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NM_004360.5(CDH1):c.1569T>G (p.Tyr523Ter) AND Hereditary cancer-predisposing syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 14, 2024
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:
RCV004037643.1

Allele description [Variation Report for NM_004360.5(CDH1):c.1569T>G (p.Tyr523Ter)]

NM_004360.5(CDH1):c.1569T>G (p.Tyr523Ter)

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.1569T>G (p.Tyr523Ter)
HGVS:
  • NC_000016.10:g.68819283T>G
  • NG_008021.1:g.86992T>G
  • NM_001317184.2:c.1386T>G
  • NM_001317185.2:c.21T>G
  • NM_001317186.2:c.-254-2718T>G
  • NM_004360.3:c.1569T>G
  • NM_004360.5:c.1569T>GMANE SELECT
  • NP_001304113.1:p.Tyr462Ter
  • NP_001304114.1:p.Tyr7Ter
  • NP_004351.1:p.Tyr523Ter
  • LRG_301t1:c.1569T>G
  • LRG_301:g.86992T>G
  • NC_000016.9:g.68853186T>G
Protein change:
Y462*
Links:
dbSNP: rs876659716
NCBI 1000 Genomes Browser:
rs876659716
Molecular consequence:
  • NM_001317186.2:c.-254-2718T>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317184.2:c.1386T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001317185.2:c.21T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_004360.5:c.1569T>G - 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
SCV005022263Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(Mar 14, 2024) 		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, SCV005022263.1

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

Description

The p.Y523* pathogenic mutation (also known as c.1569T>G), located in coding exon 11 of the CDH1 gene, results from a T to G substitution at nucleotide position 1569. This changes the amino acid from a tyrosine to a stop codon within coding exon 11. This variant has been observed in at least one individual with a personal and/or family history that is consistent with CDH1-related diffuse gastric and lobular breast cancer (Ambry internal data). 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