NM_004360.5(CDH1):c.2530A>G (p.Ser844Gly) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 28, 2019
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:: RCV001015857.3

Allele description [Variation Report for NM_004360.5(CDH1):c.2530A>G (p.Ser844Gly)]

NM_004360.5(CDH1):c.2530A>G (p.Ser844Gly)

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.2530A>G (p.Ser844Gly)

HGVS:

NC_000016.10:g.68833380A>G
NG_008021.1:g.101089A>G
NM_001317184.2:c.2347A>G
NM_001317185.2:c.982A>G
NM_001317186.2:c.565A>G
NM_004360.5:c.2530A>GMANE SELECT
NP_001304113.1:p.Ser783Gly
NP_001304114.1:p.Ser328Gly
NP_001304115.1:p.Ser189Gly
NP_004351.1:p.Ser844Gly
LRG_301t1:c.2530A>G
LRG_301:g.101089A>G
NC_000016.9:g.68867283A>G
NM_004360.3:c.2530A>G

Protein change:

S189G

Links:

dbSNP: rs761400928

NCBI 1000 Genomes Browser:

rs761400928

Molecular consequence:

NM_001317184.2:c.2347A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001317185.2:c.982A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001317186.2:c.565A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.2530A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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uncharacterized protein E5676_scaffold447G001250 [Cucumis melo var. makuwa]
uncharacterized protein E5676_scaffold447G001250 [Cucumis melo var. makuwa]
gi|1731021904|gb|TYK09709.1||gnl|WG D|E5676_scaffold447G001250

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001176737	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Sep 28, 2019)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 15313375, 30287823 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001176737

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Sep 28, 2019)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

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

The unsolved enigma of CDH1 down-regulation in hereditary diffuse gastric cancer.

Concolino P, Papa V, Mozzetti S, Ferlini C, Pacelli F, Martinelli E, Ricci R, Filippetti F, Scambia G, Doglietto GB.

J Surg Res. 2004 Sep;121(1):50-5.

PubMed [citation]

PMID:: 15313375

Germline pathogenic variants of 11 breast cancer genes in 7,051 Japanese patients and 11,241 controls.

Momozawa Y, Iwasaki Y, Parsons MT, Kamatani Y, Takahashi A, Tamura C, Katagiri T, Yoshida T, Nakamura S, Sugano K, Miki Y, Hirata M, Matsuda K, Spurdle AB, Kubo M.

Nat Commun. 2018 Oct 4;9(1):4083. doi: 10.1038/s41467-018-06581-8.

PubMed [citation]

PMID:: 30287823
PMCID:: PMC6172276

Details of each submission

From Ambry Genetics, SCV001176737.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

The p.S844G variant (also known as c.2530A>G), located in coding exon 16 of the CDH1 gene, results from an A to G substitution at nucleotide position 2530. The serine at codon 844 is replaced by glycine, an amino acid with similar properties. This alteration has been reported with a carrier frequency of 0.00028 in 7051 unselected female breast cancer patients, 0.00 in 53 unselected male breast cancer patients, 0.00018 in 11241 female controls, and 0.0002 in 12490 male controls of Japanese ancestry (Momozawa Y et al. Nat Commun, 2018 10;9:4083). This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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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