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NM_004360.5(CDH1):c.2416G>T (p.Glu806Ter) AND Hereditary cancer-predisposing syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Dec 1, 2022
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:
RCV003182774.2

Allele description [Variation Report for NM_004360.5(CDH1):c.2416G>T (p.Glu806Ter)]

NM_004360.5(CDH1):c.2416G>T (p.Glu806Ter)

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.2416G>T (p.Glu806Ter)
HGVS:
  • NC_000016.10:g.68829774G>T
  • NG_008021.1:g.97483G>T
  • NM_001317184.2:c.2233G>T
  • NM_001317185.2:c.868G>T
  • NM_001317186.2:c.451G>T
  • NM_004360.5:c.2416G>TMANE SELECT
  • NP_001304113.1:p.Glu745Ter
  • NP_001304114.1:p.Glu290Ter
  • NP_001304115.1:p.Glu151Ter
  • NP_004351.1:p.Glu806Ter
  • NP_004351.1:p.Glu806Ter
  • LRG_301t1:c.2416G>T
  • LRG_301:g.97483G>T
  • LRG_301p1:p.Glu806Ter
  • NC_000016.9:g.68863677G>T
  • NM_004360.3:c.2416G>T
Protein change:
E151*
Molecular consequence:
  • NM_001317184.2:c.2233G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001317185.2:c.868G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001317186.2:c.451G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_004360.5:c.2416G>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

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003867732Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely pathogenic
(Dec 1, 2022) 		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, SCV003867732.2

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

Description

The p.E806* variant (also known as c.2416G>T), located in coding exon 15 of the CDH1 gene, results from a G to T substitution at nucleotide position 2416. This changes the amino acid from a glutamic acid to a stop codon within coding exon 15. This alteration occurs at the 3' terminus of theCDH1 gene, is not expected to trigger nonsense-mediated mRNA decay, and only impacts the last 77 amino acids of the protein. However, premature stop codons are typically deleterious in nature, the impacted region is critical for protein function and a significant portion of the protein is affected (Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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: Dec 22, 2024