ATPAF2 p.Arg168=
c.504A>G · rs1008083351 · VCV1943327
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0201%, eas)
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 -1.6 | GERP -3.5 |
| Overall | ||
| CADD | 2.008 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0201%
East Asian · 9/44,884 alleles
Filtering AF
0.0104%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00779%
Overall
0.00062%
10/1,613,684 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0201% | 4,987 |
| South Asian | 0.0011% | 91,070 |
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.Arg168=
- Coding
- c.504A>G
- MANE Select
- NM_145691
- dbSNP
- rs1008083351
- Type
- single nucleotide variant
- Location
- chr17:18021857 (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-arg168 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown