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NM_004360.5(CDH1):c.2396C>G (p.Pro799Arg) AND Hereditary diffuse gastric adenocarcinoma

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 22, 2022
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:
RCV000167901.10

Allele description [Variation Report for NM_004360.5(CDH1):c.2396C>G (p.Pro799Arg)]

NM_004360.5(CDH1):c.2396C>G (p.Pro799Arg)

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.2396C>G (p.Pro799Arg)
Other names:
NM_004360.4(CDH1):c.2396C>G
HGVS:
  • NC_000016.10:g.68829754C>G
  • NG_008021.1:g.97463C>G
  • NM_001317184.2:c.2213C>G
  • NM_001317185.2:c.848C>G
  • NM_001317186.2:c.431C>G
  • NM_004360.5:c.2396C>GMANE SELECT
  • NP_001304113.1:p.Pro738Arg
  • NP_001304114.1:p.Pro283Arg
  • NP_001304115.1:p.Pro144Arg
  • NP_004351.1:p.Pro799Arg
  • LRG_301t1:c.2396C>G
  • LRG_301:g.97463C>G
  • NC_000016.9:g.68863657C>G
  • NM_004360.3:c.2396C>G
  • NM_004360.4:c.2396C>G
  • p.P799R
Protein change:
P144R
Links:
dbSNP: rs587781335
NCBI 1000 Genomes Browser:
rs587781335
Molecular consequence:
  • NM_001317184.2:c.2213C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317185.2:c.848C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317186.2:c.431C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.2396C>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
SCV000218548Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Feb 22, 2022) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

De novo and DNA primer-mediated initiation of cDNA synthesis by the mauriceville retroplasmid reverse transcriptase involve recognition of a 3' CCA sequence.

Chen B, Lambowitz AM.

J Mol Biol. 1997 Aug 22;271(3):311-32.

PubMed [citation]
PMID:
9268661

EGFR regulates RhoA-GTP dependent cell motility in E-cadherin mutant cells.

Mateus AR, Seruca R, Machado JC, Keller G, Oliveira MJ, Suriano G, Luber B.

Hum Mol Genet. 2007 Jul 1;16(13):1639-47. Epub 2007 May 17.

PubMed [citation]
PMID:
17510211
See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000218548.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

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. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on CDH1 function (PMID: 9268661, 15173255, 17510211, 22850631). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 140871). This missense change has been observed in individual(s) with gastric cancer (PMID: 15173255). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 799 of the CDH1 protein (p.Pro799Arg).

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

Last Updated: Sep 29, 2024