VSIR

V-set immunoregulatory receptor, the group of V-set domain containing|B7 family

Basic information

Region (hg38): 10:71747555-71773520

Previous symbols: [ "C10orf54" ]

Links

ENSG00000107738 ∙ NCBI:64115 ∙ OMIM:615608 ∙ HGNC:30085 ∙ Uniprot:Q9H7M9 ∙ 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 VSIR gene.

• Retinitis pigmentosa-deafness syndrome (2 variants)
• not specified (1 variants)
• Usher syndrome type 1D;Autosomal recessive nonsyndromic hearing loss 12;Pituitary adenoma 5, multiple types (1 variants)
• not provided (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VSIR 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			1	1	2	4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	1	2

Variants in VSIR

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

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

Position	Type	Phenotype	Significance	ClinVar
10-71751727-G-A		not specified • Usher syndrome type 1D;Autosomal recessive nonsyndromic hearing loss 12;Pituitary adenoma 5, multiple types	Benign/Likely benign (Oct 01, 2023)
10-71752985-G-A		See cases	Uncertain significance (May 07, 2019)
10-71755398-G-A		not specified	Uncertain significance (Jul 26, 2021)
10-71760875-A-C		Retinitis pigmentosa-deafness syndrome	Benign (May 28, 2019)
10-71761615-T-G		not specified	Uncertain significance (Aug 30, 2021)
10-71761773-G-T		not specified	Uncertain significance (Jul 20, 2021)
10-71761877-C-T		not specified	Uncertain significance (Sep 17, 2021)
10-71762023-G-A		not specified	Likely benign (Jul 26, 2021)
10-71773420-A-G		Retinitis pigmentosa-deafness syndrome	Benign (May 28, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VSIR	protein_coding	protein_coding	ENST00000394957	7	25940

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.761	0.239	125587	0	7	125594	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.717	160	188	0.853	0.0000116	1972
Missense in Polyphen		53	63.656	0.8326		663
Synonymous	-0.868	96	85.8	1.12	0.00000570	658
Loss of Function	2.90	2	13.5	0.148	6.63e-7	151

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000513	0.0000462
European (Non-Finnish)	0.0000482	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000201	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Immunoregulatory receptor which inhibits the T-cell response (PubMed:24691993). May promote differentiation of embryonic stem cells, by inhibiting BMP4 signaling (By similarity). May stimulate MMP14-mediated MMP2 activation (PubMed:20666777). {ECO:0000250|UniProtKB:Q9D659, ECO:0000269|PubMed:20666777, ECO:0000269|PubMed:24691993}.

Recessive Scores

• pRec: 0.0989

Intolerance Scores

• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.36

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.351
• ghis: 0.542

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Vsir
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; liver/biliary system phenotype; respiratory system phenotype; immune system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: positive regulation of gene expression;positive regulation of endopeptidase activity;positive regulation of cell migration;zymogen activation;negative regulation of interferon-gamma production;negative regulation of interleukin-10 production;negative regulation of interleukin-17 production;negative regulation of tumor necrosis factor production;positive regulation of regulatory T cell differentiation;positive regulation of collagen catabolic process;negative regulation of CD4-positive, alpha-beta T cell proliferation;negative regulation of CD8-positive, alpha-beta T cell proliferation
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: enzyme binding;identical protein binding;endopeptidase activator activity