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NM_004360.5(CDH1):c.337A>G (p.Lys113Glu) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 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:
RCV000217135.9

Allele description [Variation Report for NM_004360.5(CDH1):c.337A>G (p.Lys113Glu)]

NM_004360.5(CDH1):c.337A>G (p.Lys113Glu)

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.337A>G (p.Lys113Glu)
HGVS:
  • NC_000016.10:g.68801843A>G
  • NG_008021.1:g.69552A>G
  • NM_001317184.2:c.337A>G
  • NM_001317185.2:c.-1279A>G
  • NM_001317186.2:c.-1483A>G
  • NM_004360.5:c.337A>GMANE SELECT
  • NP_001304113.1:p.Lys113Glu
  • NP_004351.1:p.Lys113Glu
  • LRG_301t1:c.337A>G
  • LRG_301:g.69552A>G
  • NC_000016.9:g.68835746A>G
  • NM_004360.3:c.337A>G
  • NM_004360.4:c.337A>G
Protein change:
K113E
Links:
dbSNP: rs876661106
NCBI 1000 Genomes Browser:
rs876661106
Molecular consequence:
  • NM_001317185.2:c.-1279A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1483A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.337A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.337A>G - 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
SCV000279836GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Apr 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, SCV000279836.10

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

Description

This variant is denoted CDH1 c.337A>G at the cDNA level, p.Lys113Glu (K113E) at the protein level, and results in the change of a Lysine to a Glutamic Acid (AAA>GAA). This variant has been observed in co-occurrence with a pathogenic MSH6 variant, in one individual with endometrial cancer and a diagnosis of Lynch syndrome (Jori 2015). This variant has also been observed in at least one individual with non-syndromic orofacial cleft, with no specific information about cancer history (Vogelaar 2013). CDH1 Lys113Glu was not observed at a significant allele frequency in large population cohorts (Lek 2016). CDH1 Lys113Glu is located in the precursor sequence domain Brooks-WIlson 2004). 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 Lys113Glu 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: Sep 29, 2024