APTX p.Val230=
c.690G>A · rs180809113 · VCV2419334
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.243%, 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 -6.9 | GERP -3.4 |
| Overall | ||
| CADD | 1.354 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.243%
East Asian · 109/44,874 alleles
Filtering AF
0.206%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.192%
Overall
0.00694%
112/1,614,208 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.243% | 412 |
| South Asian | 0.0011% | 91,086 |
| European (non-Finnish) | 0.000169% | 590,019 |
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.Val230=
- Coding
- c.690G>A
- MANE Select
- NM_001195248
- dbSNP
- rs180809113
- Type
- single nucleotide variant
- Location
- chr9:32984711 (GRCh38)
- Gene constraint
- LOEUF 0.973 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.52 · 11 PDB
- Residue 230
- the hit domain
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-val230 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown