SWSAP1

Summary

SWSAP1 (SWIM-type zinc finger 7 associated protein 1, HGNC:26638) is a protein-coding gene on chromosome 19p13.2, encoding ATPase SWSAP1 (Q6NVH7). ATPase which is preferentially stimulated by single-stranded DNA and is involved in homologous recombination repair (HRR).

Enables ATP hydrolysis activity and single-stranded DNA binding activity. Involved in double-strand break repair via homologous recombination and protein stabilization. Part of Shu complex.

Source: NCBI Gene 126074 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 39 total
• MANE Select transcript: NM_175871

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26638
Approved symbol	SWSAP1
Name	SWIM-type zinc finger 7 associated protein 1
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ35119, ZSWIM7AP1, SWS1AP1
Ensembl gene	ENSG00000173928
Ensembl biotype	protein_coding
OMIM	614536
Entrez	126074

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000312423, ENST00000674460, ENST00000884600

RefSeq mRNA: 1 — MANE Select: NM_175871 NM_175871

CCDS: CCDS12259

Canonical transcript exons

ENST00000674460 — 2 exons

Exon	Start	End
ENSE00001186021	11374666	11374929
ENSE00003898849	11375513	11376169

Expression profiles

Bgee: expression breadth ubiquitous, 180 present calls, max score 84.87.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.5299 / max 43.3160, expressed in 1441 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
173916	3.5299	1441

Top tissues by expression

231 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.87	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.94	gold quality
monocyte	CL:0000576	82.83	gold quality
leukocyte	CL:0000738	82.52	gold quality
granulocyte	CL:0000094	80.45	gold quality
right lobe of liver	UBERON:0001114	78.74	gold quality
right adrenal gland cortex	UBERON:0035827	78.44	gold quality
spleen	UBERON:0002106	78.11	gold quality
right adrenal gland	UBERON:0001233	77.91	gold quality
mucosa of transverse colon	UBERON:0004991	77.88	gold quality
left adrenal gland cortex	UBERON:0035825	76.93	gold quality
left adrenal gland	UBERON:0001234	76.92	gold quality
apex of heart	UBERON:0002098	76.38	gold quality
adrenal cortex	UBERON:0001235	76.23	gold quality
metanephros cortex	UBERON:0010533	76.17	gold quality
blood	UBERON:0000178	76.15	gold quality
right uterine tube	UBERON:0001302	74.90	gold quality
adrenal gland	UBERON:0002369	74.37	gold quality
metanephros	UBERON:0000081	74.20	gold quality
transverse colon	UBERON:0001157	73.70	gold quality
body of stomach	UBERON:0001161	73.69	gold quality
right coronary artery	UBERON:0001625	73.67	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	73.47	gold quality
left coronary artery	UBERON:0001626	73.38	gold quality
lymph node	UBERON:0000029	73.18	gold quality
left uterine tube	UBERON:0001303	72.84	gold quality
coronary artery	UBERON:0001621	72.80	gold quality
gastrocnemius	UBERON:0001388	72.74	gold quality
cerebellar vermis	UBERON:0004720	72.74	gold quality
bone marrow	UBERON:0002371	72.56	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.80
E-MTAB-7303	no	331.75
E-GEOD-110499	no	50.04

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

44 targeting SWSAP1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4295	99.90	73.11	1838
HSA-MIR-8076	99.78	68.52	1170
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-4502	99.65	66.99	1021
HSA-MIR-561-3P	99.64	70.90	3647
HSA-MIR-802	99.61	67.70	1254
HSA-MIR-142-5P	99.48	70.92	2416
HSA-MIR-5590-3P	99.48	70.91	2429
HSA-MIR-125A-5P	99.36	70.59	1640
HSA-MIR-125B-5P	99.36	70.36	1662
HSA-MIR-4685-5P	99.25	65.99	1563
HSA-MIR-6837-5P	99.25	65.47	1632

Literature-anchored findings (GeneRIF, showing 4)

• the human Shu complex (hSWS1.SWSAP1) has an evolutionarily conserved function in homologous recombination (PMID:21965664)
• SWSAP1 protects RAD51 filaments by antagonizing the anti-recombinase, FIGNL1. (PMID:30926776)
• our study uncovers a protein complex, which consists of SWS1, SWSAP1, SPIDR and PDS5B, involved in DNA repair and provides insight into Shu complex function and composition. (PMID:31665741)
• The human Shu complex promotes RAD51 activity by modulating RPA dynamics on ssDNA. (PMID:39169038)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Swsap1	ENSMUSG00000051238
rattus_norvegicus	Swsap1	ENSRNOG00000012604

Protein

Protein identifiers

ATPase SWSAP1 — Q6NVH7 (reviewed: Q6NVH7)

Alternative names: SWIM-type zinc finger 7-associated protein 1, SWS1-associated protein 1, ZSWIM7-associated protein 1

All UniProt accessions (2): Q6NVH7, A0A6I8PRB2

UniProt curated annotations — full annotation on UniProt →

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.

Subunit / interactions. Interacts with ZSWIM7; they form a functional complex involved in homologous recombination repair and stabilize each other. Interacts with RAD51, RAD51B, RAD51C, RAD51D and XRCC3; involved in homologous recombination repair.

Subcellular location. Nucleus.

RefSeq proteins (1): NP_787067* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027417	P-loop_NTPase	Homologous_superfamily

UniProt features (6 total): mutagenesis site 2, chain 1, region of interest 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6NVH7-F1	83.34	0.48

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Mutagenesis-validated functional residues (2):

Position	Phenotype
18	loss of function in hrr associated with altered ssdna-stimulated atpase activity.
96	loss of function in hrr associated with altered ssdna-stimulated atpase activity.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 83 (showing top): MARTINEZ_RB1_TARGETS_UP, GOBP_PROTEIN_STABILIZATION, GOBP_DNA_DAMAGE_RESPONSE, GOBP_REGULATION_OF_PROTEIN_STABILITY, GOBP_RECOMBINATIONAL_REPAIR, MARTINEZ_RB1_AND_TP53_TARGETS_UP, GOMF_SINGLE_STRANDED_DNA_BINDING, RFX1_01, chr19p13, GOBP_DNA_METABOLIC_PROCESS, GOBP_DNA_REPAIR, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ACID_ANHYDRIDES, ATGGYGGA_UNKNOWN, GOBP_DNA_RECOMBINATION, DODD_NASOPHARYNGEAL_CARCINOMA_DN

GO Biological Process (5): double-strand break repair via homologous recombination (GO:0000724), protein stabilization (GO:0050821), DNA repair (GO:0006281), DNA recombination (GO:0006310), DNA damage response (GO:0006974)

GO Molecular Function (4): single-stranded DNA binding (GO:0003697), ATP hydrolysis activity (GO:0016887), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), Shu complex (GO:0097196)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA metabolic process	2
recombinational repair	1
double-strand break repair	1
regulation of protein stability	1
DNA damage response	1
cellular response to stress	1
DNA binding	1
ribonucleoside triphosphate phosphatase activity	1
ATP-dependent activity	1
nucleic acid binding	1
binding	1
intracellular membrane-bounded organelle	1
protein-containing complex	1

Protein interactions and networks

STRING

439 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SWSAP1	SPIDR	Q14159	753
SWSAP1	ZSWIM7	Q19AV6	749
SWSAP1	XRCC3	O43542	711
SWSAP1	K7EN88	K7EN88	671
SWSAP1	RAD51D	O75771	671
SWSAP1	PDS5B	Q9NTI5	654
SWSAP1	MEIOB	Q8N635	642
SWSAP1	RAD51B	O15315	622
SWSAP1	FIGNL1	Q6PIW4	571
SWSAP1	RMND5A	Q9H871	556
SWSAP1	RAD51C	O43502	555
SWSAP1	HSF2BP	O75031	534
SWSAP1	BRCA2	P51587	531
SWSAP1	XRCC2	O43543	489
SWSAP1	CCDC159	P0C7I6	479

IntAct

54 interactions, top by confidence:

A	B	Type	Score
ZSWIM7	SWSAP1	psi-mi:“MI:0915”(physical association)	0.900
SWSAP1	ZSWIM7	psi-mi:“MI:0915”(physical association)	0.900
SWSAP1	SPIDR	psi-mi:“MI:0915”(physical association)	0.720
SPIDR	SWSAP1	psi-mi:“MI:0915”(physical association)	0.720
SPIDR	SWSAP1	psi-mi:“MI:0914”(association)	0.720
SPIDR	ZSWIM7	psi-mi:“MI:0915”(physical association)	0.660
ZSWIM7	SPIDR	psi-mi:“MI:0915”(physical association)	0.660
SWSAP1	SPG21	psi-mi:“MI:0915”(physical association)	0.560
SWSAP1	EPM2AIP1	psi-mi:“MI:0915”(physical association)	0.560
SWSAP1	GAPDHS	psi-mi:“MI:0914”(association)	0.530
PLA2G10	CHEK1	psi-mi:“MI:0914”(association)	0.530
REEP1	PLSCR1	psi-mi:“MI:0914”(association)	0.530

BioGRID (54): SWSAP1 (Two-hybrid), ZSWIM7 (Affinity Capture-MS), SWSAP1 (Affinity Capture-MS), GAPDHS (Affinity Capture-MS), UBB (Affinity Capture-MS), SWSAP1 (Affinity Capture-Western), SWSAP1 (Affinity Capture-Western), FIGNL1 (Synthetic Rescue), ZSWIM7 (Two-hybrid), SWSAP1 (Two-hybrid), SWSAP1 (Two-hybrid), EPM2AIP1 (Two-hybrid), ZSWIM7 (Two-hybrid), UBB (Affinity Capture-MS), GAPDHS (Affinity Capture-MS)

ESM2 similar proteins: A4GXA9, A7E3N7, A8VU90, D3KCC4, D3ZZN9, G3V8H4, O08672, O95382, Q13608, Q13671, Q14296, Q17RN3, Q28616, Q3UR50, Q3UR97, Q3V3V9, Q4KM32, Q53GL7, Q56A04, Q58CQ5, Q58EX7, Q5BK61, Q5NVA9, Q62893, Q643R3, Q66H85, Q6F5E8, Q6NVH7, Q6ZW31, Q7T0L4, Q80UU1, Q80XL1, Q8BJW7, Q8BTN6, Q8CIE4, Q8CJ00, Q8K592, Q8N2G8, Q8NAG6, Q8VCI7

Diamond homologs: Q6NVH7, Q8VCI7

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
SWSAP1	“form complex”	“SHU complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 21 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA)	5	123.1×	5e-09
Homologous DNA Pairing and Strand Exchange	5	119.0×	5e-09
Resolution of D-loop Structures through Holliday Junction Intermediates	6	112.7×	4e-10
Presynaptic phase of homologous DNA pairing and strand exchange	6	102.0×	4e-10
HDR through Homologous Recombination (HRR)	6	71.4×	3e-09

GO biological processes:

GO term	Partners	Fold	FDR
double-strand break repair via homologous recombination	7	52.0×	9e-09
DNA repair	7	21.3×	2e-06
DNA damage response	5	12.7×	8e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

39 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	34
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

103 predictions. Top by Δscore:

Variant	Effect	Δscore
19:11374926:CCAGG:C	donor_loss	1.0000
19:11374927:CAGGT:C	donor_loss	1.0000
19:11374928:AGGT:A	donor_loss	1.0000
19:11374930:GT:G	donor_loss	1.0000
19:11374931:T:G	donor_loss	1.0000
19:11375511:A:AG	acceptor_gain	1.0000
19:11375512:G:GG	acceptor_gain	1.0000
19:11375512:GAA:G	acceptor_gain	1.0000
19:11375512:GA:G	acceptor_gain	0.9900
19:11375512:GAAGA:G	acceptor_gain	0.9900
19:11375498:T:TA	acceptor_gain	0.9800
19:11375507:TTCTA:T	acceptor_loss	0.9800
19:11375508:TCTA:T	acceptor_loss	0.9800
19:11375509:CTA:C	acceptor_loss	0.9800
19:11375510:TAGAA:T	acceptor_gain	0.9800
19:11375511:AGA:A	acceptor_loss	0.9800
19:11375511:AGAAG:A	acceptor_gain	0.9800
19:11375512:G:GC	acceptor_loss	0.9800
19:11374930:G:GG	donor_gain	0.9700
19:11374780:ACACC:A	donor_gain	0.9300
19:11375514:A:AG	acceptor_gain	0.8700
19:11375515:G:GA	acceptor_gain	0.8700
19:11375513:AAG:A	acceptor_loss	0.8400
19:11375514:A:C	acceptor_loss	0.8400
19:11375515:GATCC:G	acceptor_gain	0.7700
19:11375428:A:T	donor_gain	0.7500
19:11375654:G:GT	donor_gain	0.7400
19:11375427:G:GT	donor_gain	0.7200
19:11374787:G:GT	donor_gain	0.7000
19:11374925:TCCAG:T	donor_gain	0.6800

AlphaMissense

1562 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:11375523:T:C	F66S	0.991
19:11374859:T:C	F39S	0.980
19:11374858:T:C	F39L	0.977
19:11374860:C:A	F39L	0.977
19:11374860:C:G	F39L	0.977
19:11375522:T:C	F66L	0.968
19:11375524:C:A	F66L	0.968
19:11375524:C:G	F66L	0.968
19:11374820:C:A	A26D	0.959
19:11375528:T:C	Y68H	0.951
19:11375517:T:C	I64T	0.949
19:11375523:T:G	F66C	0.948
19:11375685:A:T	D120V	0.948
19:11374853:T:A	V37D	0.947
19:11375529:A:G	Y68C	0.946
19:11375627:T:C	Y101H	0.946
19:11374859:T:G	F39C	0.945
19:11375517:T:G	I64S	0.941
19:11374777:G:C	G12R	0.940
19:11375528:T:G	Y68D	0.940
19:11375673:C:A	A116D	0.940
19:11375628:A:C	Y101S	0.938
19:11375610:T:A	L95H	0.934
19:11375822:T:C	C166R	0.933
19:11375628:A:G	Y101C	0.928
19:11375679:T:G	L118R	0.927
19:11375699:T:C	F125L	0.924
19:11375701:C:A	F125L	0.924
19:11375701:C:G	F125L	0.924
19:11375921:T:C	F199L	0.924

dbSNP variants (sampled 300 via entrez): RS1001934794 (19:11373680 C>A), RS1002411022 (19:11374167 G>A), RS1005295343 (19:11376633 T>A,C), RS1005342984 (19:11376187 C>A), RS1005543412 (19:11374978 A>G), RS1005821572 (19:11374019 A>C), RS1005874253 (19:11373747 G>A,C), RS1009265171 (19:11372864 G>A,T), RS1009770471 (19:11374708 A>C), RS1009833186 (19:11374494 T>C), RS1010777082 (19:11376025 G>A,C), RS1010830779 (19:11375705 C>A), RS1010988942 (19:11375916 T>G), RS1013292720 (19:11374410 T>G), RS1013295257 (19:11374064 G>A)

Disease associations

OMIM: gene MIM:614536 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST005194_32	Coronary artery disease	2.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
triphenyl phosphate	affects expression	1
bisphenol A	increases methylation	1
ferrous chloride	decreases expression	1
2-palmitoylglycerol	increases expression	1
Benzo(a)pyrene	affects methylation	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Methylcholanthrene	affects binding, increases reaction	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1
Urethane	decreases expression	1
Valproic Acid	affects expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.