AXIN1 p.Pro39=
c.117C>T · rs137878236 · VCV2645787
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.758%, sas)
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 -3.1 | GERP -5.2 |
| Overall | ||
| CADD | 0.83 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.758%
South Asian · 690/91,084 alleles
Filtering AF
0.711%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.692%
Overall
0.0618%
998/1,613,816 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.758% | 132 |
| Middle Eastern | 0.264% | 379 |
| Remaining individualsnot grpmax-eligible | 0.056% | 1,786 |
| European (non-Finnish) | 0.0208% | 4,815 |
| East Asian | 0.0111% | 8,976 |
| Admixed American | 0.00666% | 15,006 |
| African / African-American | 0.004% | 25,017 |
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
- AXIN1
- Protein
- p.Pro39=
- Coding
- c.117C>T
- MANE Select
- NM_003502
- dbSNP
- rs137878236
- Type
- single nucleotide variant
- Location
- chr16:346909 (GRCh38)
- Gene constraint
- LOEUF 0.563 · pLI 0.16 (gnomAD)
- Structure
- AlphaFold pLDDT 62.32 · 22 PDB
- Residue 39
- the 'disordered' region
Similar variants
- AXIN1 p.Pro39Ser Uncertain significance ★ ⚠ same residue
- AXIN1 p.Arg373His Uncertain significance ★★ ⚠ same type
- AXIN1 c.2186+4C>T Likely benign ★★ same type
- AXIN1 c.2186+7C>T Benign/Likely benign ★★ same type
- AXIN1 p.Ala526Val Benign ★★ same type
- AXIN1 p.Ala552= Benign ★★ same type
- AXIN1 p.Arg801= Benign/Likely benign ★★ same type
- AXIN1 p.Arg803= Benign ★★ 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/axin1-p-pro39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown