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NM_004360.5(CDH1):c.2602C>T (p.Arg868Cys) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
May 1, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000478079.12

Allele description [Variation Report for NM_004360.5(CDH1):c.2602C>T (p.Arg868Cys)]

NM_004360.5(CDH1):c.2602C>T (p.Arg868Cys)

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.2602C>T (p.Arg868Cys)
HGVS:
  • NC_000016.10:g.68833452C>T
  • NG_008021.1:g.101161C>T
  • NM_001317184.2:c.2419C>T
  • NM_001317185.2:c.1054C>T
  • NM_001317186.2:c.637C>T
  • NM_004360.5:c.2602C>TMANE SELECT
  • NP_001304113.1:p.Arg807Cys
  • NP_001304114.1:p.Arg352Cys
  • NP_001304115.1:p.Arg213Cys
  • NP_004351.1:p.Arg868Cys
  • LRG_301t1:c.2602C>T
  • LRG_301:g.101161C>T
  • NC_000016.9:g.68867355C>T
  • NM_004360.3:c.2602C>T
  • NM_004360.4:c.2602C>T
Protein change:
R213C
Links:
dbSNP: rs864622630
NCBI 1000 Genomes Browser:
rs864622630
Molecular consequence:
  • NM_001317184.2:c.2419C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317185.2:c.1054C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317186.2:c.637C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.2602C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000565919GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Uncertain significance
(Dec 16, 2022)
germlineclinical testing

Citation Link,

SCV004140037CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Uncertain significance
(May 1, 2023)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000565919.5

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 15235021, 22850631)

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

From CeGaT Center for Human Genetics Tuebingen, SCV004140037.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

CDH1: PM2, PP3

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 20, 2024