SFR1

SWI5 dependent homologous recombination repair protein 1

Basic information

Region (hg38): 10:104122058-104126385

Previous symbols: [ "C10orf78", "MEIR5" ]

Links

ENSG00000156384 ∙ NCBI:119392 ∙ OMIM:616527 ∙ HGNC:29574 ∙ Uniprot:Q86XK3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SFR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SFR1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			23	2		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	0

Variants in SFR1

This is a list of pathogenic ClinVar variants found in the SFR1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-104122188-C-G		not specified	Uncertain significance (Dec 22, 2023)
10-104122190-G-C		not specified	Uncertain significance (Jan 19, 2025)
10-104122194-G-A		not specified	Uncertain significance (Nov 21, 2022)
10-104122999-T-A		not specified	Uncertain significance (Mar 15, 2024)
10-104123034-C-T		not specified	Uncertain significance (May 27, 2022)
10-104123060-C-T		not specified	Uncertain significance (Sep 26, 2023)
10-104123717-A-G		not specified	Uncertain significance (Aug 26, 2024)
10-104123789-C-T		not specified	Uncertain significance (Aug 10, 2021)
10-104123790-G-A		not specified	Uncertain significance (Sep 06, 2022)
10-104123823-C-T		not specified	Uncertain significance (Aug 29, 2022)
10-104123852-G-A		not specified	Uncertain significance (Feb 26, 2024)
10-104123858-A-G		not specified	Uncertain significance (Oct 26, 2021)
10-104123865-T-G		not specified	Uncertain significance (Sep 30, 2021)
10-104123879-A-C		not specified	Uncertain significance (Dec 10, 2024)
10-104123952-G-A		not specified	Uncertain significance (Jan 23, 2023)
10-104124112-G-A		not specified	Uncertain significance (Nov 28, 2023)
10-104124119-T-C		not specified	Uncertain significance (Dec 15, 2023)
10-104125525-C-G		not specified	Uncertain significance (Jun 29, 2023)
10-104125542-A-G		not specified	Uncertain significance (Nov 11, 2024)
10-104125556-G-A		not specified	Uncertain significance (Jan 06, 2023)
10-104125576-T-C		not specified	Uncertain significance (Nov 14, 2024)
10-104125589-C-T		not specified	Uncertain significance (Dec 20, 2022)
10-104125592-C-T		not specified	Uncertain significance (Mar 27, 2023)
10-104125594-G-A		not specified	Likely benign (Nov 01, 2022)
10-104125607-A-G		not specified	Uncertain significance (Apr 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SFR1	protein_coding	protein_coding	ENST00000369727	4	4328

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.71e-10	0.0313	125706	0	23	125729	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.425	131	118	1.11	0.00000557	1619
Missense in Polyphen		29	29.936	0.96873		467
Synonymous	0.0529	44	44.4	0.990	0.00000219	426
Loss of Function	-0.647	13	10.7	1.21	5.29e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000324	0.000324
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000620	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000663	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the SWI5-SFR1 complex, a complex required for double-strand break repair via homologous recombination (PubMed:21252223). Acts as a transcriptional modulator for ESR1 (PubMed:23874500). {ECO:0000269|PubMed:21252223, ECO:0000269|PubMed:23874500}.

Recessive Scores

• pRec: 0.0937

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.0903
• hipred: N
• hipred_score: 0.123
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sfr1

Gene ontology

• Biological process: double-strand break repair via homologous recombination;positive regulation of transcription, DNA-templated;cellular response to estrogen stimulus
• Cellular component: nucleus;Swi5-Sfr1 complex
• Molecular function: protein binding;nuclear receptor transcription coactivator activity