NM_004360.5(CDH1):c.151G>A (p.Val51Ile) AND Hereditary diffuse gastric adenocarcinoma

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 4, 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:: RCV003767180.2

Allele description [Variation Report for NM_004360.5(CDH1):c.151G>A (p.Val51Ile)]

NM_004360.5(CDH1):c.151G>A (p.Val51Ile)

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.151G>A (p.Val51Ile)

HGVS:

NC_000016.10:g.68738399G>A
NG_008021.1:g.6108G>A
NM_001317184.2:c.151G>A
NM_001317185.2:c.-1465G>A
NM_001317186.2:c.-1669G>A
NM_004360.5:c.151G>AMANE SELECT
NP_001304113.1:p.Val51Ile
NP_004351.1:p.Val51Ile
LRG_301t1:c.151G>A
LRG_301:g.6108G>A
NC_000016.9:g.68772302G>A
NM_004360.3:c.151G>A

Protein change:

V51I

Links:

dbSNP: rs1555509780

NCBI 1000 Genomes Browser:

rs1555509780

Molecular consequence:

NM_001317185.2:c.-1465G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317186.2:c.-1669G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317184.2:c.151G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.151G>A - 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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Mus musculus nuclear factor of kappa light polypeptide gene enhancer in B cells ...
Mus musculus nuclear factor of kappa light polypeptide gene enhancer in B cells inhibitor like 1 (Nfkbil1), transcript variant 1, mRNA
gi|1426138328|ref|NM_010909.5|

Nucleotide
Lake water metagenome isolate AG_325, whole genome shotgun sequencing project
Lake water metagenome isolate AG_325, whole genome shotgun sequencing project
gi|2502580670|gb|JARVMD000000000.1| D010000000

Nucleotide
Homo sapiens matrin 3 (MATR3), transcript variant 25, mRNA
Homo sapiens matrin 3 (MATR3), transcript variant 25, mRNA
gi|2182782309|ref|NM_001400461.1|

Nucleotide
MIMS Environmental/Metagenome sample from lake water metagenome
MIMS Environmental/Metagenome sample from lake water metagenome

biosample
MIMAG Metagenome-assembled Genome sample from Aquabacterium sp.
MIMAG Metagenome-assembled Genome sample from Aquabacterium sp.

biosample

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004611263	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 4, 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

SCV004611263

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 4, 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV004611263.1

#	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 valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 51 of the CDH1 protein (p.Val51Ile). 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: 483266). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The isoleucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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

ClinVar

Relating variation to medicine