SWI5

SWI5 homologous recombination repair protein

Basic information

Region (hg38): 9:128275379-128316123

Previous symbols: [ "C9orf119" ]

Links

ENSG00000175854 ∙ NCBI:375757 ∙ OMIM:616528 ∙ HGNC:31412 ∙ Uniprot:Q1ZZU3 ∙ 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 SWI5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SWI5 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			21	3		24
Total	0	0	25	3	0

Variants in SWI5

This is a list of pathogenic ClinVar variants found in the SWI5 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-128275954-G-A		not specified	Uncertain significance (Jan 23, 2024)
9-128276155-C-A		not specified	Uncertain significance (Sep 26, 2023)
9-128276155-C-T		not specified	Uncertain significance (Dec 14, 2022)
9-128276158-G-A		not specified	Uncertain significance (Jul 05, 2022)
9-128276158-G-C		not specified	Uncertain significance (Mar 28, 2024)
9-128276159-G-A		not specified	Uncertain significance (Mar 15, 2024)
9-128276221-C-G		not specified	Uncertain significance (Nov 24, 2024)
9-128276225-A-G		not specified	Uncertain significance (Apr 09, 2024)
9-128276227-A-G		not specified	Uncertain significance (Oct 03, 2022)
9-128276264-T-C		not specified	Uncertain significance (Mar 31, 2022)
9-128276276-A-C		not specified	Likely benign (Apr 07, 2023)
9-128276295-A-C		not specified	Likely benign (Apr 22, 2024)
9-128276323-C-A		not specified	Uncertain significance (Jan 25, 2023)
9-128276326-T-C		not specified	Uncertain significance (Apr 24, 2024)
9-128276347-C-T		not specified	Uncertain significance (Oct 24, 2024)
9-128276384-G-C		not specified	Uncertain significance (Dec 10, 2024)
9-128276592-T-C		not specified	Uncertain significance (May 28, 2024)
9-128284597-A-G		not specified	Uncertain significance (Jun 13, 2024)
9-128284601-T-G		not specified	Uncertain significance (Dec 17, 2021)
9-128284620-G-C		not specified	Uncertain significance (May 22, 2023)
9-128285952-G-A		not specified	Uncertain significance (Feb 06, 2024)
9-128309560-G-A		not specified	Uncertain significance (Jan 12, 2024)
9-128309590-G-A		not specified	Uncertain significance (Aug 20, 2024)
9-128309600-A-T		not specified	Uncertain significance (Aug 23, 2021)
9-128309617-G-A		not specified	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SWI5	protein_coding	protein_coding	ENST00000320188	5	13612

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00139	0.878	124787	0	9	124796	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.966	168	136	1.23	0.00000630	1495
Missense in Polyphen		46	42.44	1.0839		522
Synonymous	-2.30	80	57.7	1.39	0.00000276	503
Loss of Function	1.34	6	10.8	0.558	5.53e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000716	0.0000706
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the SWI5-SFR1 complex, a complex required for double-strand break repair via homologous recombination. {ECO:0000269|PubMed:21252223}.

Intolerance Scores

• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.53

Haploinsufficiency Scores

• pHI: 0.162
• hipred: N
• hipred_score: 0.145
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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: Swi5

Gene ontology

• Biological process: double-strand break repair via homologous recombination;DNA recombinase assembly;cellular response to ionizing radiation
• Cellular component: nucleus;Swi5-Sfr1 complex
• Molecular function: protein binding