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NM_004360.5(CDH1):c.2T>C (p.Met1Thr) AND CDH1-related diffuse gastric and lobular breast cancer syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 25, 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:
RCV003328425.1

Allele description [Variation Report for NM_004360.5(CDH1):c.2T>C (p.Met1Thr)]

NM_004360.5(CDH1):c.2T>C (p.Met1Thr)

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.2T>C (p.Met1Thr)
Other names:
NM_004360.5(CDH1):c.2T>C; p.Met1Thr
HGVS:
  • NC_000016.10:g.68737417T>C
  • NG_008021.1:g.5126T>C
  • NM_001317184.2:c.2T>C
  • NM_001317185.2:c.-1614T>C
  • NM_001317186.2:c.-1818T>C
  • NM_004360.4:c.2T>C
  • NM_004360.5:c.2T>CMANE SELECT
  • NP_001304113.1:p.Met1Thr
  • NP_004351.1:p.Met1Thr
  • LRG_301t1:c.2T>C
  • LRG_301:g.5126T>C
  • NC_000016.9:g.68771320T>C
  • NM_004360.3:c.2T>C
Protein change:
M1T
Links:
dbSNP: rs1555509623
NCBI 1000 Genomes Browser:
rs1555509623
Molecular consequence:
  • NM_001317185.2:c.-1614T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1818T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.2T>C - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_004360.5:c.2T>C - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001317184.2:c.2T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.2T>C - 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
SCV001943356ClinGen CDH1 Variant Curation Expert Panel
reviewed by expert panel

(ClinGen CDH1 ACMG Specifications V3.1)		Pathogenic
(Aug 25, 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, SCV001943356.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.2T>C (p.Met1Thr) variant alters the start codon of the CDH1 coding sequence and is predicted to lead to an absent protein (PVS1). This variant is absent in the gnomAD cohort (PM2_supporting; http://gnomad.broadinstitute.org). This variant has been reported in at least 2 probands/families meeting HDGC clinical criteria (PS4_moderate; PMID: 20373070, SCV000760804.3). In summary, this variant meets criteria to be classified as pathogenic based on the ACMG/AMP Variant Interpretation Guidelines Version 3.1 as specified by the CDH1 Variant Curation Expert Panel: PVS1, PS4_moderate, PM2_supporting.

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

Last Updated: Sep 29, 2024