NM_004360.5(CDH1):c.2555A>G (p.Glu852Gly) AND Hereditary diffuse gastric adenocarcinoma

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 22, 2023
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:
RCV002571397.4

Allele description [Variation Report for NM_004360.5(CDH1):c.2555A>G (p.Glu852Gly)]

NM_004360.5(CDH1):c.2555A>G (p.Glu852Gly)

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.2555A>G (p.Glu852Gly)
HGVS:
  • NC_000016.10:g.68833405A>G
  • NG_008021.1:g.101114A>G
  • NM_001317184.2:c.2372A>G
  • NM_001317185.2:c.1007A>G
  • NM_001317186.2:c.590A>G
  • NM_004360.5:c.2555A>GMANE SELECT
  • NP_001304113.1:p.Glu791Gly
  • NP_001304114.1:p.Glu336Gly
  • NP_001304115.1:p.Glu197Gly
  • NP_004351.1:p.Glu852Gly
  • NP_004351.1:p.Glu852Gly
  • LRG_301t1:c.2555A>G
  • LRG_301:g.101114A>G
  • LRG_301p1:p.Glu852Gly
  • NC_000016.9:g.68867308A>G
  • NM_004360.3:c.2555A>G
Protein change:
E197G
Molecular consequence:
  • NM_001317184.2:c.2372A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317185.2:c.1007A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317186.2:c.590A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.2555A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary diffuse gastric adenocarcinoma (HDGC)
Synonyms:
Hereditary diffuse gastric cancer
Identifiers:
MONDO: MONDO:0007648; MedGen: C1708349; Orphanet: 26106; OMIM: 137215

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003207127Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Feb 22, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003207127.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces glutamic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 852 of the CDH1 protein (p.Glu852Gly). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CDH1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1802899). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The glycine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024