NM_004360.5(CDH1):c.1019C>T (p.Thr340Met) AND not provided

Clinical significance:Uncertain significance (Last evaluated: Oct 30, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000219875.2

Allele description [Variation Report for NM_004360.5(CDH1):c.1019C>T (p.Thr340Met)]

NM_004360.5(CDH1):c.1019C>T (p.Thr340Met)

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.1019C>T (p.Thr340Met)
HGVS:
  • NC_000016.10:g.68812145C>T
  • NG_008021.1:g.79854C>T
  • NM_001317184.2:c.1019C>T
  • NM_001317185.2:c.-597C>T
  • NM_001317186.2:c.-801C>T
  • NM_004360.5:c.1019C>TMANE SELECT
  • NP_001304113.1:p.Thr340Met
  • NP_004351.1:p.Thr340Met
  • LRG_301t1:c.1019C>T
  • LRG_301:g.79854C>T
  • NC_000016.9:g.68846048C>T
  • NM_004360.3:c.1019C>T
  • NM_004360.4:c.1019C>T
  • p.T340M
Protein change:
T340M
Links:
dbSNP: rs61747631
NCBI 1000 Genomes Browser:
rs61747631
Molecular consequence:
  • NM_001317185.2:c.-597C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-801C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.1019C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.1019C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000278912GeneDxcriteria provided, single submitter
Uncertain significance
(Oct 30, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000278912.9

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is denoted CDH1 c.1019C>T at the cDNA level, p.Thr340Met (T340M) at the protein level, and results in the change of a Threonine to a Methionine (ACG>ATG). This variant has not, to our knowledge, been published in the literature as a germline pathogenic or benign variant. CDH1 Thr340Met was not observed at a significant allele frequency in large population cohorts (Lek 2016). Since Threonine and Methionine differ in polarity, charge, size or other properties, this is considered a non-conservative amino acid substitution. CDH1 Thr340Met is located in cadherin 2 of the extracellular domain (Brooks-Wilson 2004, Figueiredo 2013). In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function. Based on currently available evidence, it is unclear whether CDH1 Thr340Met is a pathogenic or benign variant. We consider it to be a variant of uncertain significance.

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

Last Updated: Aug 11, 2021

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