VPS13A

Chr 9

vacuolar protein sorting 13 homolog A

Also known as: BLTP5A, CHAC, CHOREIN

NCBI Gene: 23230ENSG00000197969UniProt: Q96RL7

The protein controls steps in the cycling of proteins through the trans-Golgi network to endosomes, lysosomes and the plasma membrane, and localizes to the mitochondrial outer membrane. Mutations cause chorea-acanthocytosis, an autosomal recessive movement disorder characterized by progressive chorea and acanthocytes on blood smear.

GeneReviewsResearchSummary from RefSeq, OMIM, UniProt
LOEUF 0.48
Clinical Summary— VPS13A
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
118 unique Pathogenic / Likely Pathogenic· 299 VUS of 600 total submissions
Explore recent and relevant literature in Research Assistant →
📖
GeneReview available — VPS13A
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.48LOEUF
pLI 0.000
Z-score 7.34
OE 0.40 (0.32–0.48)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
1.76Z-score
OE missense 0.88 (0.84–0.92)
1408 obs / 1606.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.40 (0.32–0.48)
0≤0.351.4
Missense OE0.88 (0.84–0.92)
0≤0.61.4
Synonymous OE0.99
0≤1.21.6
LoF obs/exp: 68 / 171.9Missense obs/exp: 1408 / 1606.3Syn Z: 0.13

ClinVar Variant Classifications

600 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic32
Likely Pathogenic86
VUS299
Likely Benign125
Benign6
Conflicting2
32
Pathogenic
86
Likely Pathogenic
299
VUS
125
Likely Benign
6
Benign
2
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
18
0
14
0
32
Likely Pathogenic
81
0
5
0
86
VUS
2
262
20
15
299
Likely Benign
0
10
79
36
125
Benign
0
0
6
0
6
Conflicting
—2
Total10127212451550

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

VPS13A · 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.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

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