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NM_004360.5(CDH1):c.1679C>G (p.Thr560Arg) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 16, 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:
RCV003477778.1

Allele description [Variation Report for NM_004360.5(CDH1):c.1679C>G (p.Thr560Arg)]

NM_004360.5(CDH1):c.1679C>G (p.Thr560Arg)

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.1679C>G (p.Thr560Arg)
Other names:
NM_004360.4(CDH1):c.1679C>G
HGVS:
  • NC_000016.10:g.68819393C>G
  • NG_008021.1:g.87102C>G
  • NM_001317184.2:c.1496C>G
  • NM_001317185.2:c.131C>G
  • NM_001317186.2:c.-254-2608C>G
  • NM_004360.5:c.1679C>GMANE SELECT
  • NP_001304113.1:p.Thr499Arg
  • NP_001304114.1:p.Thr44Arg
  • NP_004351.1:p.Thr560Arg
  • LRG_301t1:c.1679C>G
  • LRG_301:g.87102C>G
  • NC_000016.9:g.68853296C>G
  • NM_004360.3:c.1679C>G
  • NM_004360.4:c.1679C>G
Protein change:
T44R
Links:
dbSNP: rs746481984
NCBI 1000 Genomes Browser:
rs746481984
Molecular consequence:
  • NM_001317186.2:c.-254-2608C>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317184.2:c.1496C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317185.2:c.131C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.1679C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004220801Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(Quest Diagnostics criteria)		Pathogenic
(Jun 16, 2023) 		unknownclinical testing

PubMed (9)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women.

Breast Cancer Association Consortium., Dorling L, Carvalho S, Allen J, González-Neira A, Luccarini C, Wahlström C, Pooley KA, Parsons MT, Fortuno C, Wang Q, Bolla MK, Dennis J, Keeman R, Alonso MR, Álvarez N, Herraez B, Fernandez V, Núñez-Torres R, Osorio A, Valcich J, Li M, et al.

N Engl J Med. 2021 Feb 4;384(5):428-439. doi: 10.1056/NEJMoa1913948. Epub 2021 Jan 20.

PubMed [citation]
PMID:
33471991
PMCID:
PMC7611105

Genotype-first approach to identify associations between CDH1 germline variants and cancer phenotypes: a multicentre study by the European Reference Network on Genetic Tumour Risk Syndromes.

Garcia-Pelaez J, Barbosa-Matos R, Lobo S, Dias A, Garrido L, Castedo S, Sousa S, Pinheiro H, Sousa L, Monteiro R, Maqueda JJ, Fernandes S, Carneiro F, Pinto N, Lemos C, Pinto C, Teixeira MR, Aretz S, Bajalica-Lagercrantz S, Balmaña J, Blatnik A, Benusiglio PR, et al.

Lancet Oncol. 2023 Jan;24(1):91-106. doi: 10.1016/S1470-2045(22)00643-X. Epub 2022 Nov 24. Erratum in: Lancet Oncol. 2023 Jan;24(1):e10. doi: 10.1016/S1470-2045(22)00761-6.

PubMed [citation]
PMID:
36436516
PMCID:
PMC9810541
See all PubMed Citations (9)

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004220801.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (9)

Description

The CDH1 c.1679C>G (p.Thr560Arg) variant activates a cryptic splice donor site and has been shown in the published literature to cause aberrant mRNA splicing and the production of a truncated CDH1 transcript (PMID: 27880784 (2016)). Further experimental studies showed this variant has deleterious effects on CDH1 protein function (PMID: 29769627 (2018)). This variant has been reported in multiple individuals with diffused gastric cancer and lobular breast cancer (PMIDs: 36436516 (2022), 34949788 (2022), 29769627 (2018), 23709761 (2013)), and segregated with disease in at least two families with HDGC (PMIDs: 33268956 (2020), 27880784 (2016)). This variant has not been reported in large, multi-ethnic general populations (Genome Aggregation Database, http://gnomad.broadinstitute.org). Based on the available information, this variant is classified as pathogenic.

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

Last Updated: Sep 29, 2024