ATP6AP1 p.Arg337=
c.1011G>A · rs143004832 · VCV746604
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0943%, 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 -0.16 | GERP -3.1 |
| Overall | ||
| CADD | 2.694 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0943%
African / African-American · 54/57,254 alleles
Filtering AF
0.0742%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.067%
Overall
0.00471%
57/1,210,216 alleles · ultra-rare
exomes 22/1,098,100 · genomes 35/112,116 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0943% | 1,060 |
| Remaining individualsnot grpmax-eligible | 0.0042% | 23,805 |
| South Asian | 0.00176% | 56,838 |
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.Arg337=
- Coding
- c.1011G>A
- MANE Select
- NM_001183
- dbSNP
- rs143004832
- Type
- single nucleotide variant
- Location
- chrX:154435313 (GRCh38)
- Structure
- AlphaFold pLDDT 79.60 · 9 PDB
- Residue 337
- a β-strand
Similar variants
- ATP6AP1 p.Arg337Trp 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-arg337 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown