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NM_004360.5(CDH1):c.-50C>G AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 5, 2016
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:
RCV000220774.6

Allele description [Variation Report for NM_004360.5(CDH1):c.-50C>G]

NM_004360.5(CDH1):c.-50C>G

Genes:
LOC130059290:ATAC-STARR-seq lymphoblastoid silent region 7650 [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.-50C>G
HGVS:
  • NC_000016.10:g.68737366C>G
  • NG_008021.1:g.5075C>G
  • NM_001317184.2:c.-50C>G
  • NM_001317185.2:c.-1665C>G
  • NM_001317186.2:c.-1869C>G
  • NM_004360.5:c.-50C>GMANE SELECT
  • LRG_301t1:c.-50C>G
  • LRG_301:g.5075C>G
  • NC_000016.9:g.68771269C>G
  • NM_004360.3:c.-50C>G
  • NM_004360.5(CDH1):c.-50C>GMANE SELECT
Links:
dbSNP: rs876660969
NCBI 1000 Genomes Browser:
rs876660969
Molecular consequence:
  • NM_001317184.2:c.-50C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317185.2:c.-1665C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1869C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_004360.5:c.-50C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000278908GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Feb 5, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000278908.9

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

Description

This variant is denoted CDH1 c.-50C>G, and describes a nucleotide substitution 50 base pairs upstream of the CDH1 ATG translational start site in the 5Â’ untranslated region (UTR). This variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations, and the base that is altered is not conserved across species. CDH1 c.-50C>G is not predicted to affect the Kozak consensus sequence or to affect splicing. Although this particular variant has not, to our knowledge, been published in the literature, variants have been reported in this region at c.-49 and c.-54 per HGMD (Stenson 2013). Luciferase reporter assays showed that c.-49G>T contributes to a slight increase in promoter activity, while c.-54G>C significantly decreases (p = 0.003) promoter activity (Nakamura 2002, Chen 2013). Based on currently available information, we consider CDH1 c.-50C>G to be a variant of uncertain significance.

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

Last Updated: Oct 13, 2024