Is APC p.Ser873fs (c.2618_2620delinsTG) pathogenic?

APC p.Ser873fs (c.26182620delinsTG) is classified Pathogenic/Likely pathogenic in APC (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-06-18). Absent from gnomAD; Associated with hereditary neoplastic syndrome.

What condition is associated with APC p.Ser873fs (c.2618_2620delinsTG)?

APC p.Ser873fs (c.2618_2620delinsTG) is associated with hereditary neoplastic syndrome, familial adenomatous polyposis 1 (ClinVar).

How common is APC p.Ser873fs (c.2618_2620delinsTG) in the general population?

APC p.Ser873fs (c.2618_2620delinsTG) is absent from gnomAD (gnomAD).

APC p.Ser873fs

c.2618_2620delinsTG · rs2533436971 · VCV2583754

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

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.
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 7.7	GERP 2.9, phastCons 1

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.Ser873fs
Coding: c.2618_2620delinsTG
MANE Select: NM_000038
dbSNP: rs2533436971
Type: Indel
Location: chr5:112838212 (GRCh38)
Gene constraint: LOEUF 0.321 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 873: the 'disordered' 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

Also linked: familial adenomatous polyposis 1

Similar variants

APC p.Ser873Thr Uncertain significance ★ same residue
APC c.931_933+2delinsCA Pathogenic/Likely pathogenic ★★ same condition
APC c.-192_-191delinsTAGCAAGGG Likely pathogenic ★★ same condition
APC p.Ala1598fs Pathogenic/Likely pathogenic ★★ same condition
APC p.Gly253fs Pathogenic ★★ same condition
APC p.His931fs Pathogenic ★★ same condition
APC p.Ile631fs Pathogenic/Likely pathogenic ★★ same condition
APC p.Leu666_Gln667delinsTer 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-ser873fs (accessed [today's date]).

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