NM_004360.5(CDH1):c.1634G>C (p.Arg545Pro) AND Hereditary diffuse gastric adenocarcinoma

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 20, 2021
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:: RCV001899709.4

Allele description [Variation Report for NM_004360.5(CDH1):c.1634G>C (p.Arg545Pro)]

NM_004360.5(CDH1):c.1634G>C (p.Arg545Pro)

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.1634G>C (p.Arg545Pro)

HGVS:

NC_000016.10:g.68819348G>C
NG_008021.1:g.87057G>C
NM_001317184.2:c.1451G>C
NM_001317185.2:c.86G>C
NM_001317186.2:c.-254-2653G>C
NM_004360.5:c.1634G>CMANE SELECT
NP_001304113.1:p.Arg484Pro
NP_001304114.1:p.Arg29Pro
NP_004351.1:p.Arg545Pro
LRG_301:g.87057G>C
NC_000016.9:g.68853251G>C

Protein change:

R29P

Links:

dbSNP: rs587780115

NCBI 1000 Genomes Browser:

rs587780115

Molecular consequence:

NM_001317186.2:c.-254-2653G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001317184.2:c.1451G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001317185.2:c.86G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.1634G>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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thyroid hormone receptor beta isoform a [Homo sapiens]
thyroid hormone receptor beta isoform a [Homo sapiens]
gi|1765945235|ref|NP_001361753.1|

Protein
lysine-specific demethylase PHF2 isoform X4 [Homo sapiens]
lysine-specific demethylase PHF2 isoform X4 [Homo sapiens]
gi|2462625011|ref|XP_054219088.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002141301	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 20, 2021)	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

SCV002141301

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 20, 2021)

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, SCV002141301.3

#	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 arginine with proline at codon 545 of the CDH1 protein (p.Arg545Pro). The arginine residue is moderately conserved and there is a moderate physicochemical difference between arginine and proline. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with CDH1-related conditions. 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: "Possibly 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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