VPS13A p.Pro847=
c.2541A>G · rs930824912 · VCV703998
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0133%, amr)
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 -5.5 | GERP -4.4 |
| Overall | ||
| CADD | 1.359 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0133%
Admixed American · 8/59,990 alleles
Filtering AF
0.00662%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00483%
Overall
0.0018%
29/1,613,696 alleles · ultra-rare
exomes 25/1,461,548 · genomes 4/152,148 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0133% | 7,499 |
| East Asian | 0.00223% | 44,816 |
| European (non-Finnish) | 0.0017% | 58,991 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- VPS13A
- Protein
- p.Pro847=
- Coding
- c.2541A>G
- MANE Select
- NM_033305
- dbSNP
- rs930824912
- Type
- single nucleotide variant
- Location
- chr9:77275526 (GRCh38)
- Gene constraint
- LOEUF 0.696 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 847
- a UniProt-annotated variant site (in chac)
Similar variants
- VPS13A c.144+1G>C Pathogenic ★★ same type
- VPS13A c.1596-1G>C Pathogenic/Likely pathogenic ★★ same type
- VPS13A c.1596-2A>G Pathogenic ★★ same type
- VPS13A c.188-2A>G Likely pathogenic ★★ same type
- VPS13A c.2037+1G>A Likely pathogenic ★★ same type
- VPS13A c.2427+1G>A Likely pathogenic ★★ same type
- VPS13A c.2512+2T>C Likely pathogenic ★★ same type
- VPS13A c.2513-2A>T Likely pathogenic ★★ 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/vps13a-p-pro847 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown