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NM_004360.5(CDH1):c.1003C>T (p.Arg335Ter) AND CDH1-related diffuse gastric and lobular breast cancer syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 29, 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:
RCV003328190.3

Allele description [Variation Report for NM_004360.5(CDH1):c.1003C>T (p.Arg335Ter)]

NM_004360.5(CDH1):c.1003C>T (p.Arg335Ter)

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.1003C>T (p.Arg335Ter)
Other names:
NM_004360.4(CDH1):c.1003C>T
HGVS:
  • NC_000016.10:g.68811854C>T
  • NG_008021.1:g.79563C>T
  • NM_001317184.2:c.1003C>T
  • NM_001317185.2:c.-613C>T
  • NM_001317186.2:c.-817C>T
  • NM_004360.5:c.1003C>TMANE SELECT
  • NP_001304113.1:p.Arg335Ter
  • NP_004351.1:p.Arg335Ter
  • LRG_301t1:c.1003C>T
  • LRG_301:g.79563C>T
  • NC_000016.9:g.68845757C>T
  • NM_004360.3:c.1003C>T
  • NM_004360.4:c.1003C>T
  • p.R335*
Protein change:
R335*
Links:
dbSNP: rs587780784
NCBI 1000 Genomes Browser:
rs587780784
Molecular consequence:
  • NM_001317185.2:c.-613C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-817C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.1003C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_004360.5:c.1003C>T - nonsense - [Sequence Ontology: SO:0001587]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000864589ClinGen CDH1 Variant Curation Expert Panel
reviewed by expert panel

(ClinGen CDH1 ACMG Specifications V3.1)
Pathogenic
(Aug 29, 2023)
germlinecuration

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Hereditary diffuse gastric cancer: a family diagnosis and treatment.

Onitilo AA, Aryal G, Engel JM.

Clin Med Res. 2013 Feb;11(1):36-41. doi: 10.3121/cmr.2012.1071. Epub 2012 Jun 21. Review.

PubMed [citation]
PMID:
22723466
PMCID:
PMC3573088

CDH1 truncating mutations in the E-cadherin gene: an indication for total gastrectomy to treat hereditary diffuse gastric cancer.

Norton JA, Ham CM, Van Dam J, Jeffrey RB, Longacre TA, Huntsman DG, Chun N, Kurian AW, Ford JM.

Ann Surg. 2007 Jun;245(6):873-9.

PubMed [citation]
PMID:
17522512
PMCID:
PMC1876967
See all PubMed Citations (3)

Details of each submission

From ClinGen CDH1 Variant Curation Expert Panel, SCV000864589.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (3)

Description

The c.1003C>T (p.Arg335*) variant is predicted to result in a premature stop codon that leads to a truncated or absent protein (PVS1, PM5_Supporting). This variant was found to co-segregate with disease in multiple affected family members, with >7 meioses observed across at least two families (PP1_Strong; PMID: 16061854, 22723466, 17522512). In summary, this variant meets criteria to be classified as pathogenic based on the ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): PVS1, PP1_Strong, PM5_Supporting.

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

Last Updated: May 1, 2024