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NM_004360.5(CDH1):c.1615A>G (p.Thr539Ala) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 24, 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:
RCV002390540.2

Allele description [Variation Report for NM_004360.5(CDH1):c.1615A>G (p.Thr539Ala)]

NM_004360.5(CDH1):c.1615A>G (p.Thr539Ala)

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.1615A>G (p.Thr539Ala)
HGVS:
  • NC_000016.10:g.68819329A>G
  • NG_008021.1:g.87038A>G
  • NM_001317184.2:c.1432A>G
  • NM_001317185.2:c.67A>G
  • NM_001317186.2:c.-254-2672A>G
  • NM_004360.5:c.1615A>GMANE SELECT
  • NP_001304113.1:p.Thr478Ala
  • NP_001304114.1:p.Thr23Ala
  • NP_004351.1:p.Thr539Ala
  • LRG_301t1:c.1615A>G
  • LRG_301:g.87038A>G
  • NC_000016.9:g.68853232A>G
  • NM_004360.3:c.1615A>G
Protein change:
T23A
Links:
dbSNP: rs864622070
NCBI 1000 Genomes Browser:
rs864622070
Molecular consequence:
  • NM_001317186.2:c.-254-2672A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317184.2:c.1432A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317185.2:c.67A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.1615A>G - missense variant - [Sequence Ontology: SO:0001583]

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

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002703182Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Apr 24, 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, SCV002703182.2

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

Description

The p.T539A variant (also known as c.1615A>G), located in coding exon 11 of the CDH1 gene, results from an A to G substitution at nucleotide position 1615. The threonine at codon 539 is replaced by alanine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. 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