VSIR

protein-coding

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

Gene summary

Enables endopeptidase activator activity; enzyme binding activity; and identical protein binding activity. Involved in several processes, including negative regulation of cytokine production; positive regulation of collagen catabolic process; and regulation of T cell activation. Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C10orf54

MANE transcript

NM_022153.2

Inheritance

—

ClinVar variants

U:16B:3

Top phenotype

Autosomal recessive nonsyndromic hearing loss 12

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr10:71,747,556-71,773,520

External References & Databases

Ensembl (ENSG00000107738)

Transcript & Mutation Effects

hg38 • Region Span ~26.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to VSIR variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 7

not providedTotal: 3

Autosomal recessive nonsyndromic hearing loss 12Total: 1

See casesTotal: 1

Usher syndrome type 1DTotal: 1

Pituitary adenoma 5, multiple typesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022153.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			10 clinvar	2 clinvar	1 clinvar	13
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	16	2	1	19

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022153.2	RefSeq	NP_071436.1	7	MANE Select
ENST00000394957.8	Ensembl	ENSP00000378409.3	7	MANE Select
ENST00000866267.1	Ensembl	ENSP00000536326.1	6	Standard
ENST00000866267.2	Ensembl	ENSP00000536326.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

enzyme binding
identical protein binding
endopeptidase activator activity

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000394957
Coding exons: 7
Length: 25940
Individuals with no LoFs: 125587
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125594
p: 0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.717	160	188	0.853	0.0000116	1972
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000051	0.000046	rare
European (Non-Finnish)	0.000048	0.000044	rare
South Asian	0	0.0	absent
Other	0.00020	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (gene trap): N