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NM_004360.5(CDH1):c.2343A>T (p.Glu781Asp) AND CDH1-related diffuse gastric and lobular breast cancer syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Aug 17, 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:
RCV003328176.4

Allele description [Variation Report for NM_004360.5(CDH1):c.2343A>T (p.Glu781Asp)]

NM_004360.5(CDH1):c.2343A>T (p.Glu781Asp)

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.2343A>T (p.Glu781Asp)
HGVS:
  • NC_000016.10:g.68829701A>T
  • NG_008021.1:g.97410A>T
  • NM_001317184.2:c.2160A>T
  • NM_001317185.2:c.795A>T
  • NM_001317186.2:c.378A>T
  • NM_004360.5:c.2343A>TMANE SELECT
  • NP_001304113.1:p.Glu720Asp
  • NP_001304114.1:p.Glu265Asp
  • NP_001304115.1:p.Glu126Asp
  • NP_004351.1:p.Glu781Asp
  • LRG_301t1:c.2343A>T
  • LRG_301:g.97410A>T
  • NC_000016.9:g.68863604A>T
  • NM_004360.3:c.2343A>T
  • NM_004360.4(CDH1):c.2343A>T
  • NM_004360.4:c.2343A>T
  • p.E781D
Protein change:
E126D
Links:
dbSNP: rs587780119
NCBI 1000 Genomes Browser:
rs587780119
Molecular consequence:
  • NM_001317184.2:c.2160A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317185.2:c.795A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317186.2:c.378A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.2343A>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
SCV001437608ClinGen CDH1 Variant Curation Expert Panel
reviewed by expert panel

(ClinGen CDH1 ACMG Specifications V3.1)		Likely benign
(Aug 17, 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, SCV001437608.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.2343A>T (p.Glu781Asp) missense variant has a frequency of 0.00001 (4 of 282,860) in gnomAD, with a maximum allele frequency of 0.00004 (1 of 24,970) in the African subpopulation (http://gnomad.broadinstitute.org). This variant has been observed in at least 100 individuals without DGC, SRC tumours or LBC and whose families do not suggest HDGC (BS2; SCV000149761.14, SCV000185618.5, SCV000288464.7). Although functional impact of this variant was reported from in vitro assays, functional assays except splicing assay are not applicable to CDH1 according to the CDH1 specific variant interpretation criteria. In summary, the clinical significance of this variant is classified as likely benign based on BS2 alone. ACMG/AMP criteria applied, as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): BS2.

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

Last Updated: Oct 26, 2024