VIPAS39

Chr 14AR

VPS33B interacting protein, apical-basolateral polarity regulator, spe-39 homolog

NCBI Gene: 63894ENSG00000151445UniProt: Q9H9C1OMIM: 613401

The VIPAS39 protein functions in endosome to lysosome transport and vesicle tethering, playing a critical role in intracellular trafficking and maintaining cellular polarity in epithelial cells. Mutations cause arthrogryposis, renal dysfunction, and cholestasis 2, a multisystem disorder affecting joints, kidneys, and liver function. This condition follows autosomal recessive inheritance.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.801 OMIM phenotype
Clinical Summary— VIPAS39
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Gene-Disease Validity (ClinGen)
arthrogryposis, renal dysfunction, and cholestasis 2 · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.80LOEUF
pLI 0.000
Z-score 2.54
OE 0.55 (0.39–0.80)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.86Z-score
OE missense 0.85 (0.77–0.95)
229 obs / 268.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.55 (0.39–0.80)
0≤0.351.4
Missense OE0.85 (0.77–0.95)
0≤0.61.4
Synonymous OE0.89
0≤1.21.6
LoF obs/exp: 21 / 37.9Missense obs/exp: 229 / 268.6Syn Z: 0.86

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

VIPAS39 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Mild Phenotype of Arthrogryposis, Renal Dysfunction, and Cholestasis Syndrome 1 Caused by a Novel VPS33B Variant
Linhares ND et al.·Front Genet
2022
Platelet VPS16B is dependent on VPS33B expression, as determined in two siblings with arthrogryposis, renal dysfunction, and cholestasis syndrome.
Penon-Portmann M et al.·J Thromb Haemost
2022
Histomorphological Features of a Liver Explant From an Adult With Arthrogryposis-Renal Dysfunction-Cholestasis Syndrome: A Case Report and Literature Review.
Moustafa M et al.·Int J Surg Pathol
2026Review
Arthrogryposis, renal dysfunction, cholestasis syndrome in a neonate: an uncommon association of common problems.
Saad A et al.·BMJ Case Rep
2023
Novel gene mutations in three Japanese patients with ARC syndrome associated mild phenotypes: a case series
Satomura Y et al.·J Med Case Rep
2022Cohort
Top 5 full-text resultsSearch PubTator3 ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
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External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients