NM_004360.5(CDH1):c.1697T>C (p.Ile566Thr) AND not provided

Clinical significance:Uncertain significance (Last evaluated: Dec 12, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000218074.2

Allele description [Variation Report for NM_004360.5(CDH1):c.1697T>C (p.Ile566Thr)]

NM_004360.5(CDH1):c.1697T>C (p.Ile566Thr)

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.1697T>C (p.Ile566Thr)
HGVS:
  • NC_000016.10:g.68819411T>C
  • NG_008021.1:g.87120T>C
  • NM_001317184.2:c.1514T>C
  • NM_001317185.2:c.149T>C
  • NM_001317186.2:c.-254-2590T>C
  • NM_004360.5:c.1697T>CMANE SELECT
  • NP_001304113.1:p.Ile505Thr
  • NP_001304114.1:p.Ile50Thr
  • NP_004351.1:p.Ile566Thr
  • LRG_301t1:c.1697T>C
  • LRG_301:g.87120T>C
  • NC_000016.9:g.68853314T>C
  • NM_004360.3:c.1697T>C
  • NM_004360.4:c.1697T>C
  • p.I566T
Protein change:
I505T
Links:
dbSNP: rs763292288
NCBI 1000 Genomes Browser:
rs763292288
Molecular consequence:
  • NM_001317186.2:c.-254-2590T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001317184.2:c.1514T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317185.2:c.149T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.1697T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000279925GeneDxcriteria provided, single submitter
Uncertain significance
(Dec 12, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000279925.9

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

Description

This variant is denoted CDH1 c.1697T>C at the cDNA level, p.Ile566Thr (I566T) at the protein level, and results in the change of an Isoleucine to a Threonine (ATA>ACA). This variant has been reported in an individual with triple negative breast cancer (Lovejoy 2018). CDH1 Ile566Thr was not observed at a significant allele frequency in large population cohorts (Lek 2016). This variant is located in Extracellular (Cadherin 4) domain (Brooks-Wilson 2004, Figuereido 2013). In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect. Based on currently available evidence, it is unclear whether CDH1 Ile566Thr is a pathogenic or benign variant. We consider it to be a variant of uncertain significance.

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

Last Updated: Apr 12, 2021

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