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NM_004360.5(CDH1):c.1710del (p.Asn570fs) AND Hereditary cancer-predisposing syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 20, 2020
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:
RCV001189119.3

Allele description [Variation Report for NM_004360.5(CDH1):c.1710del (p.Asn570fs)]

NM_004360.5(CDH1):c.1710del (p.Asn570fs)

Gene:
CDH1:cadherin 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16q22.1
Genomic location:
Preferred name:
NM_004360.5(CDH1):c.1710del (p.Asn570fs)
HGVS:
  • NC_000016.10:g.68819424del
  • NG_008021.1:g.87133del
  • NM_001317184.2:c.1527del
  • NM_001317185.2:c.162del
  • NM_001317186.2:c.-254-2577del
  • NM_004360.5:c.1710delMANE SELECT
  • NP_001304113.1:p.Asn509fs
  • NP_001304114.1:p.Asn54fs
  • NP_004351.1:p.Asn570fs
  • LRG_301:g.87133del
  • NC_000016.9:g.68853327del
  • NM_004360.4:c.1710del
Protein change:
N509fs
Links:
dbSNP: rs1961081411
NCBI 1000 Genomes Browser:
rs1961081411
Molecular consequence:
  • NM_001317184.2:c.1527del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001317185.2:c.162del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_004360.5:c.1710del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001317186.2:c.-254-2577del - intron variant - [Sequence Ontology: SO:0001627]

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001356324Color Diagnostics, LLC DBA Color Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Sep 20, 2020) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot 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 Color Diagnostics, LLC DBA Color Health, SCV001356324.2

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

Description

This variant deletes 1 nucleotide in exon 11 of the CDH1 gene, creating a premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. To our knowledge, functional studies have not been reported for this variant. This variant has been reported in two related individuals affected with diffuse gastric cancer (PMID: 11968084). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of CDH1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.

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

Last Updated: Sep 29, 2024