ATPAF2 p.Arg143=
c.429G>A · rs765703646 · VCV2787955
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.26 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.6 | GERP -0.91, phastCons 1 |
| Overall | ||
| CADD | 15.51 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,878 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000276%
Overall
0.000137%
2/1,460,714 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
- ATPAF2
- Protein
- p.Arg143=
- Coding
- c.429G>A
- MANE Select
- NM_145691
- dbSNP
- rs765703646
- Type
- single nucleotide variant
- Location
- chr17:18024698 (GRCh38)
- Gene constraint
- LOEUF 1.1 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.07
Similar variants
- ATPAF2 c.-90C>A Uncertain significance ★★ same type
- ATPAF2 c.*132C>T Uncertain significance ★★ same type
- ATPAF2 p.Ala130Glu Uncertain significance ★★ ⚠ same type
- ATPAF2 p.Ala267Thr Uncertain significance ★★ ⚠ same type
- ATPAF2 p.Ala268Thr Uncertain significance ★★ ⚠ same type
- ATPAF2 p.Arg14Gly Uncertain significance ★★ ⚠ same type
- ATPAF2 p.Arg189Gln Uncertain significance ★★ ⚠ same type
- ATPAF2 p.Arg189Trp 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/atpaf2-p-arg143 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown