ATP11A p.Pro496=
c.1488G>A · VCV3389356
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.019 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -9.7 | GERP -3.8 |
| Overall | ||
| CADD | 0.079 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Middle Eastern · 1/6,004 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00108%
Overall
0.00219%
32/1,461,638 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0167% | 6,004 |
| East Asian | 0.00669% | 14,954 |
| Admixed American | 0.00333% | 30,006 |
| African / African-American | 0.00267% | 37,518 |
| European (non-Finnish) | 0.00195% | 51,301 |
| South Asian | 0.0011% | 91,066 |
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.Pro496=
- Coding
- c.1488G>A
- MANE Select
- NM_015205
- Type
- single nucleotide variant
- Location
- chr13:112832952 (GRCh38)
- Gene constraint
- LOEUF 0.596 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.48
Similar variants
- ATP11A p.Pro496Leu Uncertain significance ★ ⚠ 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-pro496 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown