AXIN1 p.Ala552=
c.1656C>T · rs115321780 · VCV712176
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.44%, afr)
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 -12 | GERP -3.1 |
| Overall | ||
| CADD | 0.093 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.44%
African / African-American · 1,820/74,488 alleles
Filtering AF
2.35%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.31%
Overall
0.173%
2,734/1,578,520 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.44% | 41 |
| Remaining individualsnot grpmax-eligible | 0.207% | 483 |
| Admixed American | 0.174% | 574 |
| Middle Eastern | 0.0674% | 1,485 |
| European (non-Finnish) | 0.0568% | 1,762 |
| East Asian | 0.0473% | 2,114 |
| South Asian | 0.00349% | 28,645 |
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.Ala552=
- Coding
- c.1656C>T
- MANE Select
- NM_003502
- dbSNP
- rs115321780
- Type
- single nucleotide variant
- Location
- chr16:297850 (GRCh38)
- Gene constraint
- LOEUF 0.563 · pLI 0.16 (gnomAD)
- Structure
- AlphaFold pLDDT 62.32 · 22 PDB
- Residue 552
- the 'interaction with rnf111' region; the 'disordered' region
Similar variants
- 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.Arg801= Benign/Likely benign ★★ same type
- AXIN1 p.Arg803= Benign ★★ same type
- AXIN1 p.Arg841Gln Benign/Likely benign ★★ ⚠ same type
- AXIN1 p.Asp254= 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-ala552 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown