VPS35 p.Ala101=
c.303T>C · VCV4929680
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP -3.5 |
| Overall | ||
| CADD | 7.215 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- VPS35
- Protein
- p.Ala101=
- Coding
- c.303T>C
- MANE Select
- NM_018206
- Type
- single nucleotide variant
- Location
- chr16:46681397 (GRCh38)
- Gene constraint
- LOEUF 0.32 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 91.40 · 14 PDB
Similar variants
- VPS35 p.Asp620Asn Pathogenic ★★ same type
- VPS35 c.-19C>T Uncertain significance ★★ same type
- VPS35 c.*283C>A Uncertain significance ★★ same type
- VPS35 p.Arg138His Uncertain significance ★★ ⚠ same type
- VPS35 p.Arg284Gln Uncertain significance ★★ ⚠ same type
- VPS35 p.Arg493Cys Uncertain significance ★★ ⚠ same type
- VPS35 p.Asn37Ser Uncertain significance ★★ ⚠ same type
- VPS35 p.Asn381Ser Uncertain significance ★★ ⚠ same type
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/vps35-p-ala101 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown