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NM_004360.5(CDH1):c.188G>A (p.Arg63Gln) AND CDH1-related diffuse gastric and lobular breast cancer syndrome

Germline classification:
Benign (1 submission)
Last evaluated:
Aug 10, 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:
RCV003328173.4

Allele description [Variation Report for NM_004360.5(CDH1):c.188G>A (p.Arg63Gln)]

NM_004360.5(CDH1):c.188G>A (p.Arg63Gln)

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.188G>A (p.Arg63Gln)
Other names:
p.R63Q:CGA>CAA; NM_004360.4(CDH1):c.188G>A
HGVS:
  • NC_000016.10:g.68801694G>A
  • NG_008021.1:g.69403G>A
  • NM_001317184.2:c.188G>A
  • NM_001317185.2:c.-1428G>A
  • NM_001317186.2:c.-1632G>A
  • NM_004360.5:c.188G>AMANE SELECT
  • NP_001304113.1:p.Arg63Gln
  • NP_004351.1:p.Arg63Gln
  • LRG_301t1:c.188G>A
  • LRG_301:g.69403G>A
  • NC_000016.9:g.68835597G>A
  • NM_004360.3:c.188G>A
  • NM_004360.4:c.188G>A
  • p.R63Q
Protein change:
R63Q
Links:
dbSNP: rs587780117
NCBI 1000 Genomes Browser:
rs587780117
Molecular consequence:
  • NM_001317185.2:c.-1428G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1632G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.188G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.188G>A - 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
SCV000864612ClinGen CDH1 Variant Curation Expert Panel
reviewed by expert panel

(ClinGen CDH1 ACMG Specifications V3.1)		Benign
(Aug 10, 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, SCV000864612.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.188G>A (p.Arg63Gln) variant has an allele frequency of 0.00109 (0.11%, 6/5486 alleles) in the Other subpopulation of the gnomAD cohort (BS1). This variant has also been observed in >10 without a diagnosis of diffuse gastric cancer, signet ring tumor or lobular breast cancer and whose family histories do not suggest HDGC (BS2; internal laboratory contributors). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the CDH1 Variant Curation Expert Panel (Variant Interpretation Guidelines Version 3.1): BS1, BS2.

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

Last Updated: Nov 3, 2024