NM_004360.5(CDH1):c.2529_2530delinsAG (p.Ser844Gly) AND Hereditary diffuse gastric adenocarcinoma

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 10, 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:: RCV001054061.7

Allele description [Variation Report for NM_004360.5(CDH1):c.2529_2530delinsAG (p.Ser844Gly)]

NM_004360.5(CDH1):c.2529_2530delinsAG (p.Ser844Gly)

Gene:

CDH1:cadherin 1 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

16q22.1

Genomic location:

Preferred name:

NM_004360.5(CDH1):c.2529_2530delinsAG (p.Ser844Gly)

HGVS:

NC_000016.10:g.68833379_68833380delinsAG
NG_008021.1:g.101088_101089delinsAG
NM_001317184.2:c.2346_2347delinsAG
NM_001317185.2:c.981_982delinsAG
NM_001317186.2:c.564_565delinsAG
NM_004360.5:c.2529_2530delinsAGMANE SELECT
NP_001304113.1:p.Ser783Gly
NP_001304114.1:p.Ser328Gly
NP_001304115.1:p.Ser189Gly
NP_004351.1:p.Ser844Gly
LRG_301t1:c.2529_2530delinsAG
LRG_301:g.101088_101089delinsAG
NC_000016.9:g.68867282_68867283delinsAG
NM_004360.3:c.2529_2530delTAinsAG
NM_004360.3:c.2529_2530delinsAG

Protein change:

S189G

Links:

dbSNP: rs1961538497

NCBI 1000 Genomes Browser:

rs1961538497

Molecular consequence:

NM_001317184.2:c.2346_2347delinsAG - missense variant - [Sequence Ontology: SO:0001583]
NM_001317185.2:c.981_982delinsAG - missense variant - [Sequence Ontology: SO:0001583]
NM_001317186.2:c.564_565delinsAG - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.2529_2530delinsAG - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001218354	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 10, 2023)	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

SCV001218354

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 10, 2023)

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 Invitae, SCV001218354.5

#	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 serine, which is neutral and polar, with glycine, which is neutral and non-polar, at codon 844 of the CDH1 protein (p.Ser844Gly). Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. 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: 849990). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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: May 1, 2024

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