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NM_004360.5(CDH1):c.100G>A (p.Ala34Thr) 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:
RCV001355198.1

Allele description [Variation Report for NM_004360.5(CDH1):c.100G>A (p.Ala34Thr)]

NM_004360.5(CDH1):c.100G>A (p.Ala34Thr)

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.100G>A (p.Ala34Thr)
HGVS:
  • NC_000016.10:g.68738348G>A
  • NG_008021.1:g.6057G>A
  • NM_001317184.2:c.100G>A
  • NM_001317185.2:c.-1516G>A
  • NM_001317186.2:c.-1720G>A
  • NM_004360.5:c.100G>AMANE SELECT
  • NP_001304113.1:p.Ala34Thr
  • NP_004351.1:p.Ala34Thr
  • LRG_301:g.6057G>A
  • NC_000016.9:g.68772251G>A
  • NM_004360.4:c.100G>A
Protein change:
A34T
Links:
dbSNP: rs1486768673
NCBI 1000 Genomes Browser:
rs1486768673
Molecular consequence:
  • NM_001317185.2:c.-1516G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1720G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.100G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.100G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001550012Department 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 providedunknownyes1not 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), SCV001550012.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The CDH1 p.Ala34Thr variant was not identified in the literature nor was it identified in the dbSNP, ClinVar, Cosmic, MutDB, Zhejiang University database, the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The p.Ala34 residue is not conserved in mammals and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a 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 provided1not providednot providednot provided

Last Updated: Jun 23, 2024