SFR1

Summary

SFR1 (SWI5 dependent homologous recombination repair protein 1, HGNC:29574) is a protein-coding gene on chromosome 10q25.1, encoding Swi5-dependent recombination DNA repair protein 1 homolog (Q86XK3). Component of the SWI5-SFR1 complex, a complex required for double-strand break repair via homologous recombination.

Enables transcription coactivator activity. Involved in cellular response to estrogen stimulus; double-strand break repair via homologous recombination; and positive regulation of DNA-templated transcription. Located in centrosome; nucleolus; and nucleoplasm. Part of Swi5-Sfr1 complex.

Source: NCBI Gene 119392 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 43 total
• MANE Select transcript: NM_001002759

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29574
Approved symbol	SFR1
Name	SWI5 dependent homologous recombination repair protein 1
Location	10q25.1
Locus type	gene with protein product
Status	Approved
Aliases	MEI5, bA373N18.1, FLJ41960
Ensembl gene	ENSG00000156384
Ensembl biotype	protein_coding
OMIM	616527
Entrez	119392

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000369727, ENST00000369729, ENST00000463224

RefSeq mRNA: 4 — MANE Select: NM_001002759 NM_001002759, NM_001384829, NM_001384830, NM_145247

CCDS: CCDS31279, CCDS31280

Canonical transcript exons

ENST00000369727 — 4 exons

Exon	Start	End
ENSE00001026104	104123714	104124124
ENSE00001450732	104122171	104122196
ENSE00003562919	104122965	104123086
ENSE00003910651	104125513	104126383

Expression profiles

Bgee: expression breadth ubiquitous, 250 present calls, max score 94.81.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.3366 / max 324.7888, expressed in 1730 samples.

FANTOM5 promoters (11 alternative TSS)

Promoter ID	TPM avg	Samples expressed
106867	3.2699	1257
106866	2.0445	1133
106865	1.5162	897
106861	0.4706	199
106862	0.4454	73
106858	0.1436	28
106860	0.1419	59
106864	0.0942	27
106868	0.0878	20
106863	0.0650	20

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
epithelial cell of pancreas	CL:0000083	94.81	gold quality
pancreatic ductal cell	CL:0002079	94.59	gold quality
secondary oocyte	CL:0000655	94.13	gold quality
oocyte	CL:0000023	90.91	gold quality
cartilage tissue	UBERON:0002418	90.12	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.06	gold quality
trabecular bone tissue	UBERON:0002483	88.76	gold quality
amniotic fluid	UBERON:0000173	88.24	gold quality
oviduct epithelium	UBERON:0004804	87.78	gold quality
palpebral conjunctiva	UBERON:0001812	85.60	gold quality
calcaneal tendon	UBERON:0003701	85.47	gold quality
gingival epithelium	UBERON:0001949	85.20	gold quality
buccal mucosa cell	CL:0002336	85.02	gold quality
germinal epithelium of ovary	UBERON:0001304	84.94	gold quality
parietal pleura	UBERON:0002400	84.74	gold quality
tibia	UBERON:0000979	84.53	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.30	gold quality
visceral pleura	UBERON:0002401	84.30	gold quality
esophagus squamous epithelium	UBERON:0006920	83.79	gold quality
gingiva	UBERON:0001828	83.59	gold quality
right testis	UBERON:0004534	83.51	gold quality
testis	UBERON:0000473	83.00	gold quality
bone marrow	UBERON:0002371	82.97	gold quality
left testis	UBERON:0004533	82.52	gold quality
monocyte	CL:0000576	82.48	gold quality
leukocyte	CL:0000738	82.34	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	81.99	gold quality
ileal mucosa	UBERON:0000331	81.84	gold quality
corpus epididymis	UBERON:0004359	81.62	gold quality
cauda epididymis	UBERON:0004360	81.36	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.40
E-GEOD-109979	no	58.03

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

52 targeting SFR1, 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-3613-3P	100.00	76.36	7965
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-432-3P	100.00	67.86	705
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-6744-5P	99.93	66.82	748
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-93-5P	99.88	73.98	2606
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-548AR-3P	99.85	71.26	3889
HSA-MIR-8084	99.73	69.57	1760
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-516B-5P	99.56	66.33	1495
HSA-MIR-513C-5P	99.50	68.42	1730
HSA-MIR-514B-5P	99.50	68.19	1766
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-372-5P	99.41	69.11	2299
HSA-MIR-4520-2-3P	99.14	69.28	1009

Literature-anchored findings (GeneRIF, showing 2)

• that human SWI5-MEI5 has an evolutionarily conserved function in homologous recombination repair. (PMID:21252223)
• SFR1 is a novel transcriptional modulator for ERalpha and a potential target in breast cancer therapy. (PMID:23874500)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	sfr1	ENSDARG00000021974
mus_musculus	Sfr1	ENSMUSG00000025066
rattus_norvegicus	Sfr1	ENSRNOG00000012641

Protein

Protein identifiers

Swi5-dependent recombination DNA repair protein 1 homolog — Q86XK3 (reviewed: Q86XK3)

Alternative names: Meiosis protein 5 homolog

All UniProt accessions (1): Q86XK3

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. Acts as a transcriptional modulator for ESR1.

Subunit / interactions. Component of the SWI5-SFR1 complex. Interacts with RAD51; the interaction is weak. Interacts with ESR1 in the ligand-independent and ligand-dependent manner.

Subcellular location. Nucleus.

Tissue specificity. Widely expressed.

Similarity. Belongs to the SFR1/MEI5 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q86XK3-1	1	yes
Q86XK3-2	2
Q86XK3-3	3

RefSeq proteins (4): NP_001002759, NP_001371758, NP_001371759, NP_660290 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018468	SFR1/Mei5	Family
IPR042429	SFR1	Family

Pfam: PF10376

UniProt features (10 total): modified residue 3, splice variant 2, chain 1, region of interest 1, coiled-coil region 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86XK3-F1	67.85	0.30

Functional residue map

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

Post-translational modifications (3): 61, 64, 1

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 158 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_ORGANELLE_FISSION, GOBP_CELLULAR_RESPONSE_TO_HORMONE_STIMULUS, RIGGI_EWING_SARCOMA_PROGENITOR_DN, GOBP_RESPONSE_TO_ESTROGEN, GOBP_DNA_DAMAGE_RESPONSE, TGANTCA_AP1_C, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, GOBP_RESPONSE_TO_HORMONE, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS, FISCHER_DREAM_TARGETS, GOBP_CELLULAR_RESPONSE_TO_ESTROGEN_STIMULUS, GOBP_MEIOTIC_CELL_CYCLE_PROCESS, GOBP_PROTEIN_DNA_COMPLEX_ORGANIZATION

GO Biological Process (5): double-strand break repair via homologous recombination (GO:0000724), positive regulation of DNA-templated transcription (GO:0045893), cellular response to estrogen stimulus (GO:0071391), DNA repair (GO:0006281), DNA damage response (GO:0006974)

GO Molecular Function (2): transcription coactivator activity (GO:0003713), protein binding (GO:0005515)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), centrosome (GO:0005813), Swi5-Sfr1 complex (GO:0032798)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nuclear lumen	2
recombinational repair	1
double-strand break repair	1
DNA-templated transcription	1
regulation of DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
cellular response to hormone stimulus	1
response to estrogen	1
DNA metabolic process	1
DNA damage response	1
cellular response to stress	1
transcription coregulator activity	1
positive regulation of DNA-templated transcription	1
binding	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1
intracellular membraneless organelle	1
centriole	1
microtubule organizing center	1
nuclear chromosome	1
chromatin	1
DNA recombinase mediator complex	1
nuclear protein-containing complex	1

Protein interactions and networks

STRING

276 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SFR1	SWI5	Q1ZZU3	997
SFR1	RAD51	Q06609	726
SFR1	MND1	Q9BWT6	602
SFR1	RAD54B	Q9Y620	527
SFR1	SPO11	Q9Y5K1	509
SFR1	RAD52	P43351	507
SFR1	MEIOB	Q8N635	497
SFR1	LSM6	P62312	434
SFR1	ATRX	P46100	402
SFR1	SFI1	A8K8P3	378
SFR1	FBH1	Q8NFZ0	370
SFR1	DNAJA3	Q96EY1	359
SFR1	RAD51AP1	Q96B01	357
SFR1	POC5	Q8NA72	352
SFR1	SKIC8	Q9GZS3	329

IntAct

44 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
RNF40	SFR1	psi-mi:“MI:0915”(physical association)	0.670
RINT1	SFR1	psi-mi:“MI:0915”(physical association)	0.670
TFIP11	SFR1	psi-mi:“MI:0915”(physical association)	0.670
SFR1	RNF40	psi-mi:“MI:0915”(physical association)	0.670
SFR1	RINT1	psi-mi:“MI:0915”(physical association)	0.670
SFR1	TFIP11	psi-mi:“MI:0915”(physical association)	0.670
NDC80	SFR1	psi-mi:“MI:0915”(physical association)	0.560
NMI	SFR1	psi-mi:“MI:0915”(physical association)	0.560
HMBOX1	SFR1	psi-mi:“MI:0915”(physical association)	0.560
CEP70	SFR1	psi-mi:“MI:0915”(physical association)	0.560
MRFAP1L1	SFR1	psi-mi:“MI:0915”(physical association)	0.560
SFR1	HMBOX1	psi-mi:“MI:0915”(physical association)	0.560
SFR1	MRFAP1L1	psi-mi:“MI:0915”(physical association)	0.560
SFR1	NDC80	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (68): SFR1 (Two-hybrid), SFR1 (Two-hybrid), SFR1 (Two-hybrid), SFR1 (Two-hybrid), SFR1 (Two-hybrid), SFR1 (Two-hybrid), SFR1 (Two-hybrid), SFR1 (Two-hybrid), SFR1 (Co-fractionation), SFR1 (Biochemical Activity), SFR1 (Two-hybrid), SFR1 (Affinity Capture-Western), ESR1 (Affinity Capture-Western), RNASE7 (Affinity Capture-MS), RBP1 (Affinity Capture-MS)

ESM2 similar proteins: A2BDB7, A2CE83, B2ZX90, D3IUT5, E1BXS0, F4IDY7, P0DPK0, P49069, P58501, Q07532, Q0P4A6, Q1JQE2, Q28GJ0, Q28GL6, Q2KJD6, Q2MJV9, Q2TBJ0, Q2WG79, Q2WG80, Q5F3D1, Q5R789, Q5TID7, Q5U3I2, Q5ZHQ6, Q640U0, Q641E3, Q66H73, Q67W65, Q68F53, Q6AYN9, Q6DRL4, Q6NZY4, Q7TPE5, Q7Z2Z1, Q7ZX27, Q80YR7, Q80ZU5, Q86XK3, Q8BQ33, Q8C6C7

Diamond homologs: B7ZD04, E1BXS0, Q68F53, Q6TXG9, Q86XK3, Q8BP27

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	38
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

549 predictions. Top by Δscore:

Variant	Effect	Δscore
10:104123087:G:GG	donor_gain	1.0000
10:104123125:GTTTC:G	donor_gain	1.0000
10:104123126:TTTCT:T	donor_gain	1.0000
10:104123777:AATGT:A	acceptor_gain	1.0000
10:104122266:T:G	donor_gain	0.9900
10:104123129:C:CG	donor_gain	0.9900
10:104123129:C:G	donor_gain	0.9900
10:104123777:A:AG	acceptor_gain	0.9900
10:104124120:CAAAG:C	donor_loss	0.9900
10:104124121:AAAG:A	donor_loss	0.9900
10:104124122:AAGG:A	donor_loss	0.9900
10:104124123:AGGTG:A	donor_loss	0.9900
10:104124124:GG:G	donor_loss	0.9900
10:104124125:GT:G	donor_loss	0.9900
10:104124126:T:A	donor_loss	0.9900
10:104125510:CA:C	acceptor_loss	0.9900
10:104125511:A:AG	acceptor_gain	0.9900
10:104125511:AG:A	acceptor_loss	0.9900
10:104125511:AGAAT:A	acceptor_gain	0.9900
10:104125512:G:GG	acceptor_gain	0.9900
10:104125512:GA:G	acceptor_gain	0.9900
10:104125512:GAAT:G	acceptor_gain	0.9900
10:104125512:GAATG:G	acceptor_gain	0.9900
10:104122194:G:T	donor_gain	0.9800
10:104125506:GTTTC:G	acceptor_loss	0.9800
10:104125512:GAA:G	acceptor_gain	0.9800
10:104122245:G:GT	donor_gain	0.9700
10:104122964:GAGAA:G	acceptor_gain	0.9700
10:104123039:GCCTC:G	donor_gain	0.9700
10:104123777:AAT:A	acceptor_gain	0.9700

AlphaMissense

1623 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:104125549:T:A	W195R	0.998
10:104125549:T:C	W195R	0.998
10:104124096:T:C	L173P	0.995
10:104125551:G:C	W195C	0.994
10:104125551:G:T	W195C	0.994
10:104125561:A:C	S199R	0.994
10:104125563:C:A	S199R	0.994
10:104125563:C:G	S199R	0.994
10:104124102:T:C	L175P	0.991
10:104125691:T:C	F242S	0.991
10:104125669:T:G	Y235D	0.989
10:104125690:T:C	F242L	0.989
10:104125692:T:A	F242L	0.989
10:104125692:T:G	F242L	0.989
10:104124090:G:C	R171P	0.987
10:104125631:T:C	L222S	0.986
10:104124124:G:C	K182N	0.984
10:104124124:G:T	K182N	0.984
10:104125550:G:C	W195S	0.984
10:104123742:T:C	L55S	0.982
10:104124087:T:C	L170P	0.982
10:104124113:T:G	Y179D	0.981
10:104124118:A:C	R180S	0.981
10:104124118:A:T	R180S	0.981
10:104125529:T:C	L188S	0.981
10:104125574:T:A	L203H	0.981
10:104125664:T:A	L233Q	0.981
10:104125574:T:C	L203P	0.980
10:104125574:T:G	L203R	0.980
10:104125670:A:C	Y235S	0.980

dbSNP variants (sampled 300 via entrez): RS1000023122 (10:104123326 T>A), RS1000545141 (10:104119060 C>T), RS1000593197 (10:104121875 C>A,T), RS1001548800 (10:104120849 T>G), RS1001936710 (10:104122303 C>G,T), RS1002526970 (10:104121983 G>A), RS1002557887 (10:104121771 G>A), RS1002655277 (10:104119714 T>C), RS1002955706 (10:104124714 G>A), RS1003532453 (10:104122883 A>G), RS1003553853 (10:104123266 C>T), RS1003563199 (10:104122597 G>A,C), RS1003925160 (10:104120579 A>C,G), RS1004012639 (10:104123580 T>G), RS1004277297 (10:104120157 A>G)

Disease associations

OMIM: gene MIM:616527 | 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
GCST001949_12	Preeclampsia	3.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	4
Cyclosporine	affects expression, increases expression	3
bisphenol S	decreases methylation, increases expression	2
methylmercuric chloride	decreases expression	1
butyraldehyde	increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
2-palmitoylglycerol	increases expression	1
ICG 001	decreases expression	1
abrine	increases expression	1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinone	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Vorinostat	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	increases expression	1
Cisplatin	increases expression	1
Coumestrol	affects cotreatment, increases expression	1
Estradiol	decreases expression	1
Hydrogen Peroxide	decreases expression	1
Rotenone	increases expression	1
Thimerosal	increases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Antirheumatic Agents	decreases expression	1
Cadmium Chloride	increases expression	1
Copper Sulfate	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Cellosaurus cell lines

5 cell lines: 5 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_TK82	HAP1 SFR1 (-) 1	Cancer cell line	Male
CVCL_XS64	HAP1 SFR1 (-) 2	Cancer cell line	Male
CVCL_XS65	HAP1 SFR1 (-) 3	Cancer cell line	Male
CVCL_XS66	HAP1 SFR1 (-) 4	Cancer cell line	Male
CVCL_XS67	HAP1 SFR1 (-) 5	Cancer cell line	Male

Clinical trials (associated diseases)

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