ATP11A p.Val503=
c.1509G>A · VCV4821589
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00769%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.017 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.5 | GERP -3.5 |
| Overall | ||
| CADD | 2.315 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00769%
South Asian · 7/91,068 alleles
Filtering AF
0.00359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00255%
Overall
0.000889%
13/1,461,562 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00769% | 13,010 |
| European (non-Finnish) | 0.000509% | 196,651 |
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
- ATP11A
- Protein
- p.Val503=
- Coding
- c.1509G>A
- MANE Select
- NM_015205
- Type
- single nucleotide variant
- Location
- chr13:112832973 (GRCh38)
- Gene constraint
- LOEUF 0.596 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.48
Similar variants
- ATP11A p.Val503Gly Benign/Likely benign ★★ ⚠ same residue
- ATP11A c.*113C>T Uncertain significance ★★ same type
- ATP11A p.Ala695Val Uncertain significance ★★ ⚠ same type
- ATP11A p.Gly136Asp Uncertain significance ★★ ⚠ same type
- ATP11A c.2418+3G>A Likely benign ★★ same type
- ATP11A c.334-6T>A Benign/Likely benign ★★ same type
- ATP11A c.*10-20C>G Benign ★★ same type
- ATP11A p.Ala276= Benign/Likely benign ★★ 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/atp11a-p-val503 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown