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NM_004360.5(CDH1):c.2595G>C (p.Trp865Cys) AND Familial cancer of breast

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 7, 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:
RCV003315418.4

Allele description [Variation Report for NM_004360.5(CDH1):c.2595G>C (p.Trp865Cys)]

NM_004360.5(CDH1):c.2595G>C (p.Trp865Cys)

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.2595G>C (p.Trp865Cys)
HGVS:
  • NC_000016.10:g.68833445G>C
  • NG_008021.1:g.101154G>C
  • NM_001317184.2:c.2412G>C
  • NM_001317185.2:c.1047G>C
  • NM_001317186.2:c.630G>C
  • NM_004360.5:c.2595G>CMANE SELECT
  • NP_001304113.1:p.Trp804Cys
  • NP_001304114.1:p.Trp349Cys
  • NP_001304115.1:p.Trp210Cys
  • NP_004351.1:p.Trp865Cys
  • LRG_301t1:c.2595G>C
  • LRG_301:g.101154G>C
  • NC_000016.9:g.68867348G>C
  • NM_004360.3:c.2595G>C
  • NM_004360.4:c.2595G>C
Protein change:
W210C
Links:
dbSNP: rs778019174
NCBI 1000 Genomes Browser:
rs778019174
Molecular consequence:
  • NM_001317184.2:c.2412G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317185.2:c.1047G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317186.2:c.630G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.2595G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Familial cancer of breast
Synonyms:
Breast cancer, familial; Hereditary breast cancer
Identifiers:
MONDO: MONDO:0016419; MedGen: C0346153; OMIM: 114480

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004015263KCCC/NGS Laboratory, Kuwait Cancer Control Center
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Jul 7, 2023) 		unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From KCCC/NGS Laboratory, Kuwait Cancer Control Center, SCV004015263.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces tryptophan, which is neutral and slightly polar, with cysteine, which is neutral and slightly polar, at codon 865 of the CDH1 protein (p.Trp865Cys).This amino acid position is highly conserved (PhyloP=9.71) . This variant is present in population databases (rs778019174, gnomAD 0.006%). This alteration has been identified via multi-gene panel testing for hereditary cancer risk assessment in a Turkish colorectal cancer cohort and a Chinese breast and/or ovarian cancer cohort (Erdem HB et al. Turk J Med Sci, 2020 06;50:1015-1021; Shao D et al. Cancer Sci, 2020 Feb;111:647-657).. ClinVar contains an entry for this variant (Variation ID: 216595). 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: "Probably Damaging"). 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024