Is APC p.Ser982fs (c.2943del) pathogenic?

APC p.Ser982fs (c.2943del) is classified Likely pathogenic in APC (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-17). No gnomAD frequency available for this variant; Associated with classic familial adenomatous polyposis.

What condition is associated with APC p.Ser982fs (c.2943del)?

APC p.Ser982fs (c.2943del) is associated with classic familial adenomatous polyposis (ClinVar).

How common is APC p.Ser982fs (c.2943del) in the general population?

APC p.Ser982fs (c.2943del) is no gnomAD frequency available for this variant (gnomAD).

How is Familial adenomatous polyposis inherited?

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

APC p.Ser982fs

c.2943del · rs2149880739 · VCV1677125

Likely pathogenic Single submitter

Classification

Likely 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

classic familial adenomatous polyposis

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	escapes	premature termination codon in the last exon (16 of 16) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.76	GERP -5.6, phastCons 0.96

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: APC
Protein: p.Ser982fs
Coding: c.2943del
MANE Select: NM_000038
dbSNP: rs2149880739
Type: Deletion
Location: chr5:112838535 (GRCh38)
Gene constraint: LOEUF 0.321 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 982: the 'disordered' region; the 'responsible for down-regulation through a process mediated by direct ubiquitination' region

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

Disease context

classic familial adenomatous polyposis — 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.Ala1050fs Pathogenic ★★ same condition
APC p.Ala1907fs Likely pathogenic ★★ same condition
APC p.Ala504_Leu505insTer Pathogenic/Likely pathogenic ★★ same condition
APC p.Arg499_Tyr500insTer Pathogenic ★★ same condition
APC p.Arg904fs Pathogenic ★★ same condition
APC p.Asn1830fs Pathogenic ★★ same condition
APC p.Asn1979fs Pathogenic ★★ same condition
APC p.Asp1860_Ser1861insTer 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-ser982fs (accessed [today's date]).

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