ATP6AP1 p.Ser352=
c.1056C>T · VCV4701321
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00526%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -13 | GERP -3.1 |
| Overall | ||
| CADD | 2.85 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00526%
South Asian · 3/57,022 alleles
Filtering AF
0.0014%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000687%
Overall
0.00124%
15/1,211,966 alleles · very rare
exomes 15/1,098,173 · genomes 0/113,793 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00526% | 19,007 |
| European (non-Finnish) | 0.00134% | 74,627 |
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.Ser352=
- Coding
- c.1056C>T
- MANE Select
- NM_001183
- Type
- single nucleotide variant
- Location
- chrX:154435358 (GRCh38)
- Structure
- AlphaFold pLDDT 79.60 · 9 PDB
Similar variants
- 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
- ATP6AP1 p.Asn170Ile 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-ser352 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown