AXIN2 p.Val539=
c.1617G>A · rs2509412160 · VCV1776513
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 6.84e-05%)
Conditions
2
hereditary neoplastic syndrome
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 -2 | GERP -3.7 |
| Overall | ||
| CADD | 1.988 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.84e-05%
Overall
6.84e-05%
1/1,461,880 alleles · very rare
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
- AXIN2
- Protein
- p.Val539=
- Coding
- c.1617G>A
- MANE Select
- NM_004655
- dbSNP
- rs2509412160
- Type
- single nucleotide variant
- Location
- chr17:65537419 (GRCh38)
- Gene constraint
- LOEUF 0.397 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 61.71 · 1 PDB
Similar variants
- AXIN2 p.Val539Leu Uncertain significance ★★ ⚠ same residue
- AXIN2 p.Val539Met Benign/Likely benign ★★ same residue
- AXIN2 p.Val539fs Pathogenic ★ 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
- AXIN2 c.1713-1G>A Likely pathogenic ★★ same condition
- AXIN2 c.815+1G>A Pathogenic/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-val539 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown