SWI5

Summary

SWI5 (SWI5 homologous recombination repair protein, HGNC:31412) is a protein-coding gene on chromosome 9q34.11, encoding DNA repair protein SWI5 homolog (Q1ZZU3). Component of the SWI5-SFR1 complex, a complex required for double-strand break repair via homologous recombination.

Involved in cellular response to ionizing radiation and double-strand break repair via homologous recombination. Part of Swi5-Sfr1 complex.

Source: NCBI Gene 375757 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 47 total
• MANE Select transcript: NM_001318089

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31412
Approved symbol	SWI5
Name	SWI5 homologous recombination repair protein
Location	9q34.11
Locus type	gene with protein product
Status	Approved
Aliases	bA395P17.9, SAE3
Ensembl gene	ENSG00000175854
Ensembl biotype	protein_coding
OMIM	616528
Entrez	375757

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 2 nonsense_mediated_decay

ENST00000372898, ENST00000418976, ENST00000419867, ENST00000495313, ENST00000608796, ENST00000652598, ENST00000696406

RefSeq mRNA: 4 — MANE Select: NM_001318089 NM_001040011, NM_001318089, NM_001318092, NM_001379267

CCDS: CCDS43883, CCDS83422, CCDS94496

Canonical transcript exons

ENST00000418976 — 5 exons

Exon	Start	End
ENSE00001221432	128285939	128286033
ENSE00001458936	128276707	128276755
ENSE00001605401	128288652	128288989
ENSE00001609381	128276276	128276402
ENSE00003703274	128284510	128284631

Expression profiles

Bgee: expression breadth ubiquitous, 221 present calls, max score 98.36.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.1505 / max 216.6662, expressed in 1818 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
98744	31.5092	1818
98743	0.6412	418

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	98.36	gold quality
right testis	UBERON:0004534	98.22	gold quality
testis	UBERON:0000473	96.75	gold quality
adenohypophysis	UBERON:0002196	94.34	gold quality
pituitary gland	UBERON:0000007	93.58	gold quality
right lobe of thyroid gland	UBERON:0001119	92.59	gold quality
stromal cell of endometrium	CL:0002255	92.45	gold quality
left lobe of thyroid gland	UBERON:0001120	92.41	gold quality
lower esophagus mucosa	UBERON:0035834	92.38	gold quality
left ovary	UBERON:0002119	92.16	gold quality
endocervix	UBERON:0000458	91.84	gold quality
apex of heart	UBERON:0002098	91.76	gold quality
thyroid gland	UBERON:0002046	91.72	gold quality
ectocervix	UBERON:0012249	91.61	gold quality
right ovary	UBERON:0002118	91.41	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	91.26	gold quality
right atrium auricular region	UBERON:0006631	91.21	gold quality
right lobe of liver	UBERON:0001114	90.63	gold quality
body of uterus	UBERON:0009853	90.59	gold quality
islet of Langerhans	UBERON:0000006	90.20	gold quality
right uterine tube	UBERON:0001302	90.18	gold quality
cardiac atrium	UBERON:0002081	90.15	gold quality
right adrenal gland	UBERON:0001233	89.93	gold quality
putamen	UBERON:0001874	89.71	gold quality
hypothalamus	UBERON:0001898	89.60	gold quality
ovary	UBERON:0000992	89.56	gold quality
right adrenal gland cortex	UBERON:0035827	89.55	gold quality
left coronary artery	UBERON:0001626	89.46	gold quality
nucleus accumbens	UBERON:0001882	89.42	gold quality
ascending aorta	UBERON:0001496	89.41	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	12.97
E-GEOD-36552	no	57.97

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): PRDM2

miRNA regulators (miRDB)

25 targeting SWI5, 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-6508-5P	99.92	70.67	2465
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-548AV-5P	99.60	70.84	2107
HSA-MIR-548K	99.60	70.84	2107
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-8054	99.48	70.81	2084
HSA-MIR-5590-3P	99.48	70.91	2429
HSA-MIR-142-5P	99.48	70.92	2416
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-4292	99.16	65.57	1767
HSA-MIR-6791-5P	99.16	65.92	1844
HSA-MIR-4801	98.96	69.42	2096
HSA-MIR-873-5P	98.84	66.90	1348
HSA-MIR-3138	98.41	67.53	744
HSA-MIR-660-3P	98.14	66.04	1434
HSA-MIR-3620-5P	97.42	63.95	792
HSA-MIR-10400-3P	97.29	64.66	597
HSA-MIR-4674	97.29	64.62	597
HSA-MIR-517-5P	97.13	68.43	781
HSA-MIR-1587	96.95	64.03	932
HSA-MIR-3664-5P	96.74	66.56	770
HSA-MIR-125B-2-3P	96.69	68.38	1210
HSA-MIR-3683	91.74	64.69	58
HSA-MIR-5195-5P	90.84	65.09	287

Literature-anchored findings (GeneRIF, showing 2)

• that human SWI5-MEI5 has an evolutionarily conserved function in homologous recombination repair. (PMID:21252223)
• HBV DNAPTP1 downregulated the expression of SWI5 and CTC1 at translation level. (PMID:27265469)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	swi5	ENSDARG00000078492
mus_musculus	Swi5	ENSMUSG00000044627
rattus_norvegicus	Swi5	ENSRNOG00000022860
rattus_norvegicus	AC134087.1	ENSRNOG00000048439

Protein

Protein identifiers

DNA repair protein SWI5 homolog — Q1ZZU3 (reviewed: Q1ZZU3)

Alternative names: HBV DNAPTP1-transactivated protein A, Protein SAE3 homolog

All UniProt accessions (7): A0A494C0Z4, A0A8Q3SIQ2, H3BLW9, H7C3F2, H7C5E9, V9GYD7, V9GZ11

UniProt curated annotations — full annotation on UniProt →

Function. Component of the SWI5-SFR1 complex, a complex required for double-strand break repair via homologous recombination.

Subunit / interactions. Component of the SWI5-SFR1 complex. Interacts with RAD51.

Subcellular location. Nucleus.

Similarity. Belongs to the SWI5/SAE3 family.

RefSeq proteins (4): NP_001035100, NP_001305018, NP_001305021, NP_001366196 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010760	DNA-repair_Swi5	Family

Pfam: PF07061

UniProt features (4 total): chain 1, region of interest 1, coiled-coil region 1, mutagenesis site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q1ZZU3-F1	58.61	0.16

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 (1):

Position	Phenotype
173	does not affect interaction with sfr1/mei5.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 85 (showing top): GOBP_RESPONSE_TO_IONIZING_RADIATION, GOBP_ORGANELLE_FISSION, GOBP_DNA_DAMAGE_RESPONSE, GOBP_RESPONSE_TO_RADIATION, GOBP_CELLULAR_RESPONSE_TO_IONIZING_RADIATION, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_CELLULAR_RESPONSE_TO_RADIATION, GOBP_MEIOTIC_CELL_CYCLE_PROCESS, GOBP_PROTEIN_DNA_COMPLEX_ORGANIZATION, GOBP_RECOMBINATIONAL_REPAIR, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, BRACHAT_RESPONSE_TO_CAMPTOTHECIN_DN, GOBP_CELLULAR_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_MEIOTIC_CELL_CYCLE, NUYTTEN_EZH2_TARGETS_DN

GO Biological Process (4): double-strand break repair via homologous recombination (GO:0000724), cellular response to ionizing radiation (GO:0071479), DNA repair (GO:0006281), DNA damage response (GO:0006974)

GO Molecular Function (0):

GO Cellular Component (2): nucleus (GO:0005634), Swi5-Sfr1 complex (GO:0032798)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
recombinational repair	1
double-strand break repair	1
response to ionizing radiation	1
cellular response to radiation	1
DNA metabolic process	1
DNA damage response	1
cellular response to stress	1
intracellular membrane-bounded organelle	1
nuclear chromosome	1
chromatin	1
DNA recombinase mediator complex	1
nuclear protein-containing complex	1

Protein interactions and networks

STRING

456 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SWI5	SFR1	Q86XK3	997
SWI5	SMARCA2	P51531	772
SWI5	SMARCA4	P51532	745
SWI5	MND1	Q9BWT6	735
SWI5	SPATA6	Q9NWH7	717
SWI5	RAD51	Q06609	689
SWI5	ACE2	Q9BYF1	689
SWI5	SPO11	Q9Y5K1	640
SWI5	FLI1	Q01543	596
SWI5	LGALS4	P56470	595
SWI5	SMARCC1	Q92922	587
SWI5	RAD52	P43351	586
SWI5	SRF	P11831	572
SWI5	FOXO1	Q12778	553
SWI5	FOXG1	P55315	544

IntAct

9 interactions, top by confidence:

A	B	Type	Score
SWI5	SFR1	psi-mi:“MI:0915”(physical association)	0.700
SFR1	SWI5	psi-mi:“MI:0915”(physical association)	0.700
SWI5	SFR1	psi-mi:“MI:0407”(direct interaction)	0.700
SFR1	SWI5	psi-mi:“MI:0407”(direct interaction)	0.700
RAD51	SWI5	psi-mi:“MI:0407”(direct interaction)	0.440
SWI5	S100A10	psi-mi:“MI:0915”(physical association)	0.400
SFR1	CTSV	psi-mi:“MI:0914”(association)	0.350

BioGRID (7): RAD51 (Affinity Capture-Western), SWI5 (Proximity Label-MS), SWI5 (Affinity Capture-MS), SFR1 (Affinity Capture-Western), SFR1 (Reconstituted Complex), SWI5 (Reconstituted Complex), RAD51 (Reconstituted Complex)

ESM2 similar proteins: A0A5N6H279, A4D2B8, D3ZML2, O76081, O91531, P03327, P0C678, P0C733, P79348, Q00731, Q09PK2, Q13670, Q1HVB5, Q1ZZU3, Q4KL35, Q4R1S1, Q52993, Q5JLA7, Q5JN07, Q5MFW3, Q63553, Q64902, Q6DN03, Q6NUI1, Q6P050, Q6SW81, Q86UQ5, Q8AZJ3, Q8BG31, Q8BVZ5, Q8CE90, Q8CEZ0, Q8K3M5, Q8LN49, Q8N5Z5, Q8TE04, Q8VDU5, Q8WTX9, Q8WXT5, Q9BTV7

Diamond homologs: A9UL70, B5X601, C3KJF2, Q1ZZU3, Q63ZV7, Q8K3D3, Q9UUB7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	36
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1627 predictions. Top by Δscore:

Variant	Effect	Δscore
9:128275888:TTTA:T	donor_loss	1.0000
9:128275889:TTACC:T	donor_loss	1.0000
9:128275890:TACC:T	donor_loss	1.0000
9:128276756:G:GG	donor_gain	1.0000
9:128284505:CTCA:C	acceptor_loss	1.0000
9:128284506:TCA:T	acceptor_loss	1.0000
9:128284507:CA:C	acceptor_loss	1.0000
9:128284508:A:AG	acceptor_gain	1.0000
9:128284508:AGAG:A	acceptor_gain	1.0000
9:128284509:G:GA	acceptor_gain	1.0000
9:128284509:G:GT	acceptor_loss	1.0000
9:128284509:GA:G	acceptor_gain	1.0000
9:128284509:GAGG:G	acceptor_gain	1.0000
9:128284509:GAGGC:G	acceptor_gain	1.0000
9:128284620:G:GG	donor_gain	1.0000
9:128284627:TCTGA:T	donor_gain	1.0000
9:128284628:CTGA:C	donor_gain	1.0000
9:128284629:TGA:T	donor_gain	1.0000
9:128284630:GA:G	donor_gain	1.0000
9:128284630:GAG:G	donor_gain	1.0000
9:128284631:AG:A	donor_loss	1.0000
9:128284632:G:GG	donor_gain	1.0000
9:128285925:A:AG	acceptor_gain	1.0000
9:128285925:ATC:A	acceptor_gain	1.0000
9:128285926:T:G	acceptor_gain	1.0000
9:128285927:C:CA	acceptor_gain	1.0000
9:128285932:A:AG	acceptor_gain	1.0000
9:128285933:T:G	acceptor_gain	1.0000
9:128285934:CCCA:C	acceptor_loss	1.0000
9:128285937:A:AG	acceptor_gain	1.0000

AlphaMissense

851 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:128286002:G:C	K204N	0.998
9:128286002:G:T	K204N	0.998
9:128285980:T:C	L197P	0.997
9:128285988:T:C	Y200H	0.997
9:128286003:G:C	D205H	0.997
9:128286004:A:C	D205A	0.996
9:128285993:T:A	N201K	0.995
9:128285993:T:G	N201K	0.995
9:128286005:T:A	D205E	0.995
9:128286005:T:G	D205E	0.995
9:128288693:T:C	F229L	0.995
9:128288695:T:A	F229L	0.995
9:128288695:T:G	F229L	0.995
9:128286004:A:T	D205V	0.994
9:128286024:G:C	G212R	0.994
9:128285959:T:C	L190P	0.993
9:128285989:A:C	Y200S	0.993
9:128286004:A:G	D205G	0.993
9:128286033:G:C	A215P	0.993
9:128285980:T:A	L197H	0.992
9:128286000:A:G	K204E	0.992
9:128286014:G:C	Q208H	0.992
9:128286014:G:T	Q208H	0.992
9:128286019:T:C	L210P	0.992
9:128288652:C:A	A215D	0.992
9:128285982:C:G	H198D	0.990
9:128285988:T:G	Y200D	0.990
9:128286013:A:C	Q208P	0.990
9:128288700:T:C	L231P	0.989
9:128285989:A:G	Y200C	0.988

dbSNP variants (sampled 300 via entrez): RS1000116511 (9:128286227 G>A), RS1000328117 (9:128280600 C>T), RS1000329079 (9:128274335 G>A,C,T), RS1000371851 (9:128283148 C>G,T), RS1000425640 (9:128274686 G>A), RS1000520924 (9:128288461 C>G,T), RS1000570637 (9:128289240 C>G,T), RS1000629819 (9:128281596 C>A,T), RS1000666890 (9:128275729 T>A,C), RS1001104502 (9:128281898 C>T), RS1001544714 (9:128285434 C>T), RS1001649492 (9:128288079 A>T), RS1001734078 (9:128279557 A>G), RS1001878428 (9:128287019 T>A), RS1001909528 (9:128287723 G>A)

Disease associations

OMIM: gene MIM:616528 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST002783_274	Body mass index	3.000000e-07
GCST002783_629	Body mass index	3.000000e-07
GCST002783_71	Body mass index	6.000000e-06
GCST004904_142	Body mass index	9.000000e-12

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tretinoin	decreases expression, increases expression	2
Cyclosporine	increases expression	2
aristolochic acid I	increases expression	1
trichostatin A	affects expression	1
arsenite	affects binding, increases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	increases expression	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	increases expression	1
Leflunomide	decreases expression	1
Acetaminophen	affects response to substance	1
Benzo(a)pyrene	affects methylation	1
Cisplatin	increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Diethylstilbestrol	increases expression	1
Doxorubicin	increases expression	1
Ketoconazole	increases expression	1
Methyl Methanesulfonate	increases expression	1
Smoke	decreases expression	1
Valproic Acid	increases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	increases expression	1
Okadaic Acid	increases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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