Is APC p.Asp1794= (c.5382C>T) pathogenic?

APC p.Asp1794= (c.5382C>T) is classified Benign/Likely benign in APC (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-10-13). Ultra-rare (popmax 0.0187%, sas); Associated with familial adenomatous polyposis 1.

What condition is associated with APC p.Asp1794= (c.5382C>T)?

APC p.Asp1794= (c.5382C>T) is associated with familial adenomatous polyposis 1, hereditary neoplastic syndrome (ClinVar).

How common is APC p.Asp1794= (c.5382C>T) in the general population?

APC p.Asp1794= (c.5382C>T) is ultra-rare (popmax 0.0187%, sas) (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.Asp1794=

c.5382C>T · rs566370229 · VCV490306

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0187%, sas)

Conditions

familial adenomatous polyposis 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.1	GERP -2.6, phastCons 1
Overall
CADD	4.641	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0187% South Asian · 17/90,952 alleles

Filtering AF 0.0119% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00977%

Overall 0.00105% 17/1,612,544 alleles · ultra-rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: APC
Protein: p.Asp1794=
Coding: c.5382C>T
MANE Select: NM_000038
dbSNP: rs566370229
Type: single nucleotide variant
Location: chr5:112840976 (GRCh38)
Gene constraint: LOEUF 0.321 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Residue 1794: 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

Also linked: hereditary neoplastic syndrome

For Familial adenomatous polyposis (Orphanet):

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

Similar variants

APC p.Asp1794Ala Uncertain significance ★★ ⚠ same residue
APC p.Asp1794Gly Uncertain significance ★★ same residue
APC p.Asp1794Val Uncertain significance ★★ same residue
APC p.Asp1794Glu Uncertain significance ★ ⚠ same residue
APC p.Asp1794His 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-asp1794 (accessed [today's date]).

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