VASN

protein-coding

vasorin

Gene summary

Enables transforming growth factor beta binding activity. Involved in negative regulation of epithelial to mesenchymal transition and negative regulation of transforming growth factor beta receptor signaling pathway. Located in cell surface; extracellular exosome; and obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

SLITL2

MANE transcript

NM_138440.3

Inheritance

—

ClinVar variants

U:154B:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr16:4,371,848-4,383,538

External References & Databases

Ensembl (ENSG00000168140)

Transcript & Mutation Effects

hg38 • Region Span ~11.7 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 VASN variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 164

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138440.3. 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			153 clinvar	14 clinvar		167
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	154	14	1	169

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138440.3	RefSeq	NP_612449.2	1	MANE Select
ENST00000304735.4	Ensembl	ENSP00000306864.3	1	MANE Select
ENST00000899068.1	Ensembl	ENSP00000569127.1	1	Standard
ENST00000899068.2	Ensembl	ENSP00000569127.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of epithelial to mesenchymal transition
negative regulation of transforming growth factor beta receptor signaling pathway
cellular response to hypoxia
cellular response to redox state

Molecular Function

protein binding
cadherin binding
transforming growth factor beta binding

Cellular Component

extracellular space
mitochondrion
lysosomal membrane
plasma membrane
cell surface

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000304735
Coding exons: 1
Length: 11681
Individuals with no LoFs: 124611
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 124625
p: 0.0000562

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.295	411	428	0.960	0.0000310	4089
Missense (PolyPhen)		102	121.31	0.8408		1394
Synonymous	-1.44	237	211	1.13	0.0000153	1599
Loss of Function	2.72	2	12.3	0.163	6.95e-7	116

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000032	0.000029	rare
Ashkenazi Jewish	0.00010	0.00010	rare
East Asian	0.000056	0.000055	rare
Finnish	0.00012	0.000093	rare
European (Non-Finnish)	0.000069	0.000062	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as an inhibitor of TGF-beta signaling. {ECO:0000269|PubMed:15247411}.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.104
RVIS EVS: 0.05
RVIS percentile EVS: 57.48

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.866

Gene Damage Prediction

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