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NM_004360.5(CDH1):c.1682dup (p.Tyr561Ter) AND Hereditary cancer-predisposing syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 15, 2021
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:
RCV002406052.2

Allele description [Variation Report for NM_004360.5(CDH1):c.1682dup (p.Tyr561Ter)]

NM_004360.5(CDH1):c.1682dup (p.Tyr561Ter)

Gene:
CDH1:cadherin 1 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
16q22.1
Genomic location:
Preferred name:
NM_004360.5(CDH1):c.1682dup (p.Tyr561Ter)
HGVS:
  • NC_000016.10:g.68819396dup
  • NG_008021.1:g.87105dup
  • NM_001317184.2:c.1499dup
  • NM_001317185.2:c.134dup
  • NM_001317186.2:c.-254-2605dup
  • NM_004360.5:c.1682dupMANE SELECT
  • NP_001304113.1:p.Tyr500Ter
  • NP_001304114.1:p.Tyr45Ter
  • NP_004351.1:p.Tyr561Ter
  • NP_004351.1:p.Tyr561Terfs
  • LRG_301t1:c.1682dup
  • LRG_301:g.87105dup
  • LRG_301p1:p.Tyr561Terfs
  • NC_000016.9:g.68853298_68853299insA
  • NC_000016.9:g.68853299dup
  • NM_004360.3:c.1682dup
  • NM_004360.3:c.1682dupA
Protein change:
Y45*
Molecular consequence:
  • NM_001317186.2:c.-254-2605dup - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317184.2:c.1499dup - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001317185.2:c.134dup - nonsense - [Sequence Ontology: SO:0001587]
  • NM_004360.5:c.1682dup - 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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002710678Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Sep 15, 2021) 		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, SCV002710678.2

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

Description

The c.1682dupA pathogenic mutation, located in coding exon 11 of the CDH1 gene, results from a duplication of A at nucleotide position 1682, causing a translational frameshift with a predicted alternate stop codon (p.Y561*). This mutation was reported in one of thirty-eight families clinically diagnosed with hereditary diffuse gastric cancer (HDGC) (Kaurah P et al. JAMA. 2007 Jun 6;297(21):2360-72). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

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

Last Updated: Sep 29, 2024