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NM_018249.6(CDK5RAP2):c.4041G>A (p.Leu1347=) AND not specified

Germline classification:
Benign (5 submissions)
Last evaluated:
Dec 18, 2013
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000145480.15

Allele description [Variation Report for NM_018249.6(CDK5RAP2):c.4041G>A (p.Leu1347=)]

NM_018249.6(CDK5RAP2):c.4041G>A (p.Leu1347=)

Gene:
CDK5RAP2:CDK5 regulatory subunit associated protein 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q33.2
Genomic location:
Preferred name:
NM_018249.6(CDK5RAP2):c.4041G>A (p.Leu1347=)
Other names:
p.L1347L:CTG>CTA
HGVS:
  • NC_000009.12:g.120419924C>T
  • NG_008999.1:g.165236G>A
  • NM_001011649.3:c.4041G>A
  • NM_001272039.2:c.3351G>A
  • NM_018249.6:c.4041G>AMANE SELECT
  • NP_001011649.1:p.Leu1347=
  • NP_001258968.1:p.Leu1117=
  • NP_060719.4:p.Leu1347=
  • NC_000009.11:g.123182202C>T
  • NM_018249.4:c.4041G>A
  • NM_018249.5:c.4041G>A
  • NR_073554.2:n.4307G>A
  • NR_073555.2:n.4230G>A
  • NR_073556.2:n.4437G>A
  • NR_073557.2:n.4310G>A
  • NR_073558.2:n.4307G>A
Links:
dbSNP: rs6478475
NCBI 1000 Genomes Browser:
rs6478475
Molecular consequence:
  • NR_073554.2:n.4307G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_073555.2:n.4230G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_073556.2:n.4437G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_073557.2:n.4310G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_073558.2:n.4307G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001011649.3:c.4041G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001272039.2:c.3351G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_018249.6:c.4041G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000167636GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Benign
(Dec 18, 2013)
germlineclinical testing

Citation Link,

SCV000192565Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2007)
Benign
(Feb 8, 2013)
germlineclinical testing

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

SCV000313212PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Benigngermlineclinical testing

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

SCV001953812Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Benigngermlineclinical testing

SCV001969489Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus

See additional submitters

no assertion criteria provided
Benigngermlineclinical testing

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

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee..

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]
PMID:
18414213

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From GeneDx, SCV000167636.10

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From Genetic Services Laboratory, University of Chicago, SCV000192565.1

#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 PreventionGenetics, part of Exact Sciences, SCV000313212.1

#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 Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001953812.1

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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001969489.1

#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: Mar 10, 2024