Is APC p.Arg1069Lys (c.3206G>A) pathogenic?

APC p.Arg1069Lys (c.3206G>A) is classified Uncertain significance in APC (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-03-25). AlphaMissense: likely benign (0.1066); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with APC p.Arg1069Lys (c.3206G>A)?

APC p.Arg1069Lys (c.3206G>A) is associated with hereditary neoplastic syndrome (ClinVar).

How common is APC p.Arg1069Lys (c.3206G>A) in the general population?

APC p.Arg1069Lys (c.3206G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about APC p.Arg1069Lys (c.3206G>A)?

AlphaMissense predicts likely benign (score 0.1066) — an in-silico prediction, not a clinical call.

APC p.Arg1069Lys

c.3206G>A · rs2149886840 · VCV3228114

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1066 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.1066	likely benign
REVEL	0.376	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	24.6	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: APC
Protein: p.Arg1069Lys
Coding: c.3206G>A
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

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

Similar variants

APC p.Arg1069Met 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 c.1312+3A>C Likely pathogenic ★★★ same condition
APC c.1312+3A>G Pathogenic ★★★ same condition
APC c.1312+5G>A 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/apc-p-arg1069lys (accessed [today's date]).

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