{"gene":"SWSAP1","run_date":"2026-06-10T10:51:54","timeline":{"discoveries":[{"year":2011,"finding":"SWSAP1 (C19orf39) forms a stable complex with hSWS1 in vivo and in vitro; the two proteins are mutually interdependent for their stability. The purified hSWS1·SWSAP1 complex possesses single-stranded DNA-binding activity and DNA-stimulated ATPase activity. SWSAP1 also interacts with RAD51 and RAD51 paralogs, and depletion of SWSAP1 causes defects in homologous recombination repair.","method":"Co-immunoprecipitation, in vitro reconstitution of purified complex, ssDNA-binding assay, ATPase assay, siRNA knockdown with HR reporter assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — multiple orthogonal in vitro biochemical assays (binding, ATPase) combined with in vivo Co-IP and functional HR depletion phenotype in a single rigorous study","pmids":["21965664"],"is_preprint":false},{"year":2015,"finding":"The SWIM domain (CXC…Xn…CXHXXA) of SWS1 is required for protein-protein interactions with SWSAP1 in humans; in vivo disruption of invariant residues within the canonical SWIM domain inhibits these interactions. The SWS1 family is evolutionarily conserved from early-branching eukaryotes to humans.","method":"Sequence/evolutionary analysis combined with in vivo mutagenesis of SWIM domain residues and protein-interaction assays in yeast and human cells","journal":"Genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo mutagenesis with protein-interaction readout in two organisms, single lab","pmids":["25659377"],"is_preprint":false},{"year":2018,"finding":"The SWS1-SWSAP1 complex is required in mouse meiosis to promote assembly of RAD51 and DMC1 on early meiotic HR intermediates; loss of SWSAP1 leads to male and female infertility with reduced crossover formation. Loss of CHK2 rescues female fertility without restoring crossover numbers (crossover homeostasis). Concomitant loss of the BRCA2 C-terminus aggravates meiotic defects in Swsap1 mutant spermatocytes, placing SWS1-SWSAP1 in an overlapping pathway with BRCA2.","method":"Mouse knockout, immunofluorescence of meiotic chromosome spreads for RAD51/DMC1 foci, genetic epistasis (Swsap1/Chk2 and Swsap1/Brca2 double mutants)","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean KO phenotype with defined molecular readout (recombinase foci), genetic epistasis with two independent partners, replicated across sexes","pmids":["30305635"],"is_preprint":false},{"year":2019,"finding":"SWSAP1 protects RAD51 filaments by antagonizing FIGNL1, an AAA+ ATPase anti-recombinase. FIGNL1 binds both RAD51 and SWSAP1; purified FIGNL1 promotes dissociation of RAD51 from ssDNA via its RAD51-binding activity (independent of its ATPase). Purified SWSAP1 inhibits this RAD51-dismantling activity of FIGNL1. Depletion of FIGNL1 suppresses the defective DNA damage-induced RAD51 assembly seen in SWSAP1-deficient cells during mitosis and meiosis.","method":"In vitro ssDNA dissociation assay with purified FIGNL1, purified SWSAP1 inhibition assay, Co-IP/binding assays, siRNA/shRNA knockdown with RAD51 foci quantification, genetic epistasis (double depletion)","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution of FIGNL1 dismantling and SWSAP1 inhibition, supported by genetic epistasis and cellular RAD51 foci, multiple orthogonal methods","pmids":["30926776"],"is_preprint":false},{"year":2019,"finding":"SWSAP1 and SWS1 (Shu complex) function with SPIDR and PDS5B in the same genetic pathway to regulate RAD51 recruitment to DNA repair foci and replication fork restart. CRISPR/Cas9 deletion of SWSAP1 or SWS1 sensitizes cells to MMS and MMC and reduces sister-chromatid exchanges. SPIDR and PDS5B were identified as novel Shu complex interacting partners.","method":"CRISPR/Cas9 knockout, co-immunoprecipitation (SPIDR and PDS5B interaction), clonogenic survival assays, SCE assay, RAD51 foci quantification, genetic epistasis","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP for new interactors, CRISPR KO with multiple cellular phenotypes, genetic epistasis across multiple partners","pmids":["31665741"],"is_preprint":false},{"year":2021,"finding":"The SWS1-SWSAP1-SPIDR complex specifically controls inter-homolog HDR and sister-chromatid exchange, but is not essential for intra-chromosomal HDR. It is the first mitotic factor identified specifically required for inter-homolog HR. Loss of SWSAP1 prolongs survival of BLM-deficient embryos, demonstrating a genetic interaction between the Shu complex and BLM helicase.","method":"CRISPR/Cas9 knockout, defined HDR reporter assays distinguishing intra- vs. inter-chromosomal repair, SCE assay, genetic epistasis with Blm mutants in mouse embryos","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal HR assays distinguishing pathway specificity, clean KO, genetic epistasis with BLM, replicated across labs","pmids":["34253720"],"is_preprint":false},{"year":2024,"finding":"Purified SWSAP1-SWS1 binds RAD51, maintains RAD51 filament stability, enables strand exchange, and decorates RAD51 filaments proficient for HR. SWSAP1-SWS1 also enhances RPA diffusion on ssDNA, providing a mechanism for promoting RAD51 loading. Cancer variants in SWSAP1 alter Shu complex formation. SWSAP1 and SWS1 knockout cells are sensitive to PARP and APE1 inhibition.","method":"Single-molecule confocal fluorescence microscopy combined with optical tweezers, in vitro strand exchange assay, purified protein binding assays, CRISPR KO with pharmacological sensitivity assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — single-molecule biophysical reconstitution, in vitro strand exchange, and CRISPR KO functional validation; multiple orthogonal methods in one study","pmids":["39169038"],"is_preprint":false},{"year":2025,"finding":"Purified hSWS1-SWSAP1 preferentially binds DNA with an exposed 5' end in the presence of adenine nucleotides; DNA-stimulated ATPase activity confirmed by site-specific mutagenesis with 5'-end DNA being most efficient. hSWS1-SWSAP1 initially contacts RAD51 filaments at the 5' end, induces ATP hydrolysis-dependent conformational changes in RAD51 filaments, and stabilizes filaments in an ATP binding-dependent (but hydrolysis-independent) manner.","method":"Fluorescence polarization DNA-binding assay, ATPase assay with site-specific mutagenesis of Walker motif, fluorescence-based RAD51 filament interaction assays with purified proteins","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution with purified proteins, mutagenesis validating ATPase activity, multiple biochemical assays dissecting ATP-binding vs. hydrolysis roles","pmids":["40345587"],"is_preprint":false},{"year":2025,"finding":"A homozygous frameshift deletion in SWSAP1 (c.353del) in a patient with premature ovarian insufficiency results in absence of inter-homolog HR activity in Swsap1-/- cells and destabilization of the truncated SWSAP1 protein, establishing SWSAP1 as a POI disease gene.","method":"Exome/genome sequencing, IH-HR functional assay in mouse embryonic stem cells, western blot, in silico structural modelling","journal":"Human reproduction (Oxford, England)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional IH-HR assay and protein stability western blot in a disease-relevant cellular model, single lab, limited patient number","pmids":["40991243"],"is_preprint":false}],"current_model":"SWSAP1 is a RAD51 paralog that forms the core Shu complex with SWS1 (and SPIDR/PDS5B), directly binds RAD51 filaments at their 5' ends, stimulates RAD51-mediated strand exchange by stabilizing filaments (ATP binding-dependent) and inducing conformational changes (ATP hydrolysis-dependent), enhances RPA diffusion on ssDNA to facilitate RAD51 loading, and protects RAD51 filaments by inhibiting the FIGNL1 anti-recombinase; collectively, the SWS1-SWSAP1-SPIDR complex is specifically required for inter-homolog homologous recombination, sister-chromatid exchange, and meiotic recombinase assembly, but is dispensable for intra-chromosomal HDR."},"narrative":{"mechanistic_narrative":"SWSAP1 is a RAD51 paralog that operates as the catalytic core of the human Shu complex to control the assembly and stability of RAD51 recombinase filaments during homologous recombination [PMID:21965664, PMID:39169038]. It forms a stable, mutually stabilizing heterodimer with SWS1 through the SWS1 SWIM domain, and the purified SWS1·SWSAP1 complex binds single-stranded DNA and possesses DNA-stimulated ATPase activity [PMID:21965664, PMID:25659377]. Biochemically, the complex preferentially engages DNA and RAD51 filaments at exposed 5' ends, where it stabilizes filaments in an ATP-binding-dependent manner and drives conformational changes in an ATP-hydrolysis-dependent manner, while enhancing RPA diffusion on ssDNA to facilitate RAD51 loading and strand exchange [PMID:39169038, PMID:40345587]. SWSAP1 additionally protects nascent RAD51 filaments by directly inhibiting the FIGNL1 anti-recombinase, which otherwise dismantles RAD51 from ssDNA [PMID:30926776]. Functionally, SWSAP1 acts together with SWS1, SPIDR, and PDS5B to promote RAD51 recruitment to repair foci, replication fork restart, and sister-chromatid exchange, and it is specifically required for inter-homolog HDR while being dispensable for intra-chromosomal HDR [PMID:31665741, PMID:34253720]. In meiosis the complex is needed to assemble RAD51 and DMC1 on recombination intermediates, and its loss causes infertility with reduced crossovers [PMID:30305635]. A homozygous frameshift deletion in SWSAP1 establishes it as a premature ovarian insufficiency disease gene [PMID:40991243].","teleology":[{"year":2011,"claim":"Established SWSAP1 as a partner of SWS1 with intrinsic biochemical activities and a role in HR, defining the founding members of the human Shu complex.","evidence":"Co-IP, in vitro reconstitution of purified complex with ssDNA-binding/ATPase assays, and siRNA knockdown with an HR reporter","pmids":["21965664"],"confidence":"High","gaps":["Did not resolve which subunit carries the ATPase active site","No mechanism for how the complex acts on RAD51 filaments"]},{"year":2015,"claim":"Mapped the SWS1 SWIM domain as the structural determinant of SWSAP1 binding, defining the interaction interface holding the core dimer together.","evidence":"Evolutionary/sequence analysis with in vivo SWIM-residue mutagenesis and interaction assays in yeast and human cells","pmids":["25659377"],"confidence":"Medium","gaps":["No structure of the interface","Single-lab interaction readout without orthogonal biophysical confirmation"]},{"year":2018,"claim":"Demonstrated an in vivo meiotic requirement, showing the complex promotes recombinase loading and crossover formation and placing it in a BRCA2-overlapping pathway.","evidence":"Mouse knockout with immunofluorescence of RAD51/DMC1 foci on meiotic spreads and genetic epistasis with Chk2 and Brca2","pmids":["30305635"],"confidence":"High","gaps":["Did not define the biochemical step at which recombinase loading fails","Molecular basis of overlap with BRCA2 unresolved"]},{"year":2019,"claim":"Identified the mechanism by which SWSAP1 stabilizes RAD51 filaments: direct antagonism of the FIGNL1 anti-recombinase.","evidence":"In vitro ssDNA-dissociation assays with purified FIGNL1 and SWSAP1, Co-IP, and double-depletion epistasis with RAD51 foci readout","pmids":["30926776"],"confidence":"High","gaps":["Structural basis of SWSAP1 inhibition of FIGNL1 not defined","Whether protection occurs at filament ends or along the filament unclear"]},{"year":2019,"claim":"Expanded the Shu complex to include SPIDR and PDS5B and tied the complex to RAD51 recruitment, fork restart, and sister-chromatid exchange.","evidence":"CRISPR/Cas9 knockout, reciprocal Co-IP, clonogenic survival to MMS/MMC, SCE and RAD51 foci assays with epistasis","pmids":["31665741"],"confidence":"High","gaps":["Stoichiometry and architecture of the four-subunit complex unknown","Role of PDS5B-mediated cohesin link not dissected"]},{"year":2021,"claim":"Resolved the pathway specificity of the complex, establishing it as the first mitotic factor specifically required for inter-homolog HR but not intra-chromosomal HDR.","evidence":"CRISPR KO with HDR reporters distinguishing intra- vs inter-chromosomal repair, SCE assay, and Blm epistasis in mouse embryos","pmids":["34253720"],"confidence":"High","gaps":["Molecular feature that restricts the complex to inter-homolog events unknown","Basis of the genetic interaction with BLM not mechanistically defined"]},{"year":2024,"claim":"Provided direct biophysical evidence that SWSAP1-SWS1 stabilizes RAD51 filaments, enables strand exchange, and enhances RPA diffusion to promote RAD51 loading.","evidence":"Single-molecule confocal microscopy with optical tweezers, in vitro strand exchange, purified binding assays, and CRISPR KO with PARP/APE1 inhibitor sensitivity","pmids":["39169038"],"confidence":"High","gaps":["Did not separate ATP-binding from hydrolysis contributions","Effect of cancer variants on filament biophysics not quantified"]},{"year":2025,"claim":"Dissected the ATP cycle and DNA-end preference, showing 5'-end engagement with ATP-binding-dependent stabilization and hydrolysis-dependent conformational change of RAD51 filaments.","evidence":"Fluorescence polarization DNA binding, ATPase assays with Walker-motif mutagenesis, and fluorescence-based RAD51 filament interaction assays","pmids":["40345587"],"confidence":"High","gaps":["No high-resolution structure of the complex on a RAD51 filament","Functional consequence of 5'-end specificity in cells not tested"]},{"year":2025,"claim":"Linked SWSAP1 loss-of-function to human disease, establishing it as a premature ovarian insufficiency gene.","evidence":"Exome/genome sequencing of a POI patient, IH-HR functional assay in mouse ES cells, western blot, and in silico modelling","pmids":["40991243"],"confidence":"Medium","gaps":["Single patient limits genetic certainty","Genotype-phenotype spectrum across additional families undefined"]},{"year":null,"claim":"How the full SWS1-SWSAP1-SPIDR-PDS5B complex is architecturally organized and how it is mechanistically restricted to inter-homolog recombination remain unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No structure of the assembled complex on DNA or RAD51 filaments","Molecular basis of inter-homolog vs intra-chromosomal pathway choice unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[0,7]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,7]},{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[7]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3,6]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[6,7]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[2,4]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[0,4,5]},{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[2,8]}],"complexes":["Shu complex (SWS1-SWSAP1-SPIDR-PDS5B)"],"partners":["SWS1","RAD51","SPIDR","PDS5B","FIGNL1","DMC1","BRCA2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q6NVH7","full_name":"ATPase SWSAP1","aliases":["SWIM-type zinc finger 7-associated protein 1","SWS1-associated protein 1","ZSWIM7-associated protein 1","ZSWIM7AP1"],"length_aa":229,"mass_kda":24.3,"function":"ATPase which is preferentially stimulated by single-stranded DNA and is involved in homologous recombination repair (HRR). Has a DNA-binding activity which is independent of its ATPase activity","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q6NVH7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SWSAP1","classification":"Not Classified","n_dependent_lines":21,"n_total_lines":1208,"dependency_fraction":0.0173841059602649},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SWSAP1","total_profiled":1310},"omim":[{"mim_id":"614536","title":"SWIM-TYPE ZINC FINGER DOMAIN-CONTAINING PROTEIN 7-ASSOCIATED PROTEIN 1; SWSAP1","url":"https://www.omim.org/entry/614536"},{"mim_id":"614535","title":"ZINC FINGER SWIM DOMAIN-CONTAINING PROTEIN 7; ZSWIM7","url":"https://www.omim.org/entry/614535"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SWSAP1"},"hgnc":{"alias_symbol":["FLJ35119","ZSWIM7AP1","SWS1AP1"],"prev_symbol":["C19orf39"]},"alphafold":{"accession":"Q6NVH7","domains":[{"cath_id":"3.40.50.300","chopping":"9-166","consensus_level":"high","plddt":88.3006,"start":9,"end":166}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6NVH7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q6NVH7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q6NVH7-F1-predicted_aligned_error_v6.png","plddt_mean":82.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SWSAP1","jax_strain_url":"https://www.jax.org/strain/search?query=SWSAP1"},"sequence":{"accession":"Q6NVH7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q6NVH7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q6NVH7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6NVH7"}},"corpus_meta":[{"pmid":"30551670","id":"PMC_30551670","title":"RAD-ical New Insights into RAD51 Regulation.","date":"2018","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/30551670","citation_count":105,"is_preprint":false},{"pmid":"21965664","id":"PMC_21965664","title":"hSWS1·SWSAP1 is an evolutionarily conserved complex required for efficient homologous recombination repair.","date":"2011","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21965664","citation_count":63,"is_preprint":false},{"pmid":"30926776","id":"PMC_30926776","title":"Human RAD51 paralogue SWSAP1 fosters RAD51 filament by regulating the anti-recombinase FIGNL1 AAA+ ATPase.","date":"2019","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/30926776","citation_count":56,"is_preprint":false},{"pmid":"30305635","id":"PMC_30305635","title":"Shu complex SWS1-SWSAP1 promotes early steps in mouse meiotic recombination.","date":"2018","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/30305635","citation_count":45,"is_preprint":false},{"pmid":"34253720","id":"PMC_34253720","title":"Distinct pathways of homologous recombination controlled by the SWS1-SWSAP1-SPIDR complex.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/34253720","citation_count":38,"is_preprint":false},{"pmid":"31665741","id":"PMC_31665741","title":"The human Shu complex functions with PDS5B and SPIDR to promote homologous recombination.","date":"2019","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/31665741","citation_count":36,"is_preprint":false},{"pmid":"25659377","id":"PMC_25659377","title":"Evolutionary and functional analysis of the invariant SWIM domain in the conserved Shu2/SWS1 protein family from Saccharomyces cerevisiae to Homo sapiens.","date":"2015","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/25659377","citation_count":33,"is_preprint":false},{"pmid":"39169038","id":"PMC_39169038","title":"The human Shu complex promotes RAD51 activity by modulating RPA dynamics on ssDNA.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/39169038","citation_count":9,"is_preprint":false},{"pmid":"38405734","id":"PMC_38405734","title":"The human Shu complex promotes RAD51 activity by modulating RPA dynamics on ssDNA.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38405734","citation_count":3,"is_preprint":false},{"pmid":"40991243","id":"PMC_40991243","title":"SWS1-complex in premature ovarian insufficiency: SWSAP1 as a new POI gene.","date":"2025","source":"Human reproduction (Oxford, England)","url":"https://pubmed.ncbi.nlm.nih.gov/40991243","citation_count":1,"is_preprint":false},{"pmid":"40345587","id":"PMC_40345587","title":"The role of human Shu complex in ATP-dependent regulation of RAD51 filaments during homologous recombination-associated DNA damage response.","date":"2025","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/40345587","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7728,"output_tokens":2789,"usd":0.032509,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10025,"output_tokens":3242,"usd":0.065588,"stage2_stop_reason":"end_turn"},"total_usd":0.098097,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2011,\n      \"finding\": \"SWSAP1 (C19orf39) forms a stable complex with hSWS1 in vivo and in vitro; the two proteins are mutually interdependent for their stability. The purified hSWS1·SWSAP1 complex possesses single-stranded DNA-binding activity and DNA-stimulated ATPase activity. SWSAP1 also interacts with RAD51 and RAD51 paralogs, and depletion of SWSAP1 causes defects in homologous recombination repair.\",\n      \"method\": \"Co-immunoprecipitation, in vitro reconstitution of purified complex, ssDNA-binding assay, ATPase assay, siRNA knockdown with HR reporter assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — multiple orthogonal in vitro biochemical assays (binding, ATPase) combined with in vivo Co-IP and functional HR depletion phenotype in a single rigorous study\",\n      \"pmids\": [\"21965664\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The SWIM domain (CXC…Xn…CXHXXA) of SWS1 is required for protein-protein interactions with SWSAP1 in humans; in vivo disruption of invariant residues within the canonical SWIM domain inhibits these interactions. The SWS1 family is evolutionarily conserved from early-branching eukaryotes to humans.\",\n      \"method\": \"Sequence/evolutionary analysis combined with in vivo mutagenesis of SWIM domain residues and protein-interaction assays in yeast and human cells\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo mutagenesis with protein-interaction readout in two organisms, single lab\",\n      \"pmids\": [\"25659377\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"The SWS1-SWSAP1 complex is required in mouse meiosis to promote assembly of RAD51 and DMC1 on early meiotic HR intermediates; loss of SWSAP1 leads to male and female infertility with reduced crossover formation. Loss of CHK2 rescues female fertility without restoring crossover numbers (crossover homeostasis). Concomitant loss of the BRCA2 C-terminus aggravates meiotic defects in Swsap1 mutant spermatocytes, placing SWS1-SWSAP1 in an overlapping pathway with BRCA2.\",\n      \"method\": \"Mouse knockout, immunofluorescence of meiotic chromosome spreads for RAD51/DMC1 foci, genetic epistasis (Swsap1/Chk2 and Swsap1/Brca2 double mutants)\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean KO phenotype with defined molecular readout (recombinase foci), genetic epistasis with two independent partners, replicated across sexes\",\n      \"pmids\": [\"30305635\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"SWSAP1 protects RAD51 filaments by antagonizing FIGNL1, an AAA+ ATPase anti-recombinase. FIGNL1 binds both RAD51 and SWSAP1; purified FIGNL1 promotes dissociation of RAD51 from ssDNA via its RAD51-binding activity (independent of its ATPase). Purified SWSAP1 inhibits this RAD51-dismantling activity of FIGNL1. Depletion of FIGNL1 suppresses the defective DNA damage-induced RAD51 assembly seen in SWSAP1-deficient cells during mitosis and meiosis.\",\n      \"method\": \"In vitro ssDNA dissociation assay with purified FIGNL1, purified SWSAP1 inhibition assay, Co-IP/binding assays, siRNA/shRNA knockdown with RAD51 foci quantification, genetic epistasis (double depletion)\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution of FIGNL1 dismantling and SWSAP1 inhibition, supported by genetic epistasis and cellular RAD51 foci, multiple orthogonal methods\",\n      \"pmids\": [\"30926776\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"SWSAP1 and SWS1 (Shu complex) function with SPIDR and PDS5B in the same genetic pathway to regulate RAD51 recruitment to DNA repair foci and replication fork restart. CRISPR/Cas9 deletion of SWSAP1 or SWS1 sensitizes cells to MMS and MMC and reduces sister-chromatid exchanges. SPIDR and PDS5B were identified as novel Shu complex interacting partners.\",\n      \"method\": \"CRISPR/Cas9 knockout, co-immunoprecipitation (SPIDR and PDS5B interaction), clonogenic survival assays, SCE assay, RAD51 foci quantification, genetic epistasis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP for new interactors, CRISPR KO with multiple cellular phenotypes, genetic epistasis across multiple partners\",\n      \"pmids\": [\"31665741\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"The SWS1-SWSAP1-SPIDR complex specifically controls inter-homolog HDR and sister-chromatid exchange, but is not essential for intra-chromosomal HDR. It is the first mitotic factor identified specifically required for inter-homolog HR. Loss of SWSAP1 prolongs survival of BLM-deficient embryos, demonstrating a genetic interaction between the Shu complex and BLM helicase.\",\n      \"method\": \"CRISPR/Cas9 knockout, defined HDR reporter assays distinguishing intra- vs. inter-chromosomal repair, SCE assay, genetic epistasis with Blm mutants in mouse embryos\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal HR assays distinguishing pathway specificity, clean KO, genetic epistasis with BLM, replicated across labs\",\n      \"pmids\": [\"34253720\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Purified SWSAP1-SWS1 binds RAD51, maintains RAD51 filament stability, enables strand exchange, and decorates RAD51 filaments proficient for HR. SWSAP1-SWS1 also enhances RPA diffusion on ssDNA, providing a mechanism for promoting RAD51 loading. Cancer variants in SWSAP1 alter Shu complex formation. SWSAP1 and SWS1 knockout cells are sensitive to PARP and APE1 inhibition.\",\n      \"method\": \"Single-molecule confocal fluorescence microscopy combined with optical tweezers, in vitro strand exchange assay, purified protein binding assays, CRISPR KO with pharmacological sensitivity assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — single-molecule biophysical reconstitution, in vitro strand exchange, and CRISPR KO functional validation; multiple orthogonal methods in one study\",\n      \"pmids\": [\"39169038\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Purified hSWS1-SWSAP1 preferentially binds DNA with an exposed 5' end in the presence of adenine nucleotides; DNA-stimulated ATPase activity confirmed by site-specific mutagenesis with 5'-end DNA being most efficient. hSWS1-SWSAP1 initially contacts RAD51 filaments at the 5' end, induces ATP hydrolysis-dependent conformational changes in RAD51 filaments, and stabilizes filaments in an ATP binding-dependent (but hydrolysis-independent) manner.\",\n      \"method\": \"Fluorescence polarization DNA-binding assay, ATPase assay with site-specific mutagenesis of Walker motif, fluorescence-based RAD51 filament interaction assays with purified proteins\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution with purified proteins, mutagenesis validating ATPase activity, multiple biochemical assays dissecting ATP-binding vs. hydrolysis roles\",\n      \"pmids\": [\"40345587\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"A homozygous frameshift deletion in SWSAP1 (c.353del) in a patient with premature ovarian insufficiency results in absence of inter-homolog HR activity in Swsap1-/- cells and destabilization of the truncated SWSAP1 protein, establishing SWSAP1 as a POI disease gene.\",\n      \"method\": \"Exome/genome sequencing, IH-HR functional assay in mouse embryonic stem cells, western blot, in silico structural modelling\",\n      \"journal\": \"Human reproduction (Oxford, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional IH-HR assay and protein stability western blot in a disease-relevant cellular model, single lab, limited patient number\",\n      \"pmids\": [\"40991243\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SWSAP1 is a RAD51 paralog that forms the core Shu complex with SWS1 (and SPIDR/PDS5B), directly binds RAD51 filaments at their 5' ends, stimulates RAD51-mediated strand exchange by stabilizing filaments (ATP binding-dependent) and inducing conformational changes (ATP hydrolysis-dependent), enhances RPA diffusion on ssDNA to facilitate RAD51 loading, and protects RAD51 filaments by inhibiting the FIGNL1 anti-recombinase; collectively, the SWS1-SWSAP1-SPIDR complex is specifically required for inter-homolog homologous recombination, sister-chromatid exchange, and meiotic recombinase assembly, but is dispensable for intra-chromosomal HDR.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SWSAP1 is a RAD51 paralog that operates as the catalytic core of the human Shu complex to control the assembly and stability of RAD51 recombinase filaments during homologous recombination [#0, #6]. It forms a stable, mutually stabilizing heterodimer with SWS1 through the SWS1 SWIM domain, and the purified SWS1\\u00b7SWSAP1 complex binds single-stranded DNA and possesses DNA-stimulated ATPase activity [#0, #1]. Biochemically, the complex preferentially engages DNA and RAD51 filaments at exposed 5' ends, where it stabilizes filaments in an ATP-binding-dependent manner and drives conformational changes in an ATP-hydrolysis-dependent manner, while enhancing RPA diffusion on ssDNA to facilitate RAD51 loading and strand exchange [#6, #7]. SWSAP1 additionally protects nascent RAD51 filaments by directly inhibiting the FIGNL1 anti-recombinase, which otherwise dismantles RAD51 from ssDNA [#3]. Functionally, SWSAP1 acts together with SWS1, SPIDR, and PDS5B to promote RAD51 recruitment to repair foci, replication fork restart, and sister-chromatid exchange, and it is specifically required for inter-homolog HDR while being dispensable for intra-chromosomal HDR [#4, #5]. In meiosis the complex is needed to assemble RAD51 and DMC1 on recombination intermediates, and its loss causes infertility with reduced crossovers [#2]. A homozygous frameshift deletion in SWSAP1 establishes it as a premature ovarian insufficiency disease gene [#8].\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"Established SWSAP1 as a partner of SWS1 with intrinsic biochemical activities and a role in HR, defining the founding members of the human Shu complex.\",\n      \"evidence\": \"Co-IP, in vitro reconstitution of purified complex with ssDNA-binding/ATPase assays, and siRNA knockdown with an HR reporter\",\n      \"pmids\": [\"21965664\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve which subunit carries the ATPase active site\", \"No mechanism for how the complex acts on RAD51 filaments\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Mapped the SWS1 SWIM domain as the structural determinant of SWSAP1 binding, defining the interaction interface holding the core dimer together.\",\n      \"evidence\": \"Evolutionary/sequence analysis with in vivo SWIM-residue mutagenesis and interaction assays in yeast and human cells\",\n      \"pmids\": [\"25659377\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structure of the interface\", \"Single-lab interaction readout without orthogonal biophysical confirmation\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Demonstrated an in vivo meiotic requirement, showing the complex promotes recombinase loading and crossover formation and placing it in a BRCA2-overlapping pathway.\",\n      \"evidence\": \"Mouse knockout with immunofluorescence of RAD51/DMC1 foci on meiotic spreads and genetic epistasis with Chk2 and Brca2\",\n      \"pmids\": [\"30305635\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the biochemical step at which recombinase loading fails\", \"Molecular basis of overlap with BRCA2 unresolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identified the mechanism by which SWSAP1 stabilizes RAD51 filaments: direct antagonism of the FIGNL1 anti-recombinase.\",\n      \"evidence\": \"In vitro ssDNA-dissociation assays with purified FIGNL1 and SWSAP1, Co-IP, and double-depletion epistasis with RAD51 foci readout\",\n      \"pmids\": [\"30926776\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of SWSAP1 inhibition of FIGNL1 not defined\", \"Whether protection occurs at filament ends or along the filament unclear\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Expanded the Shu complex to include SPIDR and PDS5B and tied the complex to RAD51 recruitment, fork restart, and sister-chromatid exchange.\",\n      \"evidence\": \"CRISPR/Cas9 knockout, reciprocal Co-IP, clonogenic survival to MMS/MMC, SCE and RAD51 foci assays with epistasis\",\n      \"pmids\": [\"31665741\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry and architecture of the four-subunit complex unknown\", \"Role of PDS5B-mediated cohesin link not dissected\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Resolved the pathway specificity of the complex, establishing it as the first mitotic factor specifically required for inter-homolog HR but not intra-chromosomal HDR.\",\n      \"evidence\": \"CRISPR KO with HDR reporters distinguishing intra- vs inter-chromosomal repair, SCE assay, and Blm epistasis in mouse embryos\",\n      \"pmids\": [\"34253720\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular feature that restricts the complex to inter-homolog events unknown\", \"Basis of the genetic interaction with BLM not mechanistically defined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Provided direct biophysical evidence that SWSAP1-SWS1 stabilizes RAD51 filaments, enables strand exchange, and enhances RPA diffusion to promote RAD51 loading.\",\n      \"evidence\": \"Single-molecule confocal microscopy with optical tweezers, in vitro strand exchange, purified binding assays, and CRISPR KO with PARP/APE1 inhibitor sensitivity\",\n      \"pmids\": [\"39169038\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not separate ATP-binding from hydrolysis contributions\", \"Effect of cancer variants on filament biophysics not quantified\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Dissected the ATP cycle and DNA-end preference, showing 5'-end engagement with ATP-binding-dependent stabilization and hydrolysis-dependent conformational change of RAD51 filaments.\",\n      \"evidence\": \"Fluorescence polarization DNA binding, ATPase assays with Walker-motif mutagenesis, and fluorescence-based RAD51 filament interaction assays\",\n      \"pmids\": [\"40345587\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No high-resolution structure of the complex on a RAD51 filament\", \"Functional consequence of 5'-end specificity in cells not tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Linked SWSAP1 loss-of-function to human disease, establishing it as a premature ovarian insufficiency gene.\",\n      \"evidence\": \"Exome/genome sequencing of a POI patient, IH-HR functional assay in mouse ES cells, western blot, and in silico modelling\",\n      \"pmids\": [\"40991243\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single patient limits genetic certainty\", \"Genotype-phenotype spectrum across additional families undefined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the full SWS1-SWSAP1-SPIDR-PDS5B complex is architecturally organized and how it is mechanistically restricted to inter-homolog recombination remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structure of the assembled complex on DNA or RAD51 filaments\", \"Molecular basis of inter-homolog vs intra-chromosomal pathway choice unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0, 7]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 7]},\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3, 6]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [6, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [0, 4, 5]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [2, 8]}\n    ],\n    \"complexes\": [\"Shu complex (SWS1-SWSAP1-SPIDR-PDS5B)\"],\n    \"partners\": [\"SWS1\", \"RAD51\", \"SPIDR\", \"PDS5B\", \"FIGNL1\", \"DMC1\", \"BRCA2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}