Is EPCAM p.Pro178Arg (c.533C>G) pathogenic?

EPCAM p.Pro178Arg (c.533C>G) is classified Uncertain significance in EPCAM (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-27). AlphaMissense: likely benign (0.1107); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with EPCAM p.Pro178Arg (c.533C>G)?

EPCAM p.Pro178Arg (c.533C>G) is associated with hereditary neoplastic syndrome (ClinVar).

How common is EPCAM p.Pro178Arg (c.533C>G) in the general population?

EPCAM p.Pro178Arg (c.533C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EPCAM p.Pro178Arg (c.533C>G)?

AlphaMissense predicts likely benign (score 0.1107) — an in-silico prediction, not a clinical call.

EPCAM p.Pro178Arg

c.533C>G · rs772471530 · VCV3222121

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1107 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.1107	likely benign
REVEL	0.064	moderately benign-leaning
SaProt	LLR -9.22	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.52	GERP -4.4
Regional constraint	o/e 1.32	unconstrained · MANE · 17 kb · p 4.4e-10 · regional, not allelic
Overall
CADD	3.089	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: EPCAM
Protein: p.Pro178Arg
Coding: c.533C>G
MANE Select: NM_002354
dbSNP: rs772471530
Type: single nucleotide variant
Location: chr2:47377055 (GRCh38)
Gene constraint: LOEUF 1.341 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.71 · 2 PDB
Residue 178: a UniProt-annotated variant site (in diar5; likely pathogenic); an α-helix

Full EPCAM 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

Similar variants

EPCAM p.Pro178Ala Uncertain significance ★ ⚠ same residue
EPCAM p.Pro178Leu Uncertain significance ★ ⚠ same residue
EPCAM c.491+1G>A Pathogenic ★★ same condition
EPCAM p.Ala22Thr Uncertain significance ★★ ⚠ same condition
EPCAM p.Ala256Ser Uncertain significance ★★ ⚠ same condition
EPCAM p.Ala278Val Uncertain significance ★★ same condition
EPCAM p.Ala87Val Uncertain significance ★★ same condition
EPCAM p.Arg173Cys Uncertain significance ★★ ⚠ 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/epcam-p-pro178arg (accessed [today's date]).

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