APTX p.Arg126=
c.378G>A · rs149162464 · VCV1552870
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0188%, nfe)
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 -0.35 | GERP -1.4 |
| Overall | ||
| CADD | 2.368 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0188%
European (non-Finnish) · 222/1,180,044 alleles
Filtering AF
0.0167%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.016%
Overall
0.0142%
230/1,614,080 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0188% | 5,316 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,622 |
| Admixed American | 0.00333% | 30,003 |
| African / African-American | 0.00267% | 37,458 |
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
- APTX
- Protein
- p.Arg126=
- Coding
- c.378G>A
- MANE Select
- NM_001195248
- dbSNP
- rs149162464
- Type
- single nucleotide variant
- Location
- chr9:32987649 (GRCh38)
- Gene constraint
- LOEUF 0.973 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.52 · 11 PDB
- Residue 126
- the 'disordered' region
Similar variants
- APTX c.875-2A>G Pathogenic/Likely pathogenic ★★ same type
- APTX p.Ala198Val Likely pathogenic ★★ same type
- APTX p.Arg16Ter Pathogenic/Likely pathogenic ★★ same type
- APTX p.Arg247Ter Pathogenic/Likely pathogenic ★★ same type
- APTX p.Gln130Ter Pathogenic/Likely pathogenic ★★ same type
- APTX p.Gln187Ter Pathogenic ★★ same type
- APTX p.Trp279Arg Pathogenic/Likely pathogenic ★★ same type
- APTX p.Trp279Ter Pathogenic ★★ 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/aptx-p-arg126 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown