ATP6AP1 p.Pro86=
c.258C>T · VCV4953690
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.37 | GERP -2.8, phastCons 0.99 |
| Overall | ||
| CADD | 13.66 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ATP6AP1
- Protein
- p.Pro86=
- Coding
- c.258C>T
- MANE Select
- NM_001183
- Type
- single nucleotide variant
- Location
- chrX:154429144 (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-pro86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown