VCV000210634.45 - ClinVar

NM_018249.6(CDK5RAP2):c.2003A>G (p.Tyr668Cys)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(9)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Conflicting classifications of pathogenicity
Uncertain significance(5); Likely benign(2)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_018249.6(CDK5RAP2):c.2003A>G (p.Tyr668Cys)

Variation ID: 210634 Accession: VCV000210634.45

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 9q33.2 9: 120467963 (GRCh38) [ NCBI UCSC ] 9: 123230241 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Oct 5, 2015	Oct 20, 2024	Jan 30, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_018249.6:c.2003A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_060719.4:p.Tyr668Cys	missense
NM_001011649.3:c.2003A>G	NP_001011649.1:p.Tyr668Cys	missense
NM_001272039.2:c.2000A>G	NP_001258968.1:p.Tyr667Cys	missense
NR_073554.2:n.2189A>G		non-coding transcript variant
NR_073555.2:n.2192A>G		non-coding transcript variant
NR_073556.2:n.2319A>G		non-coding transcript variant
NR_073557.2:n.2192A>G		non-coding transcript variant
NR_073558.2:n.2189A>G		non-coding transcript variant
NC_000009.12:g.120467963T>C
NC_000009.11:g.123230241T>C
NG_008999.1:g.117197A>G

... more HGVS ... less HGVS

Protein change

Y668C, Y667C

Other names

Canonical SPDI

NC_000009.12:120467962:T:C

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Exome Aggregation Consortium (ExAC) 0.00027

Trans-Omics for Precision Medicine (TOPMed) 0.00028

The Genome Aggregation Database (gnomAD) 0.00029

The Genome Aggregation Database (gnomAD), exomes 0.00033

NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00046

Links

ClinGen: CA248828 dbSNP: rs137966123 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
CDK5RAP2		-	-	GRCh38 GRCh37	828	853

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not specified	Uncertain significance (2)	criteria provided, multiple submitters, no conflicts	Jul 31, 2015	RCV000194516.7
not provided	Conflicting interpretations of pathogenicity (3)	criteria provided, conflicting classifications	Jan 30, 2024	RCV000885604.33
Microcephaly 3, primary, autosomal recessive	Uncertain significance (2)	criteria provided, single submitter	Jan 13, 2018	RCV001007670.8
Inborn genetic diseases	Uncertain significance (1)	criteria provided, single submitter	May 16, 2021	RCV004020312.1
CDK5RAP2-related disorder	Likely benign (1)	no assertion criteria provided	Sep 30, 2022	RCV003947601.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (Oct 03, 2022)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV003853183.1 First in ClinVar: Apr 09, 2023 Last updated: Apr 09, 2023	Comment: In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31696992)
Uncertain significance (Jul 31, 2015)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	not specified Affected status: unknown Allele origin: germline	Genetic Services Laboratory, University of Chicago Accession: SCV000246927.1 First in ClinVar: Oct 05, 2015 Last updated: Oct 05, 2015
Likely benign (Nov 01, 2023)	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2) Method: clinical testing	not provided Affected status: yes Allele origin: germline	CeGaT Center for Human Genetics Tuebingen Accession: SCV001501041.23 First in ClinVar: Mar 14, 2021 Last updated: Oct 20, 2024	Comment: CDK5RAP2: BP4 Number of individuals with the variant: 3
Uncertain significance (Jun 11, 2015)	criteria provided, single submitter (DGD Variant Analysis Guidelines) Method: clinical testing	not specified Affected status: unknown Allele origin: unknown	Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia Accession: SCV000258130.2 First in ClinVar: Oct 05, 2015 Last updated: Oct 05, 2015
Uncertain significance (May 16, 2021)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	Inborn genetic diseases Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV004922130.1 First in ClinVar: May 01, 2024 Last updated: May 01, 2024	Comment: The c.2003A>G (p.Y668C) alteration is located in exon 18 (coding exon 18) of the CDK5RAP2 gene. This alteration results from a A to G substitution … (more) The c.2003A>G (p.Y668C) alteration is located in exon 18 (coding exon 18) of the CDK5RAP2 gene. This alteration results from a A to G substitution at nucleotide position 2003, causing the tyrosine (Y) at amino acid position 668 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (less)
Uncertain significance (Jan 13, 2018)	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019) Method: clinical testing	Microcephaly 3, primary, autosomal recessive Affected status: unknown Allele origin: germline	Illumina Laboratory Services, Illumina Accession: SCV000476943.3 First in ClinVar: Dec 06, 2016 Last updated: May 31, 2020	Comment: 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 … (more) 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. (less)
Likely benign (Jan 30, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001029063.5 First in ClinVar: Dec 17, 2019 Last updated: Feb 14, 2024
Uncertain significance (-)	no assertion criteria provided (ACMG Guidelines, 2015) Method: clinical testing	Microcephaly 3, primary, autosomal recessive Affected status: yes Allele origin: paternal	Institut de Recherche Interdisciplinaire en Biologie Humaine et Moleculaire, Universite Libre de Bruxelles Accession: SCV000998538.1 First in ClinVar: Mar 16, 2020 Last updated: Mar 16, 2020
Likely benign (Sep 30, 2022)	no assertion criteria provided Method: clinical testing	CDK5RAP2-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004761526.2 First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024	Comment: This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

Comment:

The c.2003A>G (p.Y668C) alteration is located in exon 18 (coding exon 18) of the CDK5RAP2 gene. This alteration results from a A to G substitution at nucleotide position 2003, causing the tyrosine (Y) at amino acid position 668 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

Comment:

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.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs137966123 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 20, 2024

ClinVar Genomic variation as it relates to human health

NM_018249.6(CDK5RAP2):c.2003A>G (p.Tyr668Cys)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs137966123 ...