Is AXIN2 p.Pro467= (c.1401G>A) pathogenic?

AXIN2 p.Pro467= (c.1401G>A) is classified Likely benign in AXIN2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-08-18). Ultra-rare (popmax 0.0123%, sas); Associated with hereditary neoplastic syndrome.

What condition is associated with AXIN2 p.Pro467= (c.1401G>A)?

AXIN2 p.Pro467= (c.1401G>A) is associated with hereditary neoplastic syndrome, oligodontia-cancer predisposition syndrome (ClinVar).

How common is AXIN2 p.Pro467= (c.1401G>A) in the general population?

AXIN2 p.Pro467= (c.1401G>A) is ultra-rare (popmax 0.0123%, sas) (gnomAD).

AXIN2 p.Pro467=

c.1401G>A · rs771579039 · VCV1045820

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0123%, sas)

Conditions

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 -9.5	GERP -3.7
Overall
CADD	0.233	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0123% South Asian · 11/89,208 alleles

Filtering AF 0.0069% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00532%

Overall 0.000757% 12/1,584,940 alleles · ultra-rare exomes 10/1,433,088 · genomes 2/151,852 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0123%	8,110
African / African-American	0.00134%	74,592

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.Pro467=
Coding: c.1401G>A
MANE Select: NM_004655
dbSNP: rs771579039
Type: single nucleotide variant
Location: chr17:65537635 (GRCh38)
Gene constraint: LOEUF 0.397 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 61.71 · 1 PDB
Residue 467: the 'interaction with beta-catenin' region; the 'disordered' region

Full AXIN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: oligodontia-cancer predisposition syndrome

Similar variants

AXIN2 p.Pro467Ala Uncertain significance ★★ ⚠ same residue
AXIN2 p.Pro467Leu Uncertain significance ★★ ⚠ same residue
AXIN2 p.Pro467Arg Uncertain significance ★ ⚠ same residue
AXIN2 p.Pro467Gln Uncertain significance ★ ⚠ same residue
AXIN2 p.Pro467Ser Uncertain significance ★ 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-pro467 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown