ATP5F1A p.Pro478=
c.1434C>T · VCV4699954
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0055%, 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 1.8 | GERP -4.5, phastCons 1 |
| Overall | ||
| CADD | 8.451 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0055%
African / African-American · 4/72,790 alleles
Filtering AF
0.00178%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00106%
Overall
0.000254%
4/1,575,242 alleles · very rare
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
- ATP5F1A
- Protein
- p.Pro478=
- Coding
- c.1434C>T
- MANE Select
- NM_004046
- Type
- single nucleotide variant
- Location
- chr18:46084650 (GRCh38)
- Gene constraint
- LOEUF 0.576 · pLI 0.29 (gnomAD)
- Structure
- AlphaFold pLDDT 88.47 · 9 PDB
- Residue 478
- an α-helix
Similar variants
- ATP5F1A c.1176+1G>C Likely pathogenic ★★ same type
- ATP5F1A p.Arg182Gln Pathogenic/Likely pathogenic ★★ ⚠ same type
- ATP5F1A p.Arg207His Pathogenic/Likely pathogenic ★★ same type
- ATP5F1A p.Gly418Arg Likely pathogenic ★★ same type
- ATP5F1A p.Ala49Val Uncertain significance ★★ ⚠ same type
- ATP5F1A p.Ala8Val Uncertain significance ★★ ⚠ same type
- ATP5F1A p.Arg169Cys Uncertain significance ★★ ⚠ same type
- ATP5F1A p.Arg171Gln 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/atp5f1a-p-pro478 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown