CDK5RAP2 CDK5 regulatory subunit associated protein 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CDK5RAP2provided by HGNC
Official Full Name: CDK5 regulatory subunit associated protein 2provided by HGNC
Primary source: HGNC:HGNC:18672
See related: Ensembl:ENSG00000136861 MIM:608201; AllianceGenome:HGNC:18672
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: C48; MCPH3; Cep215
Summary: This gene encodes a regulator of CDK5 (cyclin-dependent kinase 5) activity. The protein encoded by this gene is localized to the centrosome and Golgi complex, interacts with CDK5R1 and pericentrin (PCNT), plays a role in centriole engagement and microtubule nucleation, and has been linked to primary microcephaly and Alzheimer's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2013]
Expression: Ubiquitous expression in testis (RPKM 15.8), bone marrow (RPKM 9.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q33.2

Exon count:: 39

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (120388875..120580167, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (132583189..132774493, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (123151153..123342445, complement)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A novel missense variant in CDK5RAP2 associated with non-obstructive azoospermia.
Title: A novel missense variant in CDK5RAP2 associated with non-obstructive azoospermia.
CDK5RAP2 is a Wnt target gene and promotes stemness and progression of oral squamous cell carcinoma.
Title: CDK5RAP2 is a Wnt target gene and promotes stemness and progression of oral squamous cell carcinoma.
CDK5RAP2 loss-of-function causes premature cell senescence via the GSK3beta/beta-catenin-WIP1 pathway.
Title: CDK5RAP2 loss-of-function causes premature cell senescence via the GSK3β/β-catenin-WIP1 pathway.
Triple deletion of TP53, PCNT, and CEP215 promotes centriole amplification in the M phase.
Title: Triple deletion of TP53, PCNT, and CEP215 promotes centriole amplification in the M phase.
Further insights into the spectrum phenotype of TRAPPC9 and CDK5RAP2 genes, segregating independently in a large Tunisian family with intellectual disability and microcephaly.
Title: Further insights into the spectrum phenotype of TRAPPC9 and CDK5RAP2 genes, segregating independently in a large Tunisian family with intellectual disability and microcephaly.
Centromeric chromatin integrity is compromised by loss of Cdk5rap2, a transcriptional activator of CENP-A.
Title: Centromeric chromatin integrity is compromised by loss of Cdk5rap2, a transcriptional activator of CENP-A.
CDK5RAP2 primary microcephaly is associated with hypothalamic, retinal and cochlear developmental defects.
Title: CDK5RAP2 primary microcephaly is associated with hypothalamic, retinal and cochlear developmental defects.
Centriole-independent mitotic spindle assembly relies on the PCNT-CDK5RAP2 pericentriolar matrix.
Title: Centriole-independent mitotic spindle assembly relies on the PCNT-CDK5RAP2 pericentriolar matrix.
Cep215 is essential for morphological differentiation of astrocytes.
Title: Cep215 is essential for morphological differentiation of astrocytes.
The rs10984186 risk and rs4837766 protective polymorphic variants of theCDK5RAP2gene might act as potent genetic modifiers for AD risk and/or conversion by modulating the expres-sion of this gene.
Title: CDK5RAP2 gene and tau pathophysiology in late-onset sporadic Alzheimer's disease.

Submit: New GeneRIF Correction See all GeneRIFs (41)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Microcephaly 3, primary, autosomal recessive MedGen: C1858108 OMIM: 604804 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide association of lipid-lowering response to statins in combined study populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel risk loci for rheumatoid arthritis in Han Chinese and congruence with risk variants in Europeans. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH104241 (e-PCR)
- UniSTS:98566

STS-T23995 (e-PCR)
- UniSTS:32793

D9S1099 (e-PCR)
- UniSTS:51069

D9S290 (e-PCR), detects polymorphism
- UniSTS:47999

WI-15097 (e-PCR)
- UniSTS:6025

AB056817 (e-PCR)
- UniSTS:480159

G20308 (e-PCR)
- UniSTS:22221

A005L20 (e-PCR)
- UniSTS:22222

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calmodulin binding	IDA Inferred from Direct Assay more info	PubMed
enables gamma-tubulin binding	IBA Inferred from Biological aspect of Ancestor more info
enables gamma-tubulin binding	IDA Inferred from Direct Assay more info	PubMed
enables microtubule binding	IBA Inferred from Biological aspect of Ancestor more info
enables microtubule binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IEA Inferred from Electronic Annotation more info
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed
enables tubulin binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in brain development	ISS Inferred from Sequence or Structural Similarity more info
involved_in brain development	NAS Non-traceable Author Statement more info	PubMed
involved_in centriole replication	IBA Inferred from Biological aspect of Ancestor more info
involved_in centriole replication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in centrosome cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromosome segregation	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromosome segregation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in establishment of mitotic spindle orientation	IBA Inferred from Biological aspect of Ancestor more info
involved_in establishment of mitotic spindle orientation	ISS Inferred from Sequence or Structural Similarity more info
involved_in microtubule bundle formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in microtubule bundle formation	IDA Inferred from Direct Assay more info	PubMed
involved_in microtubule cytoskeleton organization	IDA Inferred from Direct Assay more info	PubMed
involved_in microtubule organizing center organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of centriole replication	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of centriole replication	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in neurogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of microtubule polymerization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mitotic cell cycle spindle assembly checkpoint	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of mitotic cell cycle spindle assembly checkpoint	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of neuron differentiation	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in cell junction	IDA Inferred from Direct Assay more info
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoskeleton	NAS Non-traceable Author Statement more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
part_of gamma-tubulin ring complex	IDA Inferred from Direct Assay more info	PubMed
located_in microtubule	IDA Inferred from Direct Assay more info	PubMed
is_active_in microtubule plus-end	IBA Inferred from Biological aspect of Ancestor more info
located_in microtubule plus-end	IDA Inferred from Direct Assay more info	PubMed
is_active_in mitotic spindle pole	IBA Inferred from Biological aspect of Ancestor more info
is_active_in pericentriolar material	IBA Inferred from Biological aspect of Ancestor more info
located_in pericentriolar material	IDA Inferred from Direct Assay more info	PubMed
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in spindle pole	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: CDK5 regulatory subunit-associated protein 2

Names: CDK5 activator-binding protein C48; centrosomal protein 215 kDa; centrosomin

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_008999.1 RefSeqGene

Range

4993..196285

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001011649.3 → NP_001011649.1 CDK5 regulatory subunit-associated protein 2 isoform b

See identical proteins and their annotated locations for NP_001011649.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (b) is shorter compared to isoform a.

Source sequence(s)

AF448860, BC136275, BX495012, BX537759, BX953750

Consensus CDS

CCDS43871.1

UniProtKB/TrEMBL

A6H8X1

Related

ENSP00000353317.4, ENST00000360190.8

Conserved Domains (3) summary

cl14654
Location:289 → 497

V_Alix_like; Protein-interacting V-domain of mammalian Alix and related domains

COG0419
Location:105 → 667

SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]

pfam07989
Location:61 → 129

Cnn_1N; Centrosomin N-terminal motif 1
NM_001272039.2 → NP_001258968.1 CDK5 regulatory subunit-associated protein 2 isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice site and lacks three in-frame exons in the coding region, compared to variant 1. The encoded isoform (c) is shorter compared to isoform a.

Source sequence(s)

AF448860, BC136275, BX495012, BX537708, BX953708

Consensus CDS

CCDS75888.1

UniProtKB/TrEMBL

A0A0A0MRG9, Q7Z3M0

Related

ENSP00000354065.4, ENST00000360822.8

Conserved Domains (2) summary

cl14654
Location:289 → 497

V_Alix_like; Protein-interacting V-domain of mammalian Alix and related domains

pfam07989
Location:61 → 129

Cnn_1N; Centrosomin N-terminal motif 1
NM_001410992.1 → NP_001397921.1 CDK5 regulatory subunit-associated protein 2 isoform d

Status: REVIEWED

Source sequence(s)

AL138836, AL353736, AL391870, AL590642

Consensus CDS

CCDS94468.1

UniProtKB/TrEMBL

A0A8I5KXG0

Related

ENSP00000510289.1, ENST00000687633.1
NM_001410993.1 → NP_001397922.1 CDK5 regulatory subunit-associated protein 2 isoform e

Status: REVIEWED

Source sequence(s)

AL138836, AL353736, AL391870, AL590642

Consensus CDS

CCDS94470.1

Related

ENSP00000400395.2, ENST00000416449.6
NM_001410994.1 → NP_001397923.1 CDK5 regulatory subunit-associated protein 2 isoform f

Status: REVIEWED

Source sequence(s)

AL138836, AL353736, AL391870, AL590642

Consensus CDS

CCDS94469.1

UniProtKB/TrEMBL

A0A8I5QKL1

Related

ENSP00000508692.1, ENST00000687279.1
NM_018249.6 → NP_060719.4 CDK5 regulatory subunit-associated protein 2 isoform a

See identical proteins and their annotated locations for NP_060719.4

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (a).

Source sequence(s)

AF448860, AK122913, BX495012

Consensus CDS

CCDS6823.1

UniProtKB/Swiss-Prot

Q5JV18, Q7Z3L4, Q7Z3U1, Q7Z7I6, Q96SN8, Q9BSW0, Q9H6J6, Q9HCD9, Q9NV90, Q9UIW9

UniProtKB/TrEMBL

A0A0C4ZLW1

Related

ENSP00000343818.4, ENST00000349780.9

Conserved Domains (3) summary

cl14654
Location:289 → 497

V_Alix_like; Protein-interacting V-domain of mammalian Alix and related domains

COG0419
Location:105 → 667

SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]

pfam07989
Location:61 → 129

Cnn_1N; Centrosomin N-terminal motif 1

RNA

NR_073554.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses three alternate splice sites in internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF448860, BC019577, BC143732, BX495012

Related

ENST00000685866.1
NR_073555.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF448860, BC019577, BC143734, BQ428975, BX495012

Related

ENST00000689688.1
NR_073556.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (6) uses two alternate splice sites in internal exons and contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF448860, BC143755, BX471011, BX495012

Related

ENST00000473282.6
NR_073557.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (7) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF448860, BC019577, BC143764, BX495012

Related

ENST00000693386.1
NR_073558.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (8) uses two alternate splice sites in internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF448860, BC143760, BX471011, BX495012

Related

ENST00000480112.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

120388875..120580167 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047423589.1 → XP_047279545.1 CDK5 regulatory subunit-associated protein 2 isoform X3
XM_047423587.1 → XP_047279543.1 CDK5 regulatory subunit-associated protein 2 isoform X1
XM_017014923.2 → XP_016870412.1 CDK5 regulatory subunit-associated protein 2 isoform X6

UniProtKB/TrEMBL

Q7Z3M0

Related

ENST00000688923.1
XM_006717185.2 → XP_006717248.1 CDK5 regulatory subunit-associated protein 2 isoform X4

UniProtKB/TrEMBL

Q7Z3M0

Conserved Domains (2) summary

cl14654
Location:289 → 497

V_Alix_like; Protein-interacting V-domain of mammalian Alix and related domains

pfam07989
Location:61 → 129

Cnn_1N; Centrosomin N-terminal motif 1
XM_047423588.1 → XP_047279544.1 CDK5 regulatory subunit-associated protein 2 isoform X2
XM_047423590.1 → XP_047279546.1 CDK5 regulatory subunit-associated protein 2 isoform X5
XM_047423591.1 → XP_047279547.1 CDK5 regulatory subunit-associated protein 2 isoform X7

Related

ENSP00000508792.1, ENST00000690814.1

Alternate T2T-CHM13v2.0

Genomic

NC_060933.1 Alternate T2T-CHM13v2.0

Range

132583189..132774493 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054363276.1 → XP_054219251.1 CDK5 regulatory subunit-associated protein 2 isoform X3
XM_054363274.1 → XP_054219249.1 CDK5 regulatory subunit-associated protein 2 isoform X1
XM_054363279.1 → XP_054219254.1 CDK5 regulatory subunit-associated protein 2 isoform X6
XM_054363277.1 → XP_054219252.1 CDK5 regulatory subunit-associated protein 2 isoform X4
XM_054363275.1 → XP_054219250.1 CDK5 regulatory subunit-associated protein 2 isoform X2
XM_054363278.1 → XP_054219253.1 CDK5 regulatory subunit-associated protein 2 isoform X5
XM_054363280.1 → XP_054219255.1 CDK5 regulatory subunit-associated protein 2 isoform X7