APTX p.Lys233Asn
c.699G>T · VCV3308921
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.24 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.5 | GERP 1.7, phastCons 1 |
| Regional constraint | o/e 1.01 | unconstrained · MANE · 16 kb · p 0.77 · regional, not allelic |
| Overall | ||
| CADD | 21.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- APTX
- Protein
- p.Lys233Asn
- Coding
- c.699G>T
- MANE Select
- NM_001195248
- Type
- single nucleotide variant
- Location
- chr9:32984702 (GRCh38)
- Gene constraint
- LOEUF 0.973 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.52 · 11 PDB
- Residue 233
- the hit domain; an α-helix
Similar variants
- APTX p.Lys233Ter Pathogenic same residue
- APTX p.Arg29His Uncertain significance ★★ same condition
- APTX p.Arg3Gln Uncertain significance ★★ same condition
- APTX p.Asn120Ser Uncertain significance ★★ same condition
- APTX p.Glu103Lys Uncertain significance ★★ same condition
- APTX p.Glu131Lys Uncertain significance ★★ same condition
- APTX p.His320Leu Uncertain significance ★★ same condition
- APTX p.Ile124Leu Uncertain significance ★★ same condition
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-lys233asn (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown