NM_004360.5(CDH1):c.344C>G (p.Thr115Arg) AND Hereditary diffuse gastric adenocarcinoma

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 30, 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:: RCV001213279.8

Allele description [Variation Report for NM_004360.5(CDH1):c.344C>G (p.Thr115Arg)]

NM_004360.5(CDH1):c.344C>G (p.Thr115Arg)

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.344C>G (p.Thr115Arg)

HGVS:

NC_000016.10:g.68801850C>G
NG_008021.1:g.69559C>G
NM_001317184.2:c.344C>G
NM_001317185.2:c.-1272C>G
NM_001317186.2:c.-1476C>G
NM_004360.5:c.344C>GMANE SELECT
NP_001304113.1:p.Thr115Arg
NP_004351.1:p.Thr115Arg
LRG_301t1:c.344C>G
LRG_301:g.69559C>G
NC_000016.9:g.68835753C>G
NM_004360.3:c.344C>G

Protein change:

T115R

Links:

dbSNP: rs370973869

NCBI 1000 Genomes Browser:

rs370973869

Molecular consequence:

NM_001317185.2:c.-1272C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317186.2:c.-1476C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317184.2:c.344C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.344C>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

Recent activity

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hypothetical protein CLOSTHATH_00022 [Hungatella hathewayi DSM 13479]
hypothetical protein CLOSTHATH_00022 [Hungatella hathewayi DSM 13479]
gi|288869465|gb|EFD01764.1||gnl|WGS |CLOSTHATH_00022

Protein
phosphocarrier, HPr family [Hungatella hathewayi DSM 13479]
phosphocarrier, HPr family [Hungatella hathewayi DSM 13479]
gi|288869463|gb|EFD01762.1||gnl|WGS |CLOSTHATH_00020

Protein
NADH dehydrogenase subunit 1 (mitochondrion) [Celyphus obtectus]
NADH dehydrogenase subunit 1 (mitochondrion) [Celyphus obtectus]
gi|1179695926|gb|ARI44185.1|

Protein
PREDICTED: Pteropus vampyrus VPS18, CORVET/HOPS core subunit (VPS18), transcript...
PREDICTED: Pteropus vampyrus VPS18, CORVET/HOPS core subunit (VPS18), transcript variant X2, mRNA
gi|1331424228|ref|XM_011354932.2|

Nucleotide
Seseli tortuosum subsp. tortuosum ribulose-1,5-bisphosphate carboxylase/oxygenas...
Seseli tortuosum subsp. tortuosum ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene, partial cds; chloroplast
gi|2076888151|gb|MW662022.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001384905	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 30, 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

SCV001384905

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 30, 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, SCV001384905.5

#	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 threonine, which is neutral and polar, with arginine, which is basic and polar, at codon 115 of the CDH1 protein (p.Thr115Arg). 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 943148). This variant has not been reported in the literature in individuals affected with CDH1-related conditions. This variant is not present in population databases (gnomAD no frequency).

#	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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