AXIN2 p.Trp663Ter
c.1988G>A · rs761870581 · VCV2583435
Pathogenic/Likely pathogenic
Multiple submitters
Classification
Pathogenic/Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
oligodontia-cancer predisposition syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 8 of 11 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.6 | GERP -0.3, phastCons 1 |
| Overall | ||
| CADD | 38.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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
- AXIN2
- Protein
- p.Trp663Ter
- Coding
- c.1988G>A
- MANE Select
- NM_004655
- dbSNP
- rs761870581
- Type
- single nucleotide variant
- Location
- chr17:65536473 (GRCh38)
- Gene constraint
- LOEUF 0.397 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 61.71 · 1 PDB
- Residue 663
- the 'disordered' region
Similar variants
- AXIN2 p.Trp663Arg Uncertain significance ★★ ⚠ same residue
- AXIN2 p.Trp663Cys Uncertain significance ★★ ⚠ same residue
- AXIN2 p.Trp663Leu Uncertain significance ★★ ⚠ same residue
- AXIN2 p.Trp663Ser Uncertain significance ★★ ⚠ same residue
- AXIN2 p.Trp663Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
- AXIN2 c.1060-1G>C Likely pathogenic ★★ same condition
- AXIN2 c.1200+1G>A Likely pathogenic ★★ same condition
- AXIN2 c.1201-1G>C Likely pathogenic ★★ 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/axin2-p-trp663ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown