Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	55755
Gene name Gene Name - the full gene name approved by the HGNC.	CDK5 regulatory subunit associated protein 2
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	CDK5RAP2
Synonyms (NCBI Gene) Gene synonyms aliases	C48, Cep215, MCPH3
Chromosome Chromosome number	9
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	9q33.2
Summary Summary of gene provided in NCBI Entrez Gene.	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 microtubu

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SNP ID	Visualize variation	Clinical significance	Consequence
rs61756286	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity, not-provided	Non coding transcript variant, upstream transcript variant, coding sequence variant, missense variant, genic upstream transcript variant
rs61758368	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Synonymous variant, non coding transcript variant, 5 prime UTR variant, coding sequence variant
rs143341041	A>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Genic downstream transcript variant, non coding transcript variant, missense variant, coding sequence variant
rs145272328	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, non coding transcript variant, 5 prime UTR variant, coding sequence variant
rs199422126	A>T	Pathogenic	Genic upstream transcript variant, coding sequence variant, non coding transcript variant, stop gained
rs373278668	G>A	Pathogenic	Stop gained, non coding transcript variant, genic downstream transcript variant, coding sequence variant
rs374351172	C>A	Pathogenic	Stop gained, non coding transcript variant, genic downstream transcript variant, coding sequence variant
rs387906274	T>C	Pathogenic	Intron variant, genic downstream transcript variant
rs398122971	C>A	Pathogenic	Stop gained, coding sequence variant, intron variant, genic upstream transcript variant, non coding transcript variant
rs587783387	C>T	Pathogenic	Splice acceptor variant, genic downstream transcript variant
rs587783390	G>A	Pathogenic-likely-pathogenic, pathogenic	Stop gained, non coding transcript variant, coding sequence variant, genic downstream transcript variant
rs587783392	G>A	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant, genic downstream transcript variant
rs587783393	TGCCT>-	Conflicting-interpretations-of-pathogenicity	5 prime UTR variant, non coding transcript variant, genic upstream transcript variant, coding sequence variant, frameshift variant
rs747831095	C>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs752092703	C>G	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant, genic upstream transcript variant
rs754282058	G>A,C	Pathogenic	Missense variant, genic downstream transcript variant, stop gained, coding sequence variant, non coding transcript variant
rs772072816	T>C	Likely-pathogenic	Coding sequence variant, non coding transcript variant, downstream transcript variant, genic downstream transcript variant, missense variant
rs786205660	A>-	Likely-pathogenic	Coding sequence variant, genic upstream transcript variant, non coding transcript variant, frameshift variant
rs797045441	C>-	Pathogenic	Coding sequence variant, 5 prime UTR variant, non coding transcript variant, frameshift variant
rs869025200	C>G	Pathogenic	Splice donor variant, genic downstream transcript variant
rs1554728351	->AC	Pathogenic	Genic downstream transcript variant, non coding transcript variant, coding sequence variant, frameshift variant
rs1554730137	GA>-	Pathogenic	Genic downstream transcript variant, non coding transcript variant, coding sequence variant, frameshift variant
rs1554755313	T>-	Likely-pathogenic	5 prime UTR variant, non coding transcript variant, coding sequence variant, frameshift variant
rs1564338190	G>A	Likely-pathogenic	Stop gained, non coding transcript variant, coding sequence variant, 5 prime UTR variant
rs1588472215	T>-	Pathogenic	Coding sequence variant, 5 prime UTR variant, frameshift variant, non coding transcript variant
rs1588634016	G>A	Pathogenic	Coding sequence variant, genic upstream transcript variant, non coding transcript variant, missense variant

Show/Hide all(79)

miRTarBase ID	miRNA	Experiments	Reference
MIRT045392	hsa-miR-149-5p	CLASH	23622248
MIRT042896	hsa-miR-324-3p	CLASH	23622248
MIRT035984	hsa-miR-1301-3p	CLASH	23622248
MIRT881315	hsa-miR-1911	CLIP-seq
MIRT881316	hsa-miR-3064-5p	CLIP-seq
MIRT881317	hsa-miR-3919	CLIP-seq
MIRT881318	hsa-miR-3942-3p	CLIP-seq
MIRT881319	hsa-miR-4271	CLIP-seq
MIRT881320	hsa-miR-4318	CLIP-seq
MIRT881321	hsa-miR-4685-5p	CLIP-seq
MIRT881322	hsa-miR-4725-3p	CLIP-seq
MIRT881323	hsa-miR-4729	CLIP-seq
MIRT881324	hsa-miR-4756-3p	CLIP-seq
MIRT881325	hsa-miR-4786-3p	CLIP-seq
MIRT881326	hsa-miR-513c	CLIP-seq
MIRT881327	hsa-miR-514b-5p	CLIP-seq
MIRT881328	hsa-miR-548g	CLIP-seq
MIRT881329	hsa-miR-549	CLIP-seq
MIRT881330	hsa-miR-570	CLIP-seq
MIRT881331	hsa-miR-580	CLIP-seq
MIRT881332	hsa-miR-7	CLIP-seq
MIRT881333	hsa-miR-892b	CLIP-seq
MIRT1961029	hsa-miR-1324	CLIP-seq
MIRT1961030	hsa-miR-4659a-3p	CLIP-seq
MIRT1961031	hsa-miR-4659b-3p	CLIP-seq
MIRT881315	hsa-miR-1911	CLIP-seq
MIRT2197788	hsa-miR-1913	CLIP-seq
MIRT881316	hsa-miR-3064-5p	CLIP-seq
MIRT881319	hsa-miR-4271	CLIP-seq
MIRT881321	hsa-miR-4685-5p	CLIP-seq
MIRT881322	hsa-miR-4725-3p	CLIP-seq
MIRT2197789	hsa-miR-4749-3p	CLIP-seq
MIRT2197790	hsa-miR-4763-5p	CLIP-seq
MIRT2197791	hsa-miR-4766-5p	CLIP-seq
MIRT881325	hsa-miR-4786-3p	CLIP-seq
MIRT2197792	hsa-miR-524-3p	CLIP-seq
MIRT2197793	hsa-miR-525-3p	CLIP-seq
MIRT881332	hsa-miR-7	CLIP-seq
MIRT881333	hsa-miR-892b	CLIP-seq
MIRT2446717	hsa-miR-3121-3p	CLIP-seq
MIRT2446718	hsa-miR-3148	CLIP-seq
MIRT2446719	hsa-miR-3179	CLIP-seq
MIRT2446720	hsa-miR-4668-5p	CLIP-seq
MIRT2446717	hsa-miR-3121-3p	CLIP-seq
MIRT2446718	hsa-miR-3148	CLIP-seq
MIRT2446719	hsa-miR-3179	CLIP-seq
MIRT2446720	hsa-miR-4668-5p	CLIP-seq
MIRT1961029	hsa-miR-1324	CLIP-seq
MIRT2446717	hsa-miR-3121-3p	CLIP-seq
MIRT2501070	hsa-miR-3121-5p	CLIP-seq
MIRT2446718	hsa-miR-3148	CLIP-seq
MIRT2446719	hsa-miR-3179	CLIP-seq
MIRT2501071	hsa-miR-3187-3p	CLIP-seq
MIRT2501072	hsa-miR-3914	CLIP-seq
MIRT881317	hsa-miR-3919	CLIP-seq
MIRT881318	hsa-miR-3942-3p	CLIP-seq
MIRT2501073	hsa-miR-4435	CLIP-seq
MIRT1961030	hsa-miR-4659a-3p	CLIP-seq
MIRT1961031	hsa-miR-4659b-3p	CLIP-seq
MIRT2446720	hsa-miR-4668-5p	CLIP-seq
MIRT2501074	hsa-miR-4701-5p	CLIP-seq
MIRT881324	hsa-miR-4756-3p	CLIP-seq
MIRT881326	hsa-miR-513c	CLIP-seq
MIRT881327	hsa-miR-514b-5p	CLIP-seq
MIRT2501075	hsa-miR-548s	CLIP-seq
MIRT881329	hsa-miR-549	CLIP-seq
MIRT881330	hsa-miR-570	CLIP-seq
MIRT2501076	hsa-miR-588	CLIP-seq
MIRT2446717	hsa-miR-3121-3p	CLIP-seq
MIRT2446718	hsa-miR-3148	CLIP-seq
MIRT2446719	hsa-miR-3179	CLIP-seq
MIRT881317	hsa-miR-3919	CLIP-seq
MIRT881318	hsa-miR-3942-3p	CLIP-seq
MIRT2446720	hsa-miR-4668-5p	CLIP-seq
MIRT881324	hsa-miR-4756-3p	CLIP-seq
MIRT881326	hsa-miR-513c	CLIP-seq
MIRT881327	hsa-miR-514b-5p	CLIP-seq
MIRT881329	hsa-miR-549	CLIP-seq
MIRT881330	hsa-miR-570	CLIP-seq

Show/Hide all(63)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000132	Process	Establishment of mitotic spindle orientation	IBA
GO:0000132	Process	Establishment of mitotic spindle orientation	IEA
GO:0000132	Process	Establishment of mitotic spindle orientation	ISS
GO:0000226	Process	Microtubule cytoskeleton organization	IDA	17959831
GO:0000226	Process	Microtubule cytoskeleton organization	IEA
GO:0000242	Component	Pericentriolar material	IBA
GO:0000242	Component	Pericentriolar material	IDA	17959831
GO:0000922	Component	Spindle pole	IDA	17959831, 19282672
GO:0000931	Component	Gamma-tubulin ring complex	IDA	29162697
GO:0000976	Function	Transcription cis-regulatory region binding	IDA	19282672
GO:0001578	Process	Microtubule bundle formation	IBA
GO:0001578	Process	Microtubule bundle formation	IDA	19553473
GO:0005515	Function	Protein binding	IPI	17959831, 19282672, 19553473, 20466722, 25503564, 26192437, 26297806, 26485573, 29162697, 35709258, 35849559
GO:0005516	Function	Calmodulin binding	IDA	20466722
GO:0005516	Function	Calmodulin binding	IEA
GO:0005737	Component	Cytoplasm	IDA	17959831, 19282672, 19553473
GO:0005737	Component	Cytoplasm	IEA
GO:0005794	Component	Golgi apparatus	IDA	20466722
GO:0005794	Component	Golgi apparatus	IEA
GO:0005813	Component	Centrosome	IDA	14654843, 17959831, 18042621, 19282672, 19543530, 19553473, 20466722, 21399614, 25657325, 26485573, 29162697, 31974111, 35849559
GO:0005813	Component	Centrosome	IEA
GO:0005815	Component	Microtubule organizing center	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005856	Component	Cytoskeleton	NAS	10721722
GO:0005874	Component	Microtubule	IDA	19553473
GO:0005874	Component	Microtubule	IEA
GO:0007059	Process	Chromosome segregation	IBA
GO:0007059	Process	Chromosome segregation	IMP	19282672
GO:0007098	Process	Centrosome cycle	IMP	18042621
GO:0007099	Process	Centriole replication	IBA
GO:0007099	Process	Centriole replication	IMP	26297806
GO:0007420	Process	Brain development	IEA
GO:0007420	Process	Brain development	ISS
GO:0007420	Process	Brain development	NAS	10915792
GO:0008017	Function	Microtubule binding	IBA
GO:0008017	Function	Microtubule binding	IDA	14654843
GO:0015631	Function	Tubulin binding	IPI	17959831
GO:0019901	Function	Protein kinase binding	IPI	10721722
GO:0022008	Process	Neurogenesis	IEA
GO:0022008	Process	Neurogenesis	ISS
GO:0030054	Component	Cell junction	IDA
GO:0031023	Process	Microtubule organizing center organization	IMP	26485573
GO:0031116	Process	Positive regulation of microtubule polymerization	IMP	29162697
GO:0035371	Component	Microtubule plus-end	IBA
GO:0035371	Component	Microtubule plus-end	IDA	26485573
GO:0036064	Component	Ciliary basal body	IDA
GO:0043015	Function	Gamma-tubulin binding	IBA
GO:0043015	Function	Gamma-tubulin binding	IDA	29162697
GO:0044877	Function	Protein-containing complex binding	IEA
GO:0045664	Process	Regulation of neuron differentiation	NAS	10721722
GO:0045665	Process	Negative regulation of neuron differentiation	IEA
GO:0045893	Process	Positive regulation of DNA-templated transcription	IDA	19282672
GO:0046600	Process	Negative regulation of centriole replication	IBA
GO:0046600	Process	Negative regulation of centriole replication	IEA
GO:0046600	Process	Negative regulation of centriole replication	ISS
GO:0048471	Component	Perinuclear region of cytoplasm	IDA	17959831
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:0090266	Process	Regulation of mitotic cell cycle spindle assembly checkpoint	IBA
GO:0090266	Process	Regulation of mitotic cell cycle spindle assembly checkpoint	IDA	19282672
GO:0097431	Component	Mitotic spindle pole	IBA
GO:0097431	Component	Mitotic spindle pole	IEA

MIM	HGNC	e!Ensembl
608201	18672	ENSG00000136861

Protein

UniProt ID

Q96SN8

Protein name

CDK5 regulatory subunit-associated protein 2 (CDK5 activator-binding protein C48) (Centrosome-associated protein 215)

Protein function

Potential regulator of CDK5 activity via its interaction with CDK5R1 (PubMed:15164053). Negative regulator of centriole disengagement (licensing) which maintains centriole engagement and cohesion. Involved in regulation of mitotic spindle orient

PDB

6X0V , 8RX1 , 9G40 , 9H9P

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF07989	Cnn_1N	59 → 131	Centrosomin N-terminal motif 1	Coiled-coil

Tissue specificity

TISSUE SPECIFICITY: Widely expressed. Expressed in heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas. {ECO:0000269|PubMed:10721722}.

Sequence

MMDLVLEEDVTVPGTLSGCSGLVPSVPDDLDGINPNAGLGNGLLPNVSEETVSPTRARNM
KDFENQITELKKENFNLKLRIYFLEERMQQEFHGPTEHIYKTNIELKVEVESLKRELQER
EQLLIKASKAVESLAEAGGSEIQRVKEDARKKVQQVEDLLTKRILLLEKDVTAAQAELEK
AFAGTETEKALRLRLESKLSEMKKMHEGDLAMALVLDEKDRLIEELKLSLKSKEALIQCL
KEEKSQMACPDENVSSGELRGLCAAPREEKERETEAAQMEHQKERNSFEERIQALEEDLR
EKEREIATEKKNSLKRDKAIQGLTMALKSKEKKVEELNSEIEKLSAAFAKAREALQKAQT
QEFQGSEDYETALSGKEALSAALRSQNLTKSTENHRLRRSIKKITQELSDLQQERERLEK
DLEEAHREKSKGDCTIRDLRNEVEKLRNEVNEREKAMENRYKSLLSESNKKLHNQEQVIK
HLTESTNQKDVLLQKFNEKDLEVIQQNCYLMAAEDLELRSEGLITEKCSSQQPPGSKTIF
SKEKKQSSDYEELIQVLKKEQDIYTHLVKSLQESDSINNLQAELNKIFALRKQLEQDVLS
YQNLRKTLEEQISEIRRREEESFSLYSDQTSYLSICLEENNRFQVEHFSQEELKKKVSDL
IQLVKELYTDNQHLKKTIFDLSCMGFQGNGFPDRLASTEQTELLASKEDEDTIKIGEDDE
INFLSDQHLQQSNEIMKDLSKGGCKNGYLRHTESKISDCDGAHAPGCLEEGAFINLLAPL
FNEKATLLLESRPDLLKVVRELLLGQLFLTEQEVSGEHLDGKTEKTPKQKGELVHFVQTN
SFSKPHDELKLSCEAQLVKAGEVPKVGLKDASVQTVATEGDLLRFKHEATREAWEEKPIN
TALSAEHRPENLHGVPGWQAALLSLPGITNREAKKSRLPILIKPSRSLGNMYRLPATQEV
VTQLQSQILELQGELKEFKTCNKQLHQKLILAEAVMEGRPTPDKTLLNAQPPVGAAYQDS
PGEQKGIKTTSSVWRDKEMDSDQQRSYEIDSEICPPDDLASLPSCKENPEDVLSPTSVAT
YLSSKSQPSAKVSVMGTDQSESINTSNETEYLKQKIHDLETELEGYQNFIFQLQKHSQCS
EAIITVLCGTEGAQDGLSKPKNGSDGEEMTFSSLHQVRYVKHVKILGPLAPEMIDSRVLE
NLKQQLEEQEYKLQKEQNLNMQLFSEIHNLQNKFRDLSPPRYDSLVQSQARELSLQRQQI
KDGHGICVISRQHMNTMIKAFEELLQASDVDYCVAEGFQEQLNQCAELLEKLEKLFLNGK
SVGVEMNTQNELMERIEEDNLTYQHLLPESPEPSASHALSDYETSEKSFFSRDQKQDNET
EKTSVMVNSFSQDLLMEHIQEIRTLRKRLEESIKTNEKLRKQLERQGSEFVQGSTSIFAS
GSELHSSLTSEIHFLRKQNQALNAMLIKGSRDKQKENDKLRESLSRKTVSLEHLQREYAS
VKEENERLQKEGSEKERHNQQLIQEVRCSGQELSRVQEEVKLRQQLLSQNDKLLQSLRVE
LKAYEKLDEEHRRLREASGEGWKGQDPFRDLHSLLMEIQALRLQLERSIETSSTLQSRLK
EQLARGAEKAQEGALTLAVQAVSIPEVPLQPDKHDGDKYPMESDNSFDLFDSSQAVTPKS
VSETPPLSGNDTDSLSCDSGSSATSTPCVSRLVTGHHLWASKNGRHVLGLIEDYEALLKQ
ISQGQRLLAEMDIQTQEAPSSTSQELGTKGPHPAPLSKFVSSVSTAKLTLEEAYRRLKLL
WRVSLPEDGQCPLHCEQIGEMKAEVTKLHKKLFEQEKKLQNTMKLLQLSKRQEKVIFDQL
VVTHKILRKARGNLELRPGGAHPGTCSPSRPGS

Sequence length

1893

Interactions

View interactions

	Reactome
			Regulation of PLK1 Activity at G2/M Transition Loss of Nlp from mitotic centrosomes Recruitment of mitotic centrosome proteins and complexes Loss of proteins required for interphase microtubule organization from the centrosome Recruitment of NuMA to mitotic centrosomes Anchoring of the basal body to the plasma membrane AURKA Activation by TPX2

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Microcephaly	Microcephaly 3, primary, autosomal recessive, microcephaly	rs587783387, rs869025200, rs747831095, rs199422126, rs754282058, rs387906274, rs797045441, rs398122971, rs1554728351, rs374351172, rs1554730137, rs373278668, rs1588472215, rs587783393, rs1588634016, rs587783392, rs746967357, rs587783390 View all (3 more)	N/A

Show/Hide Unknown Diseases (2)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Asthma	Asthma	N/A	N/A	GWAS
Rheumatoid arthritis	Rheumatoid arthritis	N/A	N/A	GWAS

Show/Hide Text Mining Associations (22)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Adrenocortical Carcinoma	Associate	36793283
Agenesis of Corpus Callosum	Associate	23587236, 26197979
Alzheimer Disease	Associate	29360470
Autosomal Recessive Primary Microcephaly	Associate	10677332, 17764569, 17959831, 19282672, 22887808, 23587236, 26197979, 26297806, 28004182, 32677750
Azoospermia	Associate	38008501
Cockayne Syndrome	Associate	31980658
Cognition Disorders	Associate	29360470
Colonic Neoplasms	Associate	38143740
Deafness	Associate	22887808
Ectodermal Dysplasia	Associate	26197979
Hearing Loss Sensorineural	Associate	22887808
Infertility Male	Associate	38008501
Lymphatic Metastasis	Associate	36774351
Microcephaly	Associate	17764569, 23587236, 26297806, 26485573, 28004182, 32677750, 35058575
Microcephaly Primary Autosomal Recessive 3	Associate	28004182
Neoplasms	Associate	19282672
Neoplasms Squamous Cell	Associate	36774351
Pathological Conditions Anatomical	Associate	22887808
Pre Eclampsia	Associate	35860693
Prostatic Hyperplasia	Associate	39694406
Prostatic Neoplasms	Associate	39694406
Squamous Cell Carcinoma of Head and Neck	Associate	36774351

CDK5RAP2 (CDK5 regulatory subunit associated protein 2)