ATP6AP1 p.Val28=
c.84G>A · rs2068677911 · VCV1572286
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00197%, afr)
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 2.6 | GERP 0.055, phastCons 1 |
| Overall | ||
| CADD | 8.163 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00197%
African / African-American · 1/50,743 alleles
Overall
0.000177%
2/1,131,327 alleles · very rare
exomes 0/1,019,807 · genomes 2/111,520 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00197% | 50,743 |
| European (non-Finnish) | 0.000116% | 863,081 |
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
- ATP6AP1
- Protein
- p.Val28=
- Coding
- c.84G>A
- MANE Select
- NM_001183
- dbSNP
- rs2068677911
- Type
- single nucleotide variant
- Location
- chrX:154428776 (GRCh38)
- Structure
- AlphaFold pLDDT 79.60 · 9 PDB
Similar variants
- ATP6AP1 p.Val28Met Uncertain significance ★ ⚠ same residue
- ATP6AP1 p.Glu346Lys Pathogenic/Likely pathogenic ★★ same type
- ATP6AP1 c.557+6G>A Uncertain significance ★★ same type
- ATP6AP1 p.Arg225His Uncertain significance ★★ ⚠ same type
- ATP6AP1 p.Arg231Cys Uncertain significance ★★ ⚠ same type
- ATP6AP1 p.Arg330Cys Uncertain significance ★★ ⚠ same type
- ATP6AP1 p.Arg344His Uncertain significance ★★ ⚠ same type
- ATP6AP1 p.Arg9Ter 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/atp6ap1-p-val28 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown