VCV002175876.5 - ClinVar

NM_018249.6(CDK5RAP2):c.1808A>T (p.Asn603Ile)

Germline

Classification

criteria provided, multiple submitters, no conflicts. Learn more about how ClinVar calculates review status.

Uncertain significance

2 out of 3 submissions contributed to this 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.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_018249.6(CDK5RAP2):c.1808A>T (p.Asn603Ile)

Variation ID: 2175876 Accession: VCV002175876.5

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 9q33.2 9: 120471798 (GRCh38) [ NCBI UCSC ] 9: 123234076 (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	Feb 8, 2023	Feb 25, 2025	Apr 1, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_018249.6:c.1808A>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_060719.4:p.Asn603Ile	missense
NM_001011649.3:c.1808A>T	NP_001011649.1:p.Asn603Ile	missense
NM_001272039.2:c.1808A>T	NP_001258968.1:p.Asn603Ile	missense
NM_001410992.1:c.1808A>T	NP_001397921.1:p.Asn603Ile	missense
NM_001410993.1:c.1808A>T	NP_001397922.1:p.Asn603Ile	missense
NM_001410994.1:c.1808A>T	NP_001397923.1:p.Asn603Ile	missense
NM_018249.4:c.1808A>T
NM_018249.5:c.1808A>T
NR_073554.2:n.1997A>T		non-coding transcript variant
NR_073555.2:n.1997A>T		non-coding transcript variant
NR_073556.2:n.2124A>T		non-coding transcript variant
NR_073557.2:n.1997A>T		non-coding transcript variant
NR_073558.2:n.1994A>T		non-coding transcript variant
NC_000009.12:g.120471798T>A
NC_000009.11:g.123234076T>A
NG_008999.1:g.113362A>T

... more HGVS ... less HGVS

Protein change

N603I

Other names

Canonical SPDI

NC_000009.12:120471797:T:A

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.

Links

ClinGen: CA5214273 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		Gene associated with autosomal recessive phenotype	Not yet evaluated	GRCh38 GRCh37	914	939

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 provided	Uncertain significance (2)	criteria provided, multiple submitters, no conflicts	Apr 1, 2024	RCV002605848.5
CDK5RAP2-related disorder	Likely benign (1)	no assertion criteria provided	Jul 14, 2022	RCV003946279.2

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 (Jan 09, 2024) C Contributing to aggregate classification	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV005332728.1 First in ClinVar: Oct 08, 2024 Last updated: Oct 08, 2024	Comment: In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to … (more) In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge (less)
Uncertain significance (Apr 01, 2024) C Contributing to aggregate classification	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: SCV003492672.3 First in ClinVar: Feb 07, 2023 Last updated: Feb 25, 2025	Comment: This sequence change replaces asparagine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 603 of the CDK5RAP2 protein (p.Asn603Ile). … (more) This sequence change replaces asparagine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 603 of the CDK5RAP2 protein (p.Asn603Ile). This variant is present in population databases (rs144564533, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with CDK5RAP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 2175876). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less)
Likely benign (Jul 14, 2022) N Not contributing to aggregate classification	no assertion criteria provided Method: clinical testing	CDK5RAP2-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004767741.2 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:

This sequence change replaces asparagine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 603 of the CDK5RAP2 protein (p.Asn603Ile). This variant is present in population databases (rs144564533, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with CDK5RAP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 2175876). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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 this variant ...

Record last updated Apr 08, 2025

ClinVar Genomic variation as it relates to human health

NM_018249.6(CDK5RAP2):c.1808A>T (p.Asn603Ile)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...