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NM_004360.5(CDH1):c.2521G>A (p.Glu841Lys) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 3, 2018
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV000481767.2

Allele description [Variation Report for NM_004360.5(CDH1):c.2521G>A (p.Glu841Lys)]

NM_004360.5(CDH1):c.2521G>A (p.Glu841Lys)

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.2521G>A (p.Glu841Lys)
HGVS:
  • NC_000016.10:g.68833371G>A
  • NG_008021.1:g.101080G>A
  • NM_001317184.2:c.2338G>A
  • NM_001317185.2:c.973G>A
  • NM_001317186.2:c.556G>A
  • NM_004360.5:c.2521G>AMANE SELECT
  • NP_001304113.1:p.Glu780Lys
  • NP_001304114.1:p.Glu325Lys
  • NP_001304115.1:p.Glu186Lys
  • NP_004351.1:p.Glu841Lys
  • LRG_301t1:c.2521G>A
  • LRG_301:g.101080G>A
  • NC_000016.9:g.68867274G>A
  • NM_004360.3:c.2521G>A
  • NM_004360.4:c.2521G>A
Protein change:
E186K
Links:
dbSNP: rs377489352
NCBI 1000 Genomes Browser:
rs377489352
Molecular consequence:
  • NM_001317184.2:c.2338G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317185.2:c.973G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317186.2:c.556G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.2521G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000564841GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Oct 3, 2018) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000564841.4

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

Description

This variant is denoted CDH1 c.2521G>A at the cDNA level, p.Glu841Lys (E841K) at the protein level, and results in the change of a Glutamic Acid to a Lysine (GAA>AAA). Although this variant has not, to our knowledge, been published in the literature as a germline variant, it has been reported as a confirmed somatic variant in colorectal and endometrial carcinomas (Giannakis 2014). CDH1 Glu841Lys was not observed at a significant allele frequency in large population cohorts (Lek 2016). This variant is located in the cytoplasmic domain as well as within a region required for binding beta-catenin and PIPKly (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 Glu841Lys 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: Jun 23, 2024