VPS13A p.Ser519fs
c.1555del · VCV4062905
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
VPS13A-related neurodegenerative disease
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 17 of 72 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.29 | GERP -1.7, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- VPS13A
- Protein
- p.Ser519fs
- Coding
- c.1555del
- MANE Select
- NM_033305
- Type
- Deletion
- Location
- chr9:77228224 (GRCh38)
- Gene constraint
- LOEUF 0.696 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 519
- a UniProt-annotated variant site (in chac)
Disease context
VPS13A-related neurodegenerative disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Choreoacanthocytosis (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adult
Similar variants
- VPS13A c.7157_7172del Pathogenic/Likely pathogenic ★★ same condition
- VPS13A c.883-1_892del Likely pathogenic ★★ same condition
- VPS13A p.Ala332fs Pathogenic/Likely pathogenic ★★ same condition
- VPS13A p.Asn73fs Pathogenic/Likely pathogenic ★★ same condition
- VPS13A p.Gly3023fs Pathogenic/Likely pathogenic ★★ same condition
- VPS13A p.Ile1152fs Pathogenic/Likely pathogenic ★★ same condition
- VPS13A p.Leu466_Tyr467insTer Pathogenic ★★ same condition
- VPS13A p.Lys1113fs Pathogenic/Likely pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/vps13a-p-ser519fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown