NM_004360.5(CDH1):c.2624T>C (p.Met875Thr) AND Hereditary diffuse gastric adenocarcinoma

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 9, 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:: RCV001338776.6

Allele description [Variation Report for NM_004360.5(CDH1):c.2624T>C (p.Met875Thr)]

NM_004360.5(CDH1):c.2624T>C (p.Met875Thr)

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.2624T>C (p.Met875Thr)

HGVS:

NC_000016.10:g.68833474T>C
NG_008021.1:g.101183T>C
NM_001317184.2:c.2441T>C
NM_001317185.2:c.1076T>C
NM_001317186.2:c.659T>C
NM_004360.5:c.2624T>CMANE SELECT
NP_001304113.1:p.Met814Thr
NP_001304114.1:p.Met359Thr
NP_001304115.1:p.Met220Thr
NP_004351.1:p.Met875Thr
LRG_301:g.101183T>C
NC_000016.9:g.68867377T>C

Protein change:

M220T

Links:

dbSNP: rs900118000

NCBI 1000 Genomes Browser:

rs900118000

Molecular consequence:

NM_001317184.2:c.2441T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001317185.2:c.1076T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001317186.2:c.659T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.2624T>C - 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

Recent activity

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autophagy-related protein 8f [Cucurbita maxima]
autophagy-related protein 8f [Cucurbita maxima]
gi|1281054974|ref|XP_022969729.1|

Protein
uncharacterized protein LOC120067824 [Benincasa hispida]
uncharacterized protein LOC120067824 [Benincasa hispida]
gi|1955838468|ref|XP_038875345.1|

Protein
uncharacterized protein LOC111789201 isoform X2 [Cucurbita pepo subsp. pepo]
uncharacterized protein LOC111789201 isoform X2 [Cucurbita pepo subsp. pepo]
gi|1333103587|ref|XP_023525663.1|

Protein
uncharacterized protein LOC111789201 isoform X3 [Cucurbita pepo subsp. pepo]
uncharacterized protein LOC111789201 isoform X3 [Cucurbita pepo subsp. pepo]
gi|1333103589|ref|XP_023525664.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001532470	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 9, 2022)	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

SCV001532470

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 9, 2022)

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, SCV001532470.3

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

Description

This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 875 of the CDH1 protein (p.Met875Thr). 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: 1035849). 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"). 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.

#	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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