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NM_018249.6(CDK5RAP2):c.574C>T (p.Arg192Trp) AND Microcephaly 3, primary, autosomal recessive

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Jan 13, 2018
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:
RCV000145505.9

Allele description [Variation Report for NM_018249.6(CDK5RAP2):c.574C>T (p.Arg192Trp)]

NM_018249.6(CDK5RAP2):c.574C>T (p.Arg192Trp)

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.574C>T (p.Arg192Trp)
HGVS:
  • NC_000009.12:g.120536460G>A
  • NG_008999.1:g.48700C>T
  • NM_001011649.3:c.574C>T
  • NM_001272039.2:c.574C>T
  • NM_018249.6:c.574C>TMANE SELECT
  • NP_001011649.1:p.Arg192Trp
  • NP_001258968.1:p.Arg192Trp
  • NP_060719.4:p.Arg192Trp
  • NC_000009.11:g.123298738G>A
  • NM_018249.4:c.574C>T
  • NM_018249.5:c.574C>T
  • NR_073554.2:n.763C>T
  • NR_073555.2:n.763C>T
  • NR_073556.2:n.760C>T
  • NR_073557.2:n.763C>T
  • NR_073558.2:n.760C>T
Protein change:
R192W
Links:
dbSNP: rs369568564
NCBI 1000 Genomes Browser:
rs369568564
Molecular consequence:
  • NM_001011649.3:c.574C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001272039.2:c.574C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_018249.6:c.574C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_073554.2:n.763C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_073555.2:n.763C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_073556.2:n.760C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_073557.2:n.763C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_073558.2:n.760C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Microcephaly 3, primary, autosomal recessive
Identifiers:
MONDO: MONDO:0011488; MedGen: C1858108; Orphanet: 2512; OMIM: 604804

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000192592Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2007)		Uncertain significance
(Feb 8, 2013) 		germlineclinical testing

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

SCV000476961Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Uncertain significance
(Jan 13, 2018) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
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

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000192592.1

#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 Illumina Laboratory Services, Illumina, SCV000476961.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

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

Last Updated: May 1, 2024