Is CDH1 p.Pro42= (c.126C>T) pathogenic?

CDH1 p.Pro42= (c.126C>T) is classified Likely benign in CDH1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-26). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with CDH1 p.Pro42= (c.126C>T)?

CDH1 p.Pro42= (c.126C>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is CDH1 p.Pro42= (c.126C>T) in the general population?

CDH1 p.Pro42= (c.126C>T) is absent from gnomAD v4.1 (gnomAD).

CDH1 p.Pro42=

c.126C>T · rs2152114440 · VCV1765021

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,550,994)

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 · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.34	GERP -1.3, phastCons 0.057
Overall
CADD	7.888	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,550,994). 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: CDH1
Protein: p.Pro42=
Coding: c.126C>T
MANE Select: NM_004360
dbSNP: rs2152114440
Type: single nucleotide variant
Location: chr16:68738374 (GRCh38)
Gene constraint: LOEUF 0.514 · pLI 0.86 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 79.13 · 22 PDB

Full CDH1 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

CDH1 p.Pro42Leu Likely benign ★★★ ⚠ same residue
CDH1 p.Pro42Ser Uncertain significance ★★ ⚠ same residue
CDH1 p.Pro42Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
CDH1 p.Pro42His Likely benign ★ same residue
CDH1 p.Pro42fs Pathogenic ★★★ same residue
CDH1 c.1008+2T>C Likely pathogenic ★★★ same condition
CDH1 c.1137+1G>A Pathogenic ★★★ same condition
CDH1 c.1137+2T>C 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/cdh1-p-pro42 (accessed [today's date]).

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