NM_004360.5(CDH1):c.164T>G (p.Val55Gly) AND Hereditary diffuse gastric cancer

Clinical significance:Uncertain significance (Last evaluated: Oct 21, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000119234.12

Allele description [Variation Report for NM_004360.5(CDH1):c.164T>G (p.Val55Gly)]

NM_004360.5(CDH1):c.164T>G (p.Val55Gly)

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.164T>G (p.Val55Gly)
HGVS:
  • NC_000016.10:g.68801670T>G
  • NG_008021.1:g.69379T>G
  • NM_001317184.2:c.164T>G
  • NM_001317185.2:c.-1452T>G
  • NM_001317186.2:c.-1656T>G
  • NM_004360.5:c.164T>GMANE SELECT
  • NP_001304113.1:p.Val55Gly
  • NP_004351.1:p.Val55Gly
  • LRG_301t1:c.164T>G
  • LRG_301:g.69379T>G
  • NC_000016.9:g.68835573T>G
  • NM_004360.3:c.164T>G
  • NM_004360.4:c.164T>G
  • p.V55G
Protein change:
V55G
Links:
dbSNP: rs587778174
NCBI 1000 Genomes Browser:
rs587778174
Molecular consequence:
  • NM_001317185.2:c.-1452T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1656T>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.164T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.164T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000153979Invitaecriteria provided, single submitter
Uncertain significance
(Oct 21, 2020)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV000785172Counsylcriteria provided, single submitter
Uncertain significance
(May 19, 2017)
unknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Counsyl_Autosomal_Dominant_Disease_Classification_criteria_(2015)_v1.pdf

Citation Link

Summary from all submissions

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

Citations

PubMed

Cancer Susceptibility Gene Mutations in Individuals With Colorectal Cancer.

Yurgelun MB, Kulke MH, Fuchs CS, Allen BA, Uno H, Hornick JL, Ukaegbu CI, Brais LK, McNamara PG, Mayer RJ, Schrag D, Meyerhardt JA, Ng K, Kidd J, Singh N, Hartman AR, Wenstrup RJ, Syngal S.

J Clin Oncol. 2017 Apr 1;35(10):1086-1095. doi: 10.1200/JCO.2016.71.0012. Epub 2017 Jan 30.

PubMed [citation]
PMID:
28135145
PMCID:
PMC5455355

Targeted sequencing of 36 known or putative colorectal cancer susceptibility genes.

DeRycke MS, Gunawardena S, Balcom JR, Pickart AM, Waltman LA, French AJ, McDonnell S, Riska SM, Fogarty ZC, Larson MC, Middha S, Eckloff BW, Asmann YW, Ferber MJ, Haile RW, Gallinger S, Clendenning M, Rosty C, Win AK, Buchanan DD, Hopper JL, Newcomb PA, et al.

Mol Genet Genomic Med. 2017 Sep;5(5):553-569. doi: 10.1002/mgg3.317.

PubMed [citation]
PMID:
28944238
PMCID:
PMC5606870
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV000153979.12

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change replaces valine with glycine at codon 55 of the CDH1 protein (p.Val55Gly). The valine residue is highly conserved and there is a moderate physicochemical difference between valine and glycine. This variant is present in population databases (rs587778174, ExAC 0.003%). This variant has been reported in the literature in individual(s) affected with breast cancer (PMID: 24969172) and colorectal cancer (PMID: 28135145, 28944238). ClinVar contains an entry for this variant (Variation ID: 132769). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: Deleterious; PolyPhen-2: Probably Damaging; Align-GVGD: Class C0). 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

From Counsyl, SCV000785172.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 19, 2021

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