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NM_004360.5(CDH1):c.406C>A (p.Gln136Lys) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 22, 2018
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:
RCV000780093.1

Allele description [Variation Report for NM_004360.5(CDH1):c.406C>A (p.Gln136Lys)]

NM_004360.5(CDH1):c.406C>A (p.Gln136Lys)

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.406C>A (p.Gln136Lys)
HGVS:
  • NC_000016.10:g.68808442C>A
  • NG_008021.1:g.76151C>A
  • NM_001317184.2:c.406C>A
  • NM_001317185.2:c.-1210C>A
  • NM_001317186.2:c.-1414C>A
  • NM_004360.5:c.406C>AMANE SELECT
  • NP_001304113.1:p.Gln136Lys
  • NP_004351.1:p.Gln136Lys
  • LRG_301t1:c.406C>A
  • LRG_301:g.76151C>A
  • NC_000016.9:g.68842345C>A
  • NM_004360.3:c.406C>A
Protein change:
Q136K
Links:
dbSNP: rs753886948
NCBI 1000 Genomes Browser:
rs753886948
Molecular consequence:
  • NM_001317185.2:c.-1210C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1414C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.406C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.406C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000917125Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Jan 22, 2018) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000917125.1

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

Description

Variant summary: The CDH1 c.406C>A (p.Gln136Lys) variant involves the alteration of a non-conserved nucleotide. 4/4 in silico tools predict a benign outcome for this variant (SNPsandGO not captured due to low reliability index). This variant was found in 4/246152 control chromosomes, predominantly observed in the South Asian subpopulation at a frequency of 0.00013 (4/30782). This frequency is about 5 times the estimated maximal expected allele frequency of a pathogenic CDH1 variant (0.0000283), suggesting this is likely a benign polymorphism found primarily in the populations of South Asian origin. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; nor evaluated for functional impact by in vivo/vitro studies. Because of the absence of clinical information and the lack of functional studies, the variant is classified as a variant of uncertain significance (VUS) until additional information becomes available.

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

Last Updated: Sep 29, 2024