NM_006727.5(CDH10):c.1885G>A (p.Val629Ile) AND not provided

Germline classification:
Uncertain significance (1 submission)
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001354411.1

Allele description [Variation Report for NM_006727.5(CDH10):c.1885G>A (p.Val629Ile)]

NM_006727.5(CDH10):c.1885G>A (p.Val629Ile)

Gene:
CDH10:cadherin 10 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5p14.2
Genomic location:
Preferred name:
NM_006727.5(CDH10):c.1885G>A (p.Val629Ile)
HGVS:
  • NC_000005.10:g.24488145C>T
  • NM_001317222.2:c.103G>A
  • NM_001317224.2:c.1879G>A
  • NM_001362460.1:c.*3G>A
  • NM_006727.5:c.1885G>AMANE SELECT
  • NP_001304151.1:p.Val35Ile
  • NP_001304153.1:p.Val627Ile
  • NP_006718.2:p.Val629Ile
  • NC_000005.9:g.24488254C>T
Protein change:
V35I
Links:
dbSNP: rs2111613494
NCBI 1000 Genomes Browser:
rs2111613494
Molecular consequence:
  • NM_001362460.1:c.*3G>A - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001317222.2:c.103G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001317224.2:c.1879G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006727.5:c.1885G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001549024Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Uncertain significanceunknownclinical testing

Help

Summary from all submissions

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

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001549024.1

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

Description

The CDH10 p.Val627Ile variant was not identified in the literature nor was it identified in dbSNP, ClinVar, Cosmic or in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, or the Genome Aggregation Database (March 6, 2019, v2.1.1). The p.Val627 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The p.(Val627Ile) variant occurs in the last three bases of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. In addition, 2 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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

Last Updated: Dec 24, 2023