Is APC c.1412dupG pathogenic?

APC c.1412dupG is classified Pathogenic in APC (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-05-13). Absent from gnomAD; Associated with hereditary neoplastic syndrome.

What condition is associated with APC c.1412dupG?

APC c.1412dupG is associated with hereditary neoplastic syndrome, familial adenomatous polyposis 1 (ClinVar).

How common is APC c.1412dupG in the general population?

APC c.1412dupG is absent from gnomAD (gnomAD).

APC c.1412dupG

rs1580564136 · VCV1772067

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.8, phastCons 1
Non-coding constraint	Z -0.54	1 kb window · o/e 1.05 · regional · uncalibrated

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: APC
Coding: c.1412dupG
MANE Select: NM_000038
dbSNP: rs1580564136
Type: Duplication
Location: chr5:112827106 (GRCh38)
Gene constraint: LOEUF 0.321 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)

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

Also linked: familial adenomatous polyposis 1

Similar variants

APC p.Ser634fs Pathogenic ★★★ same condition
APC p.Gln12fs Uncertain significance ★★★ same condition
APC p.Ser2830fs Uncertain significance ★★★ same condition
APC c.1958+1_1958+2dup Pathogenic/Likely pathogenic ★★ same condition
APC c.531+2dup Pathogenic ★★ same condition
APC p.Ala1107fs Pathogenic ★★ same condition
APC p.Ala1402fs Pathogenic ★★ same condition
APC p.Ala2004fs Pathogenic/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-c-1412dupg (accessed [today's date]).

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