Is APC p.Arg259fs (c.775dup) pathogenic?

APC p.Arg259fs (c.775dup) is classified Pathogenic in APC (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-28). Associated with familial adenomatous polyposis 1.

What condition is associated with APC p.Arg259fs (c.775dup)?

APC p.Arg259fs (c.775dup) is associated with familial adenomatous polyposis 1 (ClinVar).

How is Familial adenomatous polyposis inherited?

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

APC p.Arg259fs

c.775dup · VCV3726341

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

familial adenomatous polyposis 1

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 8 of 16
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.8	GERP -3.1, phastCons 1

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

Variant & gene context

Gene: APC
Protein: p.Arg259fs
Coding: c.775dup
MANE Select: NM_000038
Type: Duplication
Location: chr5:112801323 (GRCh38)
Gene constraint: LOEUF 0.321 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 259: the 'disordered' 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

For Familial adenomatous polyposis (Orphanet):

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

Similar variants

APC p.Arg259= Conflicting classifications of pathogenicity ★ same residue
APC p.Arg259Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
APC p.Arg259Trp Conflicting classifications of pathogenicity ★ same residue
APC p.Ser634fs Pathogenic ★★★ same condition
APC p.Gln12fs Uncertain significance ★★★ same condition
APC c.1412dupG Pathogenic ★★ same condition
APC c.531+2dup Pathogenic ★★ same condition
APC p.Ala1107fs 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-arg259fs (accessed [today's date]).

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