VSTM1

protein-coding

V-set and transmembrane domain containing 1, the group of Immunoglobulin like domain containing

Gene summary

Predicted to enable transmembrane signaling receptor activity. Predicted to be involved in signal transduction. Predicted to be located in membrane and obsolete extracellular space. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_198481.4

Inheritance

—

ClinVar variants

U:36B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr19:54,040,825-54,063,953

External References & Databases

Ensembl (ENSG00000189068)

Transcript & Mutation Effects

hg38 • Region Span ~23.1 kb

Loading mutation effect viewer...

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 VSTM1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 37

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198481.4. 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			36 clinvar	2 clinvar		38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	36	2	0	38

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198481.4	RefSeq	NP_940883.2	9	MANE Select
ENST00000338372.7	Ensembl	ENSP00000343366.2	9	MANE Select
NM_001288791.2	RefSeq	NP_001275720.1	8	Standard
NM_001288792.2	RefSeq	NP_001275721.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

immune system process
regulation of signaling receptor activity

Molecular Function

cytokine activity

Cellular Component

extracellular space
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000338372
Coding exons: 9
Length: 23129
Individuals with no LoFs: 125683
Homozygous LoFs: 0
Heterozygous LoFs: 63
Defined: 125746
p: 0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.148	136	131	1.04	0.00000720	1531
Missense (PolyPhen)		36	30.362	1.1857		405
Synonymous	0.253	52	54.4	0.956	0.00000349	441
Loss of Function	0.436	12	13.7	0.873	5.82e-7	170

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.0024	0.0024	notable
Finnish	0.00014	0.000092	rare
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0.000098	0.000098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Isoform 2: Behaves as a cytokine, promoting IL17A secretion by CD4+ T-cells, and differentiation and activation of IL17 producing helper T-cells (TH17).;

Intolerance Scores

LoFtool: 0.766
RVIS EVS: 0.08
RVIS percentile EVS: 60.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00230

Gene Damage Prediction

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