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NM_004360.5(CDH1):c.1566A>T (p.Thr522=) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 16, 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:
RCV002397435.3

Allele description [Variation Report for NM_004360.5(CDH1):c.1566A>T (p.Thr522=)]

NM_004360.5(CDH1):c.1566A>T (p.Thr522=)

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.1566A>T (p.Thr522=)
HGVS:
  • NC_000016.10:g.68819280A>T
  • NG_008021.1:g.86989A>T
  • NM_001317184.2:c.1383A>T
  • NM_001317185.2:c.18A>T
  • NM_001317186.2:c.-254-2721A>T
  • NM_004360.5:c.1566A>TMANE SELECT
  • NP_001304113.1:p.Thr461=
  • NP_001304114.1:p.Thr6=
  • NP_004351.1:p.Thr522=
  • LRG_301t1:c.1566A>T
  • LRG_301:g.86989A>T
  • NC_000016.9:g.68853183A>T
  • NM_004360.3:c.1566A>T
Links:
dbSNP: rs1555516521
NCBI 1000 Genomes Browser:
rs1555516521
Molecular consequence:
  • NM_001317186.2:c.-254-2721A>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317184.2:c.1383A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001317185.2:c.18A>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_004360.5:c.1566A>T - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV002709933Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Sep 16, 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, SCV002709933.3

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

Description

The c.1566A>T variant (also known as p.T522T), located in coding exon 11 of the CDH1 gene, results from an A to T substitution at nucleotide position 1566. This nucleotide substitution does not change the at codon 522. However, this change occurs in the first base pair of coding exon 11, which makes it likely to have some effect on normal mRNA splicing. This nucleotide position is poorly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration may weaken the native splice acceptor site. RNA studies have demonstrated that this alteration results in an incomplete splice defect involving exons excluded from naturally occurring transcripts; the clinical impact of this abnormal splicing is unknown at this time (Ambry internal data). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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

Last Updated: Sep 29, 2024