Is APC p.Arg1069Met (c.3206G>T) pathogenic?

APC p.Arg1069Met (c.3206G>T) is classified Uncertain significance in APC (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-02-20). AlphaMissense: likely benign (0.3368); Very rare (popmax 8.47e-05%, nfe); Associated with familial adenomatous polyposis 1.

What condition is associated with APC p.Arg1069Met (c.3206G>T)?

APC p.Arg1069Met (c.3206G>T) is associated with familial adenomatous polyposis 1, hereditary neoplastic syndrome (ClinVar).

How common is APC p.Arg1069Met (c.3206G>T) in the general population?

APC p.Arg1069Met (c.3206G>T) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

How is Familial adenomatous polyposis inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about APC p.Arg1069Met (c.3206G>T)?

AlphaMissense predicts likely benign (score 0.3368) — an in-silico prediction, not a clinical call.

APC p.Arg1069Met

c.3206G>T · rs2149886840 · VCV1485666

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.3368 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Conditions

familial adenomatous polyposis 1

Computational evidence

Protein change
AlphaMissense	0.3368	likely benign
REVEL	0.488	indeterminate
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.7, phastCons 1
Regional constraint	o/e 1.09	unconstrained · MANE · 1,681 bp · p 0.023 · regional, not allelic
Overall
CADD	25.3	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,020 alleles

Overall 6.2e-05% 1/1,614,100 alleles · very rare exomes 1/1,461,800 · genomes 0/152,300 · joint denominator

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: APC
Protein: p.Arg1069Met
Coding: c.3206G>T
MANE Select: NM_000038
dbSNP: rs2149886840
Type: single nucleotide variant
Location: chr5:112838800 (GRCh38)
Gene constraint: LOEUF 0.321 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 1069: the 'responsible for down-regulation through a process mediated by direct ubiquitination' region; the 'interaction with catenins' region

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

Disease context

familial adenomatous polyposis 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary neoplastic syndrome

For Familial adenomatous polyposis (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: Adult
Prevalence: 1-9 / 100 000 (Worldwide)

Similar variants

APC p.Arg1069Lys Uncertain significance ★★ same residue
APC p.Arg1069Ser Uncertain significance ★★ same residue
APC p.Arg1069= Likely benign ★★ same residue
APC p.Arg1069Gly Conflicting classifications of pathogenicity ★ same residue
APC p.Arg1069Thr Uncertain significance ★ same residue
APC p.Arg1069fs Pathogenic ★ same residue
APC c.1312+3A>C Likely pathogenic ★★★ same condition
APC c.1312+3A>G 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/apc-p-arg1069met (accessed [today's date]).

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