VPS13A p.Val1908=
c.5724A>T · VCV3644744
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.024 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -0.77 | GERP -5.5 |
| Overall | ||
| CADD | 0.649 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,904 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000124%
2/1,613,302 alleles · very rare
exomes 0/1,461,230 · genomes 2/152,072 · joint denominator
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.Val1908=
- Coding
- c.5724A>T
- MANE Select
- NM_033305
- Type
- single nucleotide variant
- Location
- chr9:77321640 (GRCh38)
- Gene constraint
- LOEUF 0.696 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 1908
- a UniProt-annotated variant site (in chac)
Similar variants
- VPS13A p.Val1908Ile Uncertain significance ★ ⚠ same residue
- 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
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-val1908 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown