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NM_004360.5(CDH1):c.2480dup (p.Tyr827Ter) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
May 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:
RCV001015647.3

Allele description [Variation Report for NM_004360.5(CDH1):c.2480dup (p.Tyr827Ter)]

NM_004360.5(CDH1):c.2480dup (p.Tyr827Ter)

Gene:
CDH1:cadherin 1 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
16q22.1
Genomic location:
Preferred name:
NM_004360.5(CDH1):c.2480dup (p.Tyr827Ter)
HGVS:
  • NC_000016.10:g.68833330dup
  • NG_008021.1:g.101039dup
  • NM_001317184.2:c.2297dup
  • NM_001317185.2:c.932dup
  • NM_001317186.2:c.515dup
  • NM_004360.5:c.2480dupMANE SELECT
  • NP_001304113.1:p.Tyr766Ter
  • NP_001304114.1:p.Tyr311Ter
  • NP_001304115.1:p.Tyr172Ter
  • NP_004351.1:p.Tyr827Ter
  • LRG_301t1:c.2480dup
  • LRG_301:g.101039dup
  • NC_000016.9:g.68867233dup
  • NM_004360.3:c.2480dupA
Protein change:
Y172*
Links:
dbSNP: rs1596976243
NCBI 1000 Genomes Browser:
rs1596976243
Molecular consequence:
  • NM_001317184.2:c.2297dup - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001317185.2:c.932dup - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001317186.2:c.515dup - nonsense - [Sequence Ontology: SO:0001587]
  • NM_004360.5:c.2480dup - nonsense - [Sequence Ontology: SO:0001587]

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

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001176504Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(May 28, 2019) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV001176504.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.2480dupA variant, located in coding exon 16 of the CDH1 gene, results from a duplication of A at nucleotide position 2480, causing a translational frameshift with a predicted alternate stop codon (p.Y827*). Frameshifts are typically deleterious in nature, however, this frameshift occurs at the 3' terminus of CDH1, is not expected to trigger nonsense-mediated mRNA decay, and impacts only the last 56 amino acids of the protein. The exact functional impact of these altered amino acids is unknown at this time; however, the deleted region eliminates the catenin-binding domain, which is important for regulating the stability of cadherin mediated cell-cell adhesion (Ishiyama N et al. Cell 2010 Apr; 141(1):117-28). Based on the majority of available evidence to date, this variant is likely to be pathogenic.

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

Last Updated: May 1, 2024