Is AXIN2 p.Leu481fs (c.1442_1449del) pathogenic?

AXIN2 p.Leu481fs (c.14421449del) is classified Pathogenic in AXIN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-18). Absent from gnomAD; Associated with oligodontia-cancer predisposition syndrome.

What condition is associated with AXIN2 p.Leu481fs (c.1442_1449del)?

AXIN2 p.Leu481fs (c.1442_1449del) is associated with oligodontia-cancer predisposition syndrome (ClinVar).

How common is AXIN2 p.Leu481fs (c.1442_1449del) in the general population?

AXIN2 p.Leu481fs (c.1442_1449del) is absent from gnomAD (gnomAD).

AXIN2 p.Leu481fs

c.1442_1449del · rs2509414713 · VCV2035953

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

oligodontia-cancer predisposition syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 6 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.5	GERP 0.65, phastCons 0.94

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: AXIN2
Protein: p.Leu481fs
Coding: c.1442_1449del
MANE Select: NM_004655
dbSNP: rs2509414713
Type: Deletion
Location: chr17:65537587 (GRCh38)
Gene constraint: LOEUF 0.397 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 61.71 · 1 PDB
Residue 481: the 'disordered' region

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

Disease context

oligodontia-cancer predisposition syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

AXIN2 p.Leu481Phe Uncertain significance ★★ ⚠ same residue
AXIN2 p.Leu481Pro Uncertain significance ★★ ⚠ same residue
AXIN2 p.Leu481= Conflicting classifications of pathogenicity ★ same residue
AXIN2 p.Ala417fs Pathogenic ★★ same condition
AXIN2 p.Ala492fs Pathogenic/Likely pathogenic ★★ same condition
AXIN2 p.Asn344fs Pathogenic ★★ same condition
AXIN2 p.Glu32fs Pathogenic/Likely pathogenic ★★ same condition
AXIN2 p.Gly546fs 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-leu481fs (accessed [today's date]).

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