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NM_004360.5(CDH1):c.125C>T (p.Pro42Leu) AND CDH1-related diffuse gastric and lobular breast cancer syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Aug 2, 2023
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003328288.1

Allele description [Variation Report for NM_004360.5(CDH1):c.125C>T (p.Pro42Leu)]

NM_004360.5(CDH1):c.125C>T (p.Pro42Leu)

Gene:
CDH1:cadherin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q22.1
Genomic location:
Preferred name:
NM_004360.5(CDH1):c.125C>T (p.Pro42Leu)
Other names:
NM_004360.5(CDH1):c.125C>T
HGVS:
  • NC_000016.10:g.68738373C>T
  • NG_008021.1:g.6082C>T
  • NM_001317184.2:c.125C>T
  • NM_001317185.2:c.-1491C>T
  • NM_001317186.2:c.-1695C>T
  • NM_004360.5:c.125C>TMANE SELECT
  • NP_001304113.1:p.Pro42Leu
  • NP_004351.1:p.Pro42Leu
  • LRG_301t1:c.125C>T
  • LRG_301:g.6082C>T
  • NC_000016.9:g.68772276C>T
  • NM_004360.3:c.125C>T
  • NM_004360.4:c.125C>T
  • p.Pro42Leu
Protein change:
P42L
Links:
dbSNP: rs876659333
NCBI 1000 Genomes Browser:
rs876659333
Molecular consequence:
  • NM_001317185.2:c.-1491C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1695C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.125C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.125C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
CDH1-related diffuse gastric and lobular breast cancer syndrome
Synonyms:
CDH1-related diffuse gastric and lobular breast cancer
Identifiers:
MONDO: MONDO:0100488; MedGen: CN311521

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004035124ClinGen CDH1 Variant Curation Expert Panel
reviewed by expert panel

(ClinGen CDH1 ACMG Specifications V3.1)		Likely benign
(Aug 2, 2023) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From ClinGen CDH1 Variant Curation Expert Panel, SCV004035124.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.125C>T (NM_004360.5) variant in CDH1 is a missense variant predicted to cause substitution of Pro by Leu at amino acid 42 (p.Pro42Leu). This variant has been observed in more than 10 heterozygous individuals with no DGC, SRC tumours and whose families do not suggest HDGC (BS2; GeneDx, Invitae, Color). In summary, the CDH1 VCEP classified the variant as likely benign for DGLBCS based on BS2 alone based on the ACMG/AMP criteria applied, as specified by the ClinGen CDH1 VCEP: BS2. (CDH1 VCEP specifications version 3.1; 04/24/2023)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024