NM_000075.4(CDK4):c.447A>G (p.Thr149=) AND not provided

Clinical significance:Benign (Last evaluated: Apr 26, 2017)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000586842.6

Allele description [Variation Report for NM_000075.4(CDK4):c.447A>G (p.Thr149=)]

NM_000075.4(CDK4):c.447A>G (p.Thr149=)

Gene:
CDK4:cyclin dependent kinase 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q14.1
Genomic location:
Preferred name:
NM_000075.4(CDK4):c.447A>G (p.Thr149=)
HGVS:
  • NC_000012.12:g.57750998T>C
  • NG_007484.2:g.6384A>G
  • NM_000075.4:c.447A>GMANE SELECT
  • NP_000066.1:p.Thr149=
  • LRG_490t1:c.447A>G
  • LRG_490:g.6384A>G
  • NC_000012.11:g.58144781T>C
  • NM_000075.2:c.447A>G
  • NM_000075.3:c.447A>G
  • p.T149T
  • p.Thr149Thr
Links:
dbSNP: rs2069501
NCBI 1000 Genomes Browser:
rs2069501
Molecular consequence:
  • NM_000075.4:c.447A>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000695317Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Benign
(Jan 25, 2016)
germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV000889266Quest Diagnostics Nichols Institute San Juan Capistranocriteria provided, single submitter
Benign
(Apr 26, 2017)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001892974GeneDxcriteria provided, single submitter
Benign
(Mar 3, 2015)
germlineclinical testing

Citation Link

Summary from all submissions

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

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000695317.1

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

Description

Variant summary: The c.447A>G in CDK4 gene is a synonymous change that involves a non-conserved nucleotide. 5/5 programs in Alamut predict that this variant does not affect normal splicing, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in the control population dataset of ExAC at an overall frequency of 0.23%, being most prevalent in individuals of African descent (2.5%), including several homozygotes. The observed frequency exceeds the maximum expected allele frequency for a pathogenic CDK4 variant of 0.002%, suggesting that it is a common polymorphism. The variant has been reported as Benign by reputable database/clinical laboratory without providing evidence to independently evaluate. Taken together, this variant has been classified as Benign.

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000889266.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV001892974.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2021

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