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NM_004360.5(CDH1):c.2446A>T (p.Lys816Ter) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Feb 2, 2018
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:
RCV000593954.4

Allele description [Variation Report for NM_004360.5(CDH1):c.2446A>T (p.Lys816Ter)]

NM_004360.5(CDH1):c.2446A>T (p.Lys816Ter)

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.2446A>T (p.Lys816Ter)
HGVS:
  • NC_000016.10:g.68833296A>T
  • NG_008021.1:g.101005A>T
  • NM_001317184.2:c.2263A>T
  • NM_001317185.2:c.898A>T
  • NM_001317186.2:c.481A>T
  • NM_004360.5:c.2446A>TMANE SELECT
  • NP_001304113.1:p.Lys755Ter
  • NP_001304114.1:p.Lys300Ter
  • NP_001304115.1:p.Lys161Ter
  • NP_004351.1:p.Lys816Ter
  • LRG_301t1:c.2446A>T
  • LRG_301:g.101005A>T
  • NC_000016.9:g.68867199A>T
  • NC_000016.9:g.68867199A>T
  • NM_004360.3:c.2446A>T
  • NM_004360.5(CDH1):c.2446A>TMANE SELECT
  • p.Lys816Ter
Protein change:
K161*
Links:
dbSNP: rs1555518211
NCBI 1000 Genomes Browser:
rs1555518211
Molecular consequence:
  • NM_001317184.2:c.2263A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001317185.2:c.898A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001317186.2:c.481A>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_004360.5:c.2446A>T - 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
SCV000700320Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Feb 2, 2018) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV000700320.5

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

Description

The p.K816* variant (also known as c.2446A>T), located in coding exon 16 of the CDH1 gene, results from an A to T substitution at nucleotide position 2446. This changes the amino acid from a lysine to a stop codon within coding exon 16. Premature stop codons are typically deleterious in nature, however, this stop codon occurs at the 3' terminus of CDH1, is not expected to trigger nonsense-mediated mRNA decay, and impacts only the last 67 amino acids of the protein. The exact functional impact of these removed 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;141:117-28). 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: Sep 29, 2024