VSIG10

protein-coding

V-set and immunoglobulin domain containing 10, the group of V-set domain containing|I-set domain containing

Gene summary

Predicted to enable cell adhesion molecule binding activity. Predicted to be involved in cell-cell adhesion and synapse assembly. Predicted to be located in membrane. Predicted to be active in cell-cell junction and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_019086.6

Inheritance

—

ClinVar variants

U:80B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr12:118,063,593-118,136,026

External References & Databases

Ensembl (ENSG00000176834)

Transcript & Mutation Effects

hg38 • Region Span ~72.4 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 VSIG10 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 78

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_019086.6. 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						0
missense			77 clinvar	5 clinvar		82
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	80	5	0	85

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_019086.6	RefSeq	NP_061959.2	9	MANE Select
ENST00000359236.10	Ensembl	ENSP00000352172.5	9	MANE Select
ENST00000538357.1	Ensembl	ENSP00000442861.1	3	Standard
ENST00000965105.1	Ensembl	ENSP00000635164.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000359236
Coding exons: 9
Length: 72434
Individuals with no LoFs: 124575
Homozygous LoFs: 1
Heterozygous LoFs: 79
Defined: 124655
p: 0.000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.583	266	294	0.904	0.0000155	3497
Missense (PolyPhen)		54	71.513	0.75511		858
Synonymous	-0.372	128	123	1.04	0.00000720	1074
Loss of Function	2.27	13	25.3	0.514	0.00000124	279

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00033	0.00032	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0.0016	0.0016	notable
Other	0.00050	0.00050	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.42
RVIS percentile EVS: 77.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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