimerization-dependent serine protease. X-ray crystal structures and mutagenesis show it dimerizes via an N-terminal helix within the serine protease domain (SPD), which induces an activation cascade from a dimerization sensor loop to the oxyanion hole through disorder-to-order transitions. FAM111A cleaves substrates with chymotrypsin-like specificity and has a narrow, recessed active site. Dimerization is required for substrate cleavage and for facilitating replication at DPC obstacles in cells, but is dispensable for autocleavage.","method":"X-ray crystallography, mutagenesis, in vitro protease assays, DPC bypass assays in cells","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus mutagenesis plus in vitro reconstitution plus cellular functional validation, multiple orthogonal methods","pmids":["38453899"],"is_preprint":false},{"year":2024,"finding":"Disruption of the FAM111A C-terminal serine protease domain in mice (frameshift or large deletion via CRISPR/Cas9) does not alter serum calcium or PTH levels, Ca2+ excretion, intestinal absorption, or overall Ca2+ balance. Only female homozygous (c.1450insA) mice showed differences in bone microarchitecture and mineral density. These results indicate the serine protease domain is not required for calcium homeostasis in mice.","method":"CRISPR/Cas9 knock-in mouse models, serum/urine Ca2+/PTH measurement, intestinal Ca2+ absorption assay, micro-CT bone analysis","journal":"Physiological reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct CRISPR mouse models with multiple physiological endpoints, single lab, confirms negative result for Ca2+ regulation","pmids":["38697929"],"is_preprint":false},{"year":2025,"finding":"SPI-1 (poxvirus serpin) directly inhibits FAM111A protease activity in vitro through covalent complex formation, a hallmark of serpin inhibition. SPI-1 shows specificity for FAM111A compared to other serine proteases. Mutagenesis of the SPI-1 reactive center loop (RCL) identified residues critical for FAM111A inhibition and covalent complex formation, and these mutations showed correlated effects on supporting RPXV replication in non-permissive cells.","method":"In vitro protease inhibition assay, covalent complex formation assay, SPI-1 RCL mutagenesis, viral replication rescue assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution of direct inhibition, mutagenesis of both partners, correlated cellular functional validation, single lab","pmids":["39798873"],"is_preprint":false},{"year":2025,"finding":"FAM111A is transcriptionally repressed by the androgen receptor (AR) via an AR binding site within the FAM111A gene. FAM111A protein subcellular localization shifts from predominantly nucleolar in castration-sensitive prostate cancer cells to more dispersed nuclear and cytoplasmic in castration-resistant cells. FAM111A depletion enhances sensitivity to PARP inhibitors olaparib and niraparib, and reduces AR target gene (PSA, TMPRSS2) transcription, indicating a FAM111A-AR co-regulatory loop.","method":"AR ChIP (AR binding site), knockdown/overexpression, xenograft models, subcellular fractionation/immunofluorescence, PARP inhibitor sensitivity assays, RT-qPCR","journal":"Neoplasia (New York, N.Y.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — AR binding site identified, multiple cellular models and in vivo xenografts, direct localization with functional consequence, single lab","pmids":["40446667"],"is_preprint":false},{"year":2025,"finding":"Biallelic hypermorphic FAM111A variants (Y414C and Y414N) cause autosomal recessive KCS/OCS. Recombinant FAM111A-Y414C showed normal dimerization but a mild gain-of-function effect in protease activity assays, indicating that quantitative hypermorphic activation (not just loss-of-function) of FAM111A protease underlies the skeletal dysplasia phenotype even in a recessive context.","method":"Exome sequencing, recombinant protein production, in vitro protease activity assays, dimerization assays","journal":"JCI insight","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro biochemical assays with recombinant protein, single lab, limited to one variant functionally characterized","pmids":["39932783"],"is_preprint":false},{"year":2025,"finding":"ATRX suppresses DNA damage during replication stress by counteracting the activity of the FAM111A protease. Genetic epistasis experiments in ATRX-deficient cells revealed that ATRX's role in replication requires its PIP-box (independent of its DAXX interaction), placing FAM111A activity downstream of ATRX in the replication stress response pathway.","method":"Genetic epistasis (double mutants), CRISPR/Cas9 KO, domain mutants (ATPase, PIP-box, DAXX-interaction), replication stress assays","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — genetic epistasis with multiple domain mutants, preprint not yet peer-reviewed, single lab","pmids":["bio_10.1101_2025.09.22.677761"],"is_preprint":true}],"current_model":"FAM111A is a nuclear, dimerization-dependent trypsin-like serine protease that associates with PCNA at replication forks, where it cleaves protein obstacles (DNA-protein crosslinks, including trapped PARP1 and topoisomerase 1 cleavage complexes) to facilitate replication fork progression; its protease activity is activated by dimerization via an N-terminal helix and follows chymotrypsin-like specificity, while disease-causing gain-of-function mutations in the catalytic domain cause hyper-autocleavage and are linked to Kenny-Caffey syndrome and osteocraniostenosis; FAM111A also functions as an antiviral restriction factor that degrades the nuclear pore complex to relocalize to the cytoplasm and degrades poxviral protein I3 via autophagy, and is directly inhibited by the poxviral serpin SPI-1 through covalent complex formation."},"narrative":{"mechanistic_narrative":"FAM111A is a nuclear, PCNA-associated trypsin-like serine protease that safeguards DNA replication by removing protein obstacles from replication forks and that doubles as a viral restriction factor [PMID:32165630, PMID:23093934]. At the fork, FAM111A binds PCNA through a PIP box and uses its protease and DNA-binding domains to clear DNA-protein crosslinks, including PARP1-DNA complexes trapped by PARP inhibitors, a function distinct from SPRTN [PMID:32165630]. It also promotes efficient activation of replication origins under normal conditions, and unrestrained protease activity drives ssDNA accumulation, DNA damage, and cell death dependent on intact peptidase activity and S-phase entry but not on PCNA binding [PMID:37793778]. Catalytic activity is governed by dimerization: FAM111A dimerizes via an N-terminal helix within the serine protease domain, triggering a disorder-to-order activation cascade that builds the oxyanion hole and confers chymotrypsin-like specificity through a narrow, recessed active site; dimerization is required for substrate cleavage and DPC bypass but is dispensable for autocleavage [PMID:38453899]. In its antiviral role, FAM111A restricts SV40 and orthopoxvirus replication, localizing to nucleoli in a cell-cycle-dependent manner and relocalizing to SV40 replication centers in a manner dependent on viral DNA replication [PMID:23093934, PMID:30333173, PMID:28320935]; against vaccinia virus it degrades the nuclear pore complex to translocate to the cytoplasm and then targets the viral DNA-binding protein I3 for autophagic degradation, an activity antagonized by the poxviral serpin SPI-1 which prevents nuclear export and directly inhibits FAM111A through covalent complex formation [PMID:37607234, PMID:39798873]. Basal FAM111A expression is set by IRF2 and is repressed by the androgen receptor [PMID:28320935, PMID:40446667]. Hypermorphic gain-of-function variants in the catalytic domain cause Kenny-Caffey syndrome and osteocraniostenosis, including biallelic recessive variants that mildly elevate protease activity without altering dimerization [PMID:39932783].","teleology":[{"year":2012,"claim":"Established FAM111A as a host factor whose removal phenocopies the SV40 large T antigen function, defining its first biological role as a viral restriction factor.","evidence":"AP-MS of SV40 LT C-terminus, siRNA depletion and viral replication rescue assays","pmids":["23093934"],"confidence":"High","gaps":["Did not define the molecular activity of FAM111A","Mechanism of restriction unresolved"]},{"year":2013,"claim":"Linked FAM111A to Kenny-Caffey syndrome and osteocraniostenosis and predicted a trypsin-like peptidase fold, framing pathogenesis as a question of catalysis versus interaction.","evidence":"Exome sequencing of patients with molecular modeling of mutation positions","pmids":["23684011"],"confidence":"Medium","gaps":["No in vitro catalytic assay performed","Mutation effect on protease activity inferred only from modeling"]},{"year":2017,"claim":"Extended FAM111A restriction to orthopoxvirus SPI-1 deletion mutants and identified IRF2 as a transcriptional regulator setting basal FAM111A levels.","evidence":"Genome-wide siRNA screen with secondary validation, microarray, qRT-PCR and immunoblotting","pmids":["28320935"],"confidence":"High","gaps":["Mechanism by which FAM111A restricts poxvirus not defined","Direct FAM111A targets in poxvirus unknown"]},{"year":2018,"claim":"Defined FAM111A's cell-cycle-dependent nucleolar localization and its replication-dependent relocalization to viral replication centers, tying restriction to DNA replication.","evidence":"Immunofluorescence, aphidicolin inhibition and replication-defective SV40 mutants with FAM111A depletion","pmids":["30333173"],"confidence":"High","gaps":["Molecular substrate at viral replication centers not identified","Trigger for nucleolar release not defined"]},{"year":2020,"claim":"Identified FAM111A as a PCNA-interacting protease that clears DNA-protein crosslinks at forks, distinguishing it from SPRTN and specifying PARP1-DNA complexes as obstacles.","evidence":"PCNA interaction assays, PIP-box and DNA-binding domain mutagenesis, PARP inhibitor and fork protection assays","pmids":["32165630"],"confidence":"High","gaps":["Direct cleavage of PARP1 not biochemically reconstituted in this study","Substrate spectrum at forks incomplete"]},{"year":2021,"claim":"Showed the IRF2-FAM111A axis restricts ZIKV and enhances RFC3-mediated restriction independently of type I IFN, broadening FAM111A's antiviral scope to an RNA virus.","evidence":"siRNA knockdown, overexpression, RT-qPCR, western blot and viral replication assays","pmids":["34930359"],"confidence":"Medium","gaps":["Mechanistic link between FAM111A and RFC3 unresolved","Single lab, ZIKV restriction mechanism not defined"]},{"year":2022,"claim":"Demonstrated that FAM111A loss alone does not recapitulate Kenny-Caffey electrolyte or skeletal phenotypes in mice, arguing against simple loss-of-function pathogenesis.","evidence":"Fam111a knockout mouse with serum/urine electrolyte, gene expression and histology readouts","pmids":["35715480"],"confidence":"High","gaps":["Does not test gain-of-function disease alleles","Possible compensation in mouse not excluded"]},{"year":2023,"claim":"Placed FAM111A in normal origin activation and showed that excess protease activity is toxic through ssDNA, DNA damage and S-phase-dependent death, decoupling toxicity from PCNA binding.","evidence":"siRNA depletion, WT and patient-mutant overexpression, ssDNA, survival and DNA damage marker assays","pmids":["37793778"],"confidence":"High","gaps":["Substrates driving origin activation not identified","Link between toxicity and disease phenotype indirect"]},{"year":2023,"claim":"Revealed an antiviral effector mechanism in which FAM111A degrades the nuclear pore complex to exit the nucleus and then drives autophagic degradation of vaccinia I3, with SPI-1 blocking nuclear export.","evidence":"Domain mutants, Co-IP, viral replication and DNA quantification, NPC degradation, autophagy assays and confocal microscopy","pmids":["37607234"],"confidence":"High","gaps":["NPC components cleaved not enumerated","Mechanism of SPI-1 export block not resolved at this stage"]},{"year":2024,"claim":"Solved the structural basis of FAM111A activation, showing dimerization via an N-terminal helix drives a disorder-to-order cascade to build the active site with chymotrypsin-like specificity, required for cleavage but not autocleavage.","evidence":"X-ray crystallography, mutagenesis, in vitro protease assays and cellular DPC bypass assays","pmids":["38453899"],"confidence":"High","gaps":["Physiological dimerization trigger not defined","Full substrate repertoire not mapped"]},{"year":2024,"claim":"Showed disruption of the FAM111A protease domain does not alter calcium homeostasis in mice, further dissociating the protease from the renal/skeletal disease phenotype.","evidence":"CRISPR/Cas9 knock-in mice with serum/urine Ca2+/PTH, intestinal absorption and micro-CT analysis","pmids":["38697929"],"confidence":"Medium","gaps":["Only one allele showed a sex-specific bone effect","Human gain-of-function not modeled directly"]},{"year":2025,"claim":"Reconstituted direct inhibition of FAM111A by the poxvirus serpin SPI-1 through covalent complex formation, defining a molecular mechanism for poxviral antagonism.","evidence":"In vitro protease inhibition and covalent complex assays, SPI-1 RCL mutagenesis and viral replication rescue","pmids":["39798873"],"confidence":"High","gaps":["Cellular stoichiometry of inhibition not quantified","Single lab"]},{"year":2025,"claim":"Connected FAM111A to androgen receptor signaling, showing AR represses FAM111A and that depletion sensitizes prostate cancer cells to PARP inhibitors, defining a co-regulatory loop with therapeutic relevance.","evidence":"AR ChIP, knockdown/overexpression, xenografts, subcellular fractionation/IF, PARP inhibitor and RT-qPCR assays","pmids":["40446667"],"confidence":"Medium","gaps":["Direct AR binding consequence on FAM111A protease not tested","Single lab"]},{"year":2025,"claim":"Demonstrated that biallelic hypermorphic variants causing recessive KCS/OCS act by quantitatively elevating protease activity without altering dimerization, establishing gain-of-function as the disease mechanism.","evidence":"Exome sequencing, recombinant protein production, in vitro protease and dimerization assays","pmids":["39932783"],"confidence":"Medium","gaps":["Only one variant functionally characterized","Tissue-specific consequence not modeled"]},{"year":null,"claim":"How FAM111A protease activity is physiologically licensed and restrained at forks, and how its gain-of-function in disease tissues produces skeletal/endocrine pathology not seen in mouse loss models, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["Endogenous dimerization/activation trigger unknown","Complete fork substrate spectrum unmapped","Mechanistic basis of tissue-specific disease phenotype undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[4,8,9]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[4,9,11]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[4,8]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[3,12]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[3,8]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[8,12]}],"pathway":[{"term_id":"R-HSA-69306","term_label":"DNA Replication","supporting_discovery_ids":[4,7]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[4,7]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,2,8]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[8]}],"complexes":[],"partners":["PCNA","PARP1","SPI-1","IRF2","AR","ATRX"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96PZ2","full_name":"Serine protease FAM111A","aliases":[],"length_aa":611,"mass_kda":70.2,"function":"Single-stranded DNA-binding serine protease that mediates the proteolytic cleavage of covalent DNA-protein cross-links (DPCs) during DNA synthesis, thereby playing a key role in maintaining genomic integrity (PubMed:32165630). DPCs are highly toxic DNA lesions that interfere with essential chromatin transactions, such as replication and transcription, and which are induced by reactive agents, such as UV light or formaldehyde (PubMed:32165630). Protects replication fork from stalling by removing DPCs, such as covalently trapped topoisomerase 1 (TOP1) adducts on DNA lesion, or poly(ADP-ribose) polymerase 1 (PARP1)-DNA complexes trapped by PARP inhibitors (PubMed:32165630). Required for PCNA loading on replication sites (PubMed:24561620). Promotes S-phase entry and DNA synthesis (PubMed:24561620). Also acts as a restriction factor for some viruses including SV40 polyomavirus and vaccinia virus (PubMed:23093934, PubMed:37607234). Mechanistically, affects nuclear barrier function during viral replication by mediating the disruption of the nuclear pore complex (NPC) via its protease activity (PubMed:33369867, PubMed:37607234). In turn, interacts with vaccinia virus DNA-binding protein OPG079 in the cytoplasm and promotes its degradation without the need of its protease activity but through autophagy (PubMed:37607234)","subcellular_location":"Nucleus; Chromosome; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q96PZ2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/FAM111A","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/FAM111A","total_profiled":1310},"omim":[{"mim_id":"615292","title":"FAMILY WITH SEQUENCE SIMILARITY 111, MEMBER A; FAM111A","url":"https://www.omim.org/entry/615292"},{"mim_id":"602361","title":"GRACILE BONE DYSPLASIA; GCLEB","url":"https://www.omim.org/entry/602361"},{"mim_id":"127000","title":"KENNY-CAFFEY SYNDROME, TYPE 2; KCS2","url":"https://www.omim.org/entry/127000"},{"mim_id":"114105","title":"PROTEIN PHOSPHATASE 3, CATALYTIC SUBUNIT, ALPHA ISOFORM; PPP3CA","url":"https://www.omim.org/entry/114105"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Nucleoli fibrillar center","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/FAM111A"},"hgnc":{"alias_symbol":["FLJ22794","KIAA1895"],"prev_symbol":[]},"alphafold":{"accession":"Q96PZ2","domains":[{"cath_id":"3.10.20.90","chopping":"74-267","consensus_level":"medium","plddt":82.8508,"start":74,"end":267},{"cath_id":"2.40.10.10","chopping":"344-456","consensus_level":"medium","plddt":92.4,"start":344,"end":456},{"cath_id":"2.40.10.10","chopping":"459-583","consensus_level":"medium","plddt":87.4829,"start":459,"end":583},{"cath_id":"1.20.5","chopping":"293-331","consensus_level":"high","plddt":80.4746,"start":293,"end":331}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96PZ2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96PZ2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96PZ2-F1-predicted_aligned_error_v6.png","plddt_mean":76.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=FAM111A","jax_strain_url":"https://www.jax.org/strain/search?query=FAM111A"},"sequence":{"accession":"Q96PZ2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96PZ2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96PZ2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96PZ2"}},"corpus_meta":[{"pmid":"23684011","id":"PMC_23684011","title":"FAM111A mutations result in hypoparathyroidism and impaired skeletal development.","date":"2013","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/23684011","citation_count":95,"is_preprint":false},{"pmid":"32165630","id":"PMC_32165630","title":"FAM111A protects replication forks from protein obstacles via its trypsin-like domain.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/32165630","citation_count":94,"is_preprint":false},{"pmid":"23093934","id":"PMC_23093934","title":"Identification of FAM111A as an SV40 host range restriction and adenovirus helper factor.","date":"2012","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/23093934","citation_count":63,"is_preprint":false},{"pmid":"23996431","id":"PMC_23996431","title":"A recurrent de novo FAM111A mutation causes Kenny-Caffey syndrome type 2.","date":"2014","source":"Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research","url":"https://pubmed.ncbi.nlm.nih.gov/23996431","citation_count":57,"is_preprint":false},{"pmid":"28320935","id":"PMC_28320935","title":"Triad of human cellular proteins, IRF2, FAM111A, and RFC3, restrict replication of orthopoxvirus SPI-1 host-range mutants.","date":"2017","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/28320935","citation_count":32,"is_preprint":false},{"pmid":"28138333","id":"PMC_28138333","title":"Short stature and hypoparathyroidism in a child with Kenny-Caffey syndrome type 2 due to a novel mutation in FAM111A gene.","date":"2017","source":"International journal of pediatric endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/28138333","citation_count":29,"is_preprint":false},{"pmid":"37607234","id":"PMC_37607234","title":"Human FAM111A inhibits vaccinia virus replication by degrading viral protein I3 and is antagonized by poxvirus host range factor SPI-1.","date":"2023","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/37607234","citation_count":21,"is_preprint":false},{"pmid":"30333173","id":"PMC_30333173","title":"Contribution of DNA Replication to the FAM111A-Mediated Simian Virus 40 Host Range Phenotype.","date":"2018","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/30333173","citation_count":20,"is_preprint":false},{"pmid":"37793778","id":"PMC_37793778","title":"FAM111A regulates replication origin activation and cell fitness.","date":"2023","source":"Life science alliance","url":"https://pubmed.ncbi.nlm.nih.gov/37793778","citation_count":18,"is_preprint":false},{"pmid":"37400994","id":"PMC_37400994","title":"N6 -methyladenosine-modified FAM111A-DT promotes hepatocellular carcinoma growth via epigenetically activating FAM111A.","date":"2023","source":"Cancer science","url":"https://pubmed.ncbi.nlm.nih.gov/37400994","citation_count":17,"is_preprint":false},{"pmid":"38474092","id":"PMC_38474092","title":"Unravelling the Intricate Roles of FAM111A and FAM111B: From Protease-Mediated Cellular Processes to Disease Implications.","date":"2024","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/38474092","citation_count":15,"is_preprint":false},{"pmid":"34930359","id":"PMC_34930359","title":"IRF2 inhibits ZIKV replication by promoting FAM111A expression to enhance the host restriction effect of RFC3.","date":"2021","source":"Virology journal","url":"https://pubmed.ncbi.nlm.nih.gov/34930359","citation_count":13,"is_preprint":false},{"pmid":"34382758","id":"PMC_34382758","title":"Compound Heterozygous Variants in FAM111A Cause Autosomal Recessive Kenny-Caffey Syndrome Type 2.","date":"2021","source":"Journal of clinical research in pediatric endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/34382758","citation_count":12,"is_preprint":false},{"pmid":"36686468","id":"PMC_36686468","title":"Case report: Late middle-aged features of FAM111A variant, Kenny-Caffey syndrome type 2-suggestive symptoms during a long follow-up.","date":"2023","source":"Frontiers in endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/36686468","citation_count":10,"is_preprint":false},{"pmid":"33750016","id":"PMC_33750016","title":"Report of a novel variant in the FAM111A gene in a fetus with multiple anomalies including gracile bones, hypoplastic spleen, and hypomineralized skull.","date":"2021","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/33750016","citation_count":10,"is_preprint":false},{"pmid":"38453899","id":"PMC_38453899","title":"Dimerization-dependent serine protease activity of FAM111A prevents replication fork stalling at topoisomerase 1 cleavage complexes.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38453899","citation_count":9,"is_preprint":false},{"pmid":"35715480","id":"PMC_35715480","title":"FAM111A is dispensable for electrolyte homeostasis in mice.","date":"2022","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/35715480","citation_count":7,"is_preprint":false},{"pmid":"38697929","id":"PMC_38697929","title":"Disruption of the c-terminal serine protease domain of Fam111a does not alter calcium homeostasis in mice.","date":"2024","source":"Physiological reports","url":"https://pubmed.ncbi.nlm.nih.gov/38697929","citation_count":4,"is_preprint":false},{"pmid":"35203468","id":"PMC_35203468","title":"FAM111A Is a Novel Molecular Marker for Oocyte Aging.","date":"2022","source":"Biomedicines","url":"https://pubmed.ncbi.nlm.nih.gov/35203468","citation_count":3,"is_preprint":false},{"pmid":"39786708","id":"PMC_39786708","title":"Long noncoding RNA FAM111A-DT promotes aggressiveness of papillary thyroid cancer via activating NF-κB signaling.","date":"2025","source":"Journal of endocrinological investigation","url":"https://pubmed.ncbi.nlm.nih.gov/39786708","citation_count":2,"is_preprint":false},{"pmid":"39501122","id":"PMC_39501122","title":"Homozygous synonymous FAM111A variant underlies an autosomal recessive form of Kenny-Caffey syndrome.","date":"2024","source":"Journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/39501122","citation_count":2,"is_preprint":false},{"pmid":"39932783","id":"PMC_39932783","title":"Quantitative hypermorphic FAM111A alleles cause autosomal recessive Kenny-Caffey syndrome type 2 and osteocraniostenosis.","date":"2025","source":"JCI insight","url":"https://pubmed.ncbi.nlm.nih.gov/39932783","citation_count":1,"is_preprint":false},{"pmid":"39798873","id":"PMC_39798873","title":"The viral serpin SPI-1 directly inhibits the host cell serine protease FAM111A.","date":"2025","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/39798873","citation_count":1,"is_preprint":false},{"pmid":"40446667","id":"PMC_40446667","title":"Alteration in expression and subcellular localization of the androgen receptor- regulated FAM111A protease is associated with emergence of castration resistant prostate cancer.","date":"2025","source":"Neoplasia (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/40446667","citation_count":0,"is_preprint":false},{"pmid":"41901222","id":"PMC_41901222","title":"The FAM111A Gene: Genetic, Epigenetic, and Pharmacological Targets and Mechanistic Insights with Clinical Relevance.","date":"2026","source":"Pharmaceuticals (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/41901222","citation_count":0,"is_preprint":false},{"pmid":"41607649","id":"PMC_41607649","title":"A Case of FAM111A-Associated Kenny-Caffey Syndrome Type 2 with New Clinical Features: Microtia, Lacunar Skull Appearance, and Arnold-Chiari Malformation.","date":"2025","source":"Molecular syndromology","url":"https://pubmed.ncbi.nlm.nih.gov/41607649","citation_count":0,"is_preprint":false},{"pmid":"41663299","id":"PMC_41663299","title":"[Prenatal phenotype and genetic analysis of two fetuses with Osteocraniostenosis due to variants of FAM111A gene].","date":"2026","source":"Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/41663299","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.08.02.606359","title":"E2F3-dependent activation of FAM111B restricts mouse cytomegalovirus replication in primate cells","date":"2024-08-02","source":"bioRxiv","url":"https://doi.org/10.1101/2024.08.02.606359","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.09.22.677761","title":"Distinct ATRX functions cooperate with 9-1-1 and CST complexes to safeguard replication and telomere integrity","date":"2025-09-22","source":"bioRxiv","url":"https://doi.org/10.1101/2025.09.22.677761","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":16792,"output_tokens":4067,"usd":0.05569,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11934,"output_tokens":4343,"usd":0.084123,"stage2_stop_reason":"end_turn"},"total_usd":0.139813,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2012,\n      \"finding\": \"FAM111A was identified as a host restriction factor for SV40 replication. Affinity purification followed by mass spectrometry revealed a specific interaction between the SV40 large T antigen (LT) C-terminal region and FAM111A. Depletion of FAM111A recapitulated the effects of heterologous expression of the LT C-terminal region, rescuing viral gene expression and lytic infection of SV40 host range mutants in restrictive cells.\",\n      \"method\": \"Affinity purification/mass spectrometry, siRNA depletion, viral replication assays\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal interaction confirmed by AP-MS, functional rescue with depletion, replicated in subsequent studies\",\n      \"pmids\": [\"23093934\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"FAM111A encodes a 611 amino acid protein with homology to trypsin-like peptidases. Disease-causing mutations in Kenny-Caffey syndrome (KCS) and osteocraniostenosis (OCS) map to a surface-exposed segment clustered away from the predicted active site, suggesting pathogenesis involves disruption of protein-protein interactions rather than impaired catalysis.\",\n      \"method\": \"Exome sequencing, molecular modeling of protein structure\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — molecular modeling with mutational mapping, replicated across multiple unrelated patients but no in vitro functional assay\",\n      \"pmids\": [\"23684011\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"FAM111A functions as a host restriction factor for orthopoxvirus SPI-1 deletion mutants. Genome-wide siRNA screen and secondary confirmation assays showed that depletion of FAM111A (along with RFC3 and IRF2) increased replication of the SPI-1 deletion mutant. IRF2 was further shown to regulate basal FAM111A expression levels by microarray, qRT-PCR, and immunoblotting, making the IRF2 effect on viral replication indirect (through FAM111A).\",\n      \"method\": \"Genome-wide siRNA screen, secondary confirmation assays, microarray, qRT-PCR, immunoblotting\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genome-wide screen with secondary validation, multiple orthogonal methods confirming IRF2→FAM111A regulatory axis\",\n      \"pmids\": [\"28320935\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"FAM111A localizes to nucleoli in uninfected cells in a cell cycle-dependent manner, and relocalizes to SV40 viral replication centers upon infection with wild-type or host range (HR) mutant SV40. FAM111A restricts HR virus replication center formation, and this restriction is dependent on viral DNA replication, as inhibition of viral DNA replication with aphidicolin or replication-defective SV40 mutants diminished the effect of FAM111A depletion on viral gene expression.\",\n      \"method\": \"Immunofluorescence localization, aphidicolin inhibition, FAM111A depletion, replication-defective mutant SV40\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiments tied to functional consequence, multiple genetic/pharmacological perturbations in a single study\",\n      \"pmids\": [\"30333173\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"FAM111A is a PCNA-interacting serine protease that protects replication forks from protein obstacles (DNA-protein crosslinks, DPCs) via its trypsin-like protease domain. FAM111A protects forks specifically from PARP1-DNA complexes trapped by PARP inhibitors, a function not shared by SPRTN. The PCNA interaction motif (PIP box) and a DNA-binding domain necessary for protease activity in vivo are required for this function.\",\n      \"method\": \"PCNA interaction assays, domain mutagenesis, PARP inhibitor treatment, replication fork protection assays, cell survival assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple domain mutants tested, PARP inhibitor DPC model with orthogonal assays, complementation experiments, replicated concept in subsequent papers\",\n      \"pmids\": [\"32165630\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"IRF2 inhibits ZIKV replication by upregulating FAM111A expression, which in turn enhances the host restriction effect of RFC3. Knockdown of IRF2 reduced FAM111A expression; overexpression of IRF2 increased it. This regulatory axis was shown to operate independently of type I IFN signaling.\",\n      \"method\": \"siRNA knockdown, plasmid overexpression, RT-qPCR, western blot, viral replication assays\",\n      \"journal\": \"Virology journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab, multiple methods but mechanistic link between FAM111A and RFC3 downstream not fully resolved\",\n      \"pmids\": [\"34930359\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"FAM111A knockout (Fam111a-/-) mice exhibit normal electrolyte homeostasis, normal serum PTH, calcium, magnesium, and phosphate, and unaffected bone morphology and density on a standard diet. This indicates FAM111A loss alone is not sufficient to recapitulate the electrolyte/skeletal phenotype of Kenny-Caffey syndrome in mice.\",\n      \"method\": \"Fam111a knockout mouse model (C57BL/6N), serum/urine electrolyte measurement, gene expression analysis, histology\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO mouse with defined phenotypic readouts, multiple electrolyte and histological endpoints, single lab\",\n      \"pmids\": [\"35715480\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"FAM111A facilitates efficient activation of DNA replication origins under normal conditions. FAM111A-depleted cells show reduced single-stranded DNA (ssDNA) formation and better survival under hydroxyurea treatment. Unrestrained FAM111A expression causes DNA damage and cell death dependent on intact peptidase activity and S-phase entry, but not on PCNA binding.\",\n      \"method\": \"siRNA depletion, overexpression of WT and patient mutants, ssDNA formation assays, cell survival assays, DNA damage markers\",\n      \"journal\": \"Life science alliance\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal assays (ssDNA, survival, damage markers), domain dissection with PCNA-binding mutant, multiple mutant constructs\",\n      \"pmids\": [\"37793778\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"FAM111A directly degrades vaccinia virus (VACV) DNA-binding protein I3 through autophagy. Upon VACV infection, FAM111A translocates from nucleus to cytoplasm by degrading the nuclear pore complex via its protease activity, then interacts with and promotes I3 degradation. This antiviral function requires the trypsin-like protease domain and DNA-binding domain but not the PCNA-interacting motif. The poxvirus virulence factor SPI-1 antagonizes FAM111A by preventing its nuclear export.\",\n      \"method\": \"FAM111A deletion/overexpression, co-immunoprecipitation, viral replication assays, viral DNA quantification, nuclear pore complex degradation assays, autophagy assays, confocal microscopy\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (CoIP, domain mutants, localization, viral replication), mechanistic pathway experimentally confirmed in a single rigorous study\",\n      \"pmids\": [\"37607234\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"FAM111A is a dimerization-dependent serine protease. X-ray crystal structures and mutagenesis show it dimerizes via an N-terminal helix within the serine protease domain (SPD), which induces an activation cascade from a dimerization sensor loop to the oxyanion hole through disorder-to-order transitions. FAM111A cleaves substrates with chymotrypsin-like specificity and has a narrow, recessed active site. Dimerization is required for substrate cleavage and for facilitating replication at DPC obstacles in cells, but is dispensable for autocleavage.\",\n      \"method\": \"X-ray crystallography, mutagenesis, in vitro protease assays, DPC bypass assays in cells\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus mutagenesis plus in vitro reconstitution plus cellular functional validation, multiple orthogonal methods\",\n      \"pmids\": [\"38453899\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Disruption of the FAM111A C-terminal serine protease domain in mice (frameshift or large deletion via CRISPR/Cas9) does not alter serum calcium or PTH levels, Ca2+ excretion, intestinal absorption, or overall Ca2+ balance. Only female homozygous (c.1450insA) mice showed differences in bone microarchitecture and mineral density. These results indicate the serine protease domain is not required for calcium homeostasis in mice.\",\n      \"method\": \"CRISPR/Cas9 knock-in mouse models, serum/urine Ca2+/PTH measurement, intestinal Ca2+ absorption assay, micro-CT bone analysis\",\n      \"journal\": \"Physiological reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct CRISPR mouse models with multiple physiological endpoints, single lab, confirms negative result for Ca2+ regulation\",\n      \"pmids\": [\"38697929\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SPI-1 (poxvirus serpin) directly inhibits FAM111A protease activity in vitro through covalent complex formation, a hallmark of serpin inhibition. SPI-1 shows specificity for FAM111A compared to other serine proteases. Mutagenesis of the SPI-1 reactive center loop (RCL) identified residues critical for FAM111A inhibition and covalent complex formation, and these mutations showed correlated effects on supporting RPXV replication in non-permissive cells.\",\n      \"method\": \"In vitro protease inhibition assay, covalent complex formation assay, SPI-1 RCL mutagenesis, viral replication rescue assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution of direct inhibition, mutagenesis of both partners, correlated cellular functional validation, single lab\",\n      \"pmids\": [\"39798873\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"FAM111A is transcriptionally repressed by the androgen receptor (AR) via an AR binding site within the FAM111A gene. FAM111A protein subcellular localization shifts from predominantly nucleolar in castration-sensitive prostate cancer cells to more dispersed nuclear and cytoplasmic in castration-resistant cells. FAM111A depletion enhances sensitivity to PARP inhibitors olaparib and niraparib, and reduces AR target gene (PSA, TMPRSS2) transcription, indicating a FAM111A-AR co-regulatory loop.\",\n      \"method\": \"AR ChIP (AR binding site), knockdown/overexpression, xenograft models, subcellular fractionation/immunofluorescence, PARP inhibitor sensitivity assays, RT-qPCR\",\n      \"journal\": \"Neoplasia (New York, N.Y.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — AR binding site identified, multiple cellular models and in vivo xenografts, direct localization with functional consequence, single lab\",\n      \"pmids\": [\"40446667\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Biallelic hypermorphic FAM111A variants (Y414C and Y414N) cause autosomal recessive KCS/OCS. Recombinant FAM111A-Y414C showed normal dimerization but a mild gain-of-function effect in protease activity assays, indicating that quantitative hypermorphic activation (not just loss-of-function) of FAM111A protease underlies the skeletal dysplasia phenotype even in a recessive context.\",\n      \"method\": \"Exome sequencing, recombinant protein production, in vitro protease activity assays, dimerization assays\",\n      \"journal\": \"JCI insight\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro biochemical assays with recombinant protein, single lab, limited to one variant functionally characterized\",\n      \"pmids\": [\"39932783\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ATRX suppresses DNA damage during replication stress by counteracting the activity of the FAM111A protease. Genetic epistasis experiments in ATRX-deficient cells revealed that ATRX's role in replication requires its PIP-box (independent of its DAXX interaction), placing FAM111A activity downstream of ATRX in the replication stress response pathway.\",\n      \"method\": \"Genetic epistasis (double mutants), CRISPR/Cas9 KO, domain mutants (ATPase, PIP-box, DAXX-interaction), replication stress assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genetic epistasis with multiple domain mutants, preprint not yet peer-reviewed, single lab\",\n      \"pmids\": [\"bio_10.1101_2025.09.22.677761\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"FAM111A is a nuclear, dimerization-dependent trypsin-like serine protease that associates with PCNA at replication forks, where it cleaves protein obstacles (DNA-protein crosslinks, including trapped PARP1 and topoisomerase 1 cleavage complexes) to facilitate replication fork progression; its protease activity is activated by dimerization via an N-terminal helix and follows chymotrypsin-like specificity, while disease-causing gain-of-function mutations in the catalytic domain cause hyper-autocleavage and are linked to Kenny-Caffey syndrome and osteocraniostenosis; FAM111A also functions as an antiviral restriction factor that degrades the nuclear pore complex to relocalize to the cytoplasm and degrades poxviral protein I3 via autophagy, and is directly inhibited by the poxviral serpin SPI-1 through covalent complex formation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"FAM111A is a nuclear, PCNA-associated trypsin-like serine protease that safeguards DNA replication by removing protein obstacles from replication forks and that doubles as a viral restriction factor [#4, #0]. At the fork, FAM111A binds PCNA through a PIP box and uses its protease and DNA-binding domains to clear DNA-protein crosslinks, including PARP1-DNA complexes trapped by PARP inhibitors, a function distinct from SPRTN [#4]. It also promotes efficient activation of replication origins under normal conditions, and unrestrained protease activity drives ssDNA accumulation, DNA damage, and cell death dependent on intact peptidase activity and S-phase entry but not on PCNA binding [#7]. Catalytic activity is governed by dimerization: FAM111A dimerizes via an N-terminal helix within the serine protease domain, triggering a disorder-to-order activation cascade that builds the oxyanion hole and confers chymotrypsin-like specificity through a narrow, recessed active site; dimerization is required for substrate cleavage and DPC bypass but is dispensable for autocleavage [#9]. In its antiviral role, FAM111A restricts SV40 and orthopoxvirus replication, localizing to nucleoli in a cell-cycle-dependent manner and relocalizing to SV40 replication centers in a manner dependent on viral DNA replication [#0, #3, #2]; against vaccinia virus it degrades the nuclear pore complex to translocate to the cytoplasm and then targets the viral DNA-binding protein I3 for autophagic degradation, an activity antagonized by the poxviral serpin SPI-1 which prevents nuclear export and directly inhibits FAM111A through covalent complex formation [#8, #11]. Basal FAM111A expression is set by IRF2 and is repressed by the androgen receptor [#2, #12]. Hypermorphic gain-of-function variants in the catalytic domain cause Kenny-Caffey syndrome and osteocraniostenosis, including biallelic recessive variants that mildly elevate protease activity without altering dimerization [#13].\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Established FAM111A as a host factor whose removal phenocopies the SV40 large T antigen function, defining its first biological role as a viral restriction factor.\",\n      \"evidence\": \"AP-MS of SV40 LT C-terminus, siRNA depletion and viral replication rescue assays\",\n      \"pmids\": [\"23093934\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the molecular activity of FAM111A\", \"Mechanism of restriction unresolved\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Linked FAM111A to Kenny-Caffey syndrome and osteocraniostenosis and predicted a trypsin-like peptidase fold, framing pathogenesis as a question of catalysis versus interaction.\",\n      \"evidence\": \"Exome sequencing of patients with molecular modeling of mutation positions\",\n      \"pmids\": [\"23684011\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No in vitro catalytic assay performed\", \"Mutation effect on protease activity inferred only from modeling\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Extended FAM111A restriction to orthopoxvirus SPI-1 deletion mutants and identified IRF2 as a transcriptional regulator setting basal FAM111A levels.\",\n      \"evidence\": \"Genome-wide siRNA screen with secondary validation, microarray, qRT-PCR and immunoblotting\",\n      \"pmids\": [\"28320935\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which FAM111A restricts poxvirus not defined\", \"Direct FAM111A targets in poxvirus unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Defined FAM111A's cell-cycle-dependent nucleolar localization and its replication-dependent relocalization to viral replication centers, tying restriction to DNA replication.\",\n      \"evidence\": \"Immunofluorescence, aphidicolin inhibition and replication-defective SV40 mutants with FAM111A depletion\",\n      \"pmids\": [\"30333173\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular substrate at viral replication centers not identified\", \"Trigger for nucleolar release not defined\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identified FAM111A as a PCNA-interacting protease that clears DNA-protein crosslinks at forks, distinguishing it from SPRTN and specifying PARP1-DNA complexes as obstacles.\",\n      \"evidence\": \"PCNA interaction assays, PIP-box and DNA-binding domain mutagenesis, PARP inhibitor and fork protection assays\",\n      \"pmids\": [\"32165630\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct cleavage of PARP1 not biochemically reconstituted in this study\", \"Substrate spectrum at forks incomplete\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showed the IRF2-FAM111A axis restricts ZIKV and enhances RFC3-mediated restriction independently of type I IFN, broadening FAM111A's antiviral scope to an RNA virus.\",\n      \"evidence\": \"siRNA knockdown, overexpression, RT-qPCR, western blot and viral replication assays\",\n      \"pmids\": [\"34930359\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic link between FAM111A and RFC3 unresolved\", \"Single lab, ZIKV restriction mechanism not defined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrated that FAM111A loss alone does not recapitulate Kenny-Caffey electrolyte or skeletal phenotypes in mice, arguing against simple loss-of-function pathogenesis.\",\n      \"evidence\": \"Fam111a knockout mouse with serum/urine electrolyte, gene expression and histology readouts\",\n      \"pmids\": [\"35715480\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not test gain-of-function disease alleles\", \"Possible compensation in mouse not excluded\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Placed FAM111A in normal origin activation and showed that excess protease activity is toxic through ssDNA, DNA damage and S-phase-dependent death, decoupling toxicity from PCNA binding.\",\n      \"evidence\": \"siRNA depletion, WT and patient-mutant overexpression, ssDNA, survival and DNA damage marker assays\",\n      \"pmids\": [\"37793778\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Substrates driving origin activation not identified\", \"Link between toxicity and disease phenotype indirect\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Revealed an antiviral effector mechanism in which FAM111A degrades the nuclear pore complex to exit the nucleus and then drives autophagic degradation of vaccinia I3, with SPI-1 blocking nuclear export.\",\n      \"evidence\": \"Domain mutants, Co-IP, viral replication and DNA quantification, NPC degradation, autophagy assays and confocal microscopy\",\n      \"pmids\": [\"37607234\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"NPC components cleaved not enumerated\", \"Mechanism of SPI-1 export block not resolved at this stage\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Solved the structural basis of FAM111A activation, showing dimerization via an N-terminal helix drives a disorder-to-order cascade to build the active site with chymotrypsin-like specificity, required for cleavage but not autocleavage.\",\n      \"evidence\": \"X-ray crystallography, mutagenesis, in vitro protease assays and cellular DPC bypass assays\",\n      \"pmids\": [\"38453899\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological dimerization trigger not defined\", \"Full substrate repertoire not mapped\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Showed disruption of the FAM111A protease domain does not alter calcium homeostasis in mice, further dissociating the protease from the renal/skeletal disease phenotype.\",\n      \"evidence\": \"CRISPR/Cas9 knock-in mice with serum/urine Ca2+/PTH, intestinal absorption and micro-CT analysis\",\n      \"pmids\": [\"38697929\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Only one allele showed a sex-specific bone effect\", \"Human gain-of-function not modeled directly\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Reconstituted direct inhibition of FAM111A by the poxvirus serpin SPI-1 through covalent complex formation, defining a molecular mechanism for poxviral antagonism.\",\n      \"evidence\": \"In vitro protease inhibition and covalent complex assays, SPI-1 RCL mutagenesis and viral replication rescue\",\n      \"pmids\": [\"39798873\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cellular stoichiometry of inhibition not quantified\", \"Single lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Connected FAM111A to androgen receptor signaling, showing AR represses FAM111A and that depletion sensitizes prostate cancer cells to PARP inhibitors, defining a co-regulatory loop with therapeutic relevance.\",\n      \"evidence\": \"AR ChIP, knockdown/overexpression, xenografts, subcellular fractionation/IF, PARP inhibitor and RT-qPCR assays\",\n      \"pmids\": [\"40446667\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct AR binding consequence on FAM111A protease not tested\", \"Single lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated that biallelic hypermorphic variants causing recessive KCS/OCS act by quantitatively elevating protease activity without altering dimerization, establishing gain-of-function as the disease mechanism.\",\n      \"evidence\": \"Exome sequencing, recombinant protein production, in vitro protease and dimerization assays\",\n      \"pmids\": [\"39932783\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Only one variant functionally characterized\", \"Tissue-specific consequence not modeled\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How FAM111A protease activity is physiologically licensed and restrained at forks, and how its gain-of-function in disease tissues produces skeletal/endocrine pathology not seen in mouse loss models, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Endogenous dimerization/activation trigger unknown\", \"Complete fork substrate spectrum unmapped\", \"Mechanistic basis of tissue-specific disease phenotype undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [4, 8, 9]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [4, 9, 11]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [4, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [3, 12]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [3, 8]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [8, 12]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-69306\", \"supporting_discovery_ids\": [4, 7]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [4, 7]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 2, 8]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"PCNA\", \"PARP1\", \"SPI-1\", \"IRF2\", \"AR\", \"ATRX\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}