NM_004360.5(CDH1):c.2480A>G (p.Tyr827Cys) AND Hereditary diffuse gastric adenocarcinoma

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 23, 2017
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:: RCV000548051.7

Allele description [Variation Report for NM_004360.5(CDH1):c.2480A>G (p.Tyr827Cys)]

NM_004360.5(CDH1):c.2480A>G (p.Tyr827Cys)

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.2480A>G (p.Tyr827Cys)

HGVS:

NC_000016.10:g.68833330A>G
NG_008021.1:g.101039A>G
NM_001317184.2:c.2297A>G
NM_001317185.2:c.932A>G
NM_001317186.2:c.515A>G
NM_004360.5:c.2480A>GMANE SELECT
NP_001304113.1:p.Tyr766Cys
NP_001304114.1:p.Tyr311Cys
NP_001304115.1:p.Tyr172Cys
NP_004351.1:p.Tyr827Cys
LRG_301t1:c.2480A>G
LRG_301:g.101039A>G
NC_000016.9:g.68867233A>G
NM_004360.3:c.2480A>G

Protein change:

Y172C

Links:

dbSNP: rs1555518224

NCBI 1000 Genomes Browser:

rs1555518224

Molecular consequence:

NM_001317184.2:c.2297A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001317185.2:c.932A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001317186.2:c.515A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.2480A>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

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CBR NADH:cytochrome B5 reductase 1 [Arabidopsis thaliana]
CBR NADH:cytochrome B5 reductase 1 [Arabidopsis thaliana]
Gene ID:831645

Gene
831645[uid] AND (alive[prop]) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000637806	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 23, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000637806

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 23, 2017)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV000637806.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

In summary, this variant has uncertain impact on CDH1 function. The available evidence is currently insufficient to determine its role in disease. Therefore, it has been classified as a Variant of Uncertain Significance. 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"). This variant has not been reported in the literature in individuals with a CDH1-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces tyrosine with cysteine at codon 827 of the CDH1 protein (p.Tyr827Cys). The tyrosine residue is highly conserved and there is a large physicochemical difference between tyrosine and cysteine.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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