VASH2

protein-coding

vasohibin 2

Gene summary

Enables actin binding activity; metallocarboxypeptidase activity; and microtubule binding activity. Involved in axon development and proteolysis. Acts upstream of or within cell-cell fusion; positive regulation of angiogenesis; and positive regulation of endothelial cell proliferation. Located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001301056.2

Inheritance

—

ClinVar variants

U:43B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr1:212,950,520-212,992,037

External References & Databases

Ensembl (ENSG00000143494)

Transcript & Mutation Effects

hg38 • Region Span ~41.5 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 VASH2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 42

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001301056.2. 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 clinvar		2
missense			42 clinvar	1 clinvar		43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	2	0	45

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 54 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001301056.2	RefSeq	NP_001287985.1	7	MANE Select
ENST00000517399.3	Ensembl	ENSP00000428324.1	7	MANE Select
NM_001136474.3	RefSeq	NP_001129946.1	7	Standard
NM_001136475.3	RefSeq	NP_001129947.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

syncytium formation by plasma membrane fusion
positive regulation of endothelial cell proliferation
proteolysis
positive regulation of angiogenesis
labyrinthine layer blood vessel development

Molecular Function

actin binding
metallocarboxypeptidase activity
protein binding

Cellular Component

extracellular region
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000366965
Coding exons: 5
Length: 41518
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125748
p: 0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.747	156	185	0.845	0.00000990	2020
Missense (PolyPhen)		55	68.426	0.80379		754
Synonymous	0.562	68	74.2	0.917	0.00000402	604
Loss of Function	2.37	3	11.8	0.255	5.82e-7	150

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000063	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Tyrosine carboxypeptidase that removes the C-terminal tyrosine residue of alpha-tubulin, thereby regulating microtubule dynamics and function (PubMed:29146869). Acts as an activator of angiogenesis: expressed in infiltrating mononuclear cells in the sprouting front to promote angiogenesis (PubMed:19204325). {ECO:0000269|PubMed:19204325, ECO:0000269|PubMed:29146869}.;

Recessive Scores

pRec: 0.114

Intolerance Scores

LoFtool: 0.0719
RVIS EVS: 0.17
RVIS percentile EVS: 65.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.261

Gene Damage Prediction

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