VSTM4

protein-coding

V-set and transmembrane domain containing 4, the group of V-set domain containing

Gene summary

Predicted to act upstream of or within several processes, including endothelial cell proliferation; retina blood vessel maintenance; and vasculature development. Predicted to be located in extracellular region and plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C10orf72

MANE transcript

NM_001031746.5

Inheritance

—

ClinVar variants

U:54B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr10:49,014,236-49,115,522

External References & Databases

Ensembl (ENSG00000165633)

Transcript & Mutation Effects

hg38 • Region Span ~101.3 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 VSTM4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 53

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001031746.5. 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			2 clinvar	1 clinvar		3
missense			50 clinvar	2 clinvar		52
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	54	3	0	57

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001031746.5	RefSeq	NP_001026916.2	8	MANE Select
ENST00000332853.9	Ensembl	ENSP00000331062.3	8	MANE Select
NM_144984.4	RefSeq	NP_659421.1	3	Standard
ENST00000298454.3	Ensembl	ENSP00000298454.3	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

extracellular region
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000332853
Coding exons: 8
Length: 101265
Individuals with no LoFs: 125725
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 125748
p: 0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.295	174	185	0.939	0.0000118	2043
Missense (PolyPhen)		54	67.727	0.79732		771
Synonymous	0.469	77	82.4	0.934	0.00000564	655
Loss of Function	2.34	5	14.7	0.341	6.20e-7	190

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000082	0.000079	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Peptide Lv enhances L-type voltage-gated calcium channel (L-VGCC) currents in retinal photoreceptors. {ECO:0000250|UniProtKB:T1NXB5}.;

Intolerance Scores

RVIS EVS: -0.16
RVIS percentile EVS: 42.16

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	Medium	Medium	Medium
Cancer	Medium	Medium	Medium