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NM_004360.5(CDH1):c.344C>T (p.Thr115Met) AND CDH1-related diffuse gastric and lobular breast cancer syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Aug 3, 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:
RCV003328206.1

Allele description [Variation Report for NM_004360.5(CDH1):c.344C>T (p.Thr115Met)]

NM_004360.5(CDH1):c.344C>T (p.Thr115Met)

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.344C>T (p.Thr115Met)
Other names:
p.T115M:ACG>ATG; NM_004360.5(CDH1):c.344C>T; p.Thr115Met
HGVS:
  • NC_000016.10:g.68801850C>T
  • NG_008021.1:g.69559C>T
  • NM_001317184.2:c.344C>T
  • NM_001317185.2:c.-1272C>T
  • NM_001317186.2:c.-1476C>T
  • NM_004360.5:c.344C>TMANE SELECT
  • NP_001304113.1:p.Thr115Met
  • NP_004351.1:p.Thr115Met
  • LRG_301t1:c.344C>T
  • LRG_301:g.69559C>T
  • NC_000016.9:g.68835753C>T
  • NM_004360.3:c.344C>T
  • NM_004360.4:c.344C>T
  • p.T115M
Protein change:
T115M
Links:
dbSNP: rs370973869
NCBI 1000 Genomes Browser:
rs370973869
Molecular consequence:
  • NM_001317185.2:c.-1272C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1476C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.344C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.344C>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
SCV004035098ClinGen CDH1 Variant Curation Expert Panel
reviewed by expert panel

(ClinGen CDH1 ACMG Specifications V3.1)		Likely benign
(Aug 3, 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, SCV004035098.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The c.344C>T (p.Thr115Met) missense variant has a maximum subpopulation frequency of 0.0097% in the gnomAD v2.1.1 cohort (http://gnomad.broadinstitute.org). This variant has been observed in over 75 probands not meeting HDGC phenotype criteria (BS2; SCV000254830.11, SCV000210896.16, SCV000183817.7). In summary, this variant meets criteria to be classified as Likely Benign based on the ACMG/AMP criteria applied as specified by the CDH1 Variant Curation Expert Panel: BS2. (CDH1 VCEP specifications version 3.1; 06/26/2023)

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

Last Updated: Sep 29, 2024