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

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	51654
Gene name	CDK5RAP1 mitochondrial tRNA methylthiotransferase
Gene symbol	CDK5RAP1
Synonyms (NCBI Gene)	C20orf34C42CGI-05HSPC167
Chromosome	20
Chromosome location	20q11.21
Summary	This gene encodes a regulator of cyclin-dependent kinase 5 activity. This protein has also been reported to modify RNA by adding a methylthio-group and may thus have a dual function as an RNA methylthiotransferase and as an inhibitor of cyclin-dependent k

Show/Hide all (72)

miRTarBase ID	miRNA	Experiments	Reference
MIRT001473	hsa-miR-16-5p	pSILAC	18668040
MIRT001473	hsa-miR-16-5p	Proteomics;Other	18668040
MIRT2197784	hsa-miR-142-5p	CLIP-seq
MIRT2197785	hsa-miR-21	CLIP-seq
MIRT2197786	hsa-miR-561	CLIP-seq
MIRT2197787	hsa-miR-590-5p	CLIP-seq
MIRT2446709	hsa-miR-2110	CLIP-seq
MIRT2446710	hsa-miR-3127-3p	CLIP-seq
MIRT2446711	hsa-miR-3147	CLIP-seq
MIRT2446712	hsa-miR-3150a-3p	CLIP-seq
MIRT2446713	hsa-miR-3175	CLIP-seq
MIRT2446714	hsa-miR-3667-3p	CLIP-seq
MIRT2446715	hsa-miR-4425	CLIP-seq
MIRT2446716	hsa-miR-939	CLIP-seq
MIRT2501054	hsa-miR-1207-5p	CLIP-seq
MIRT2501055	hsa-miR-1238	CLIP-seq
MIRT2501056	hsa-miR-1301	CLIP-seq
MIRT2197784	hsa-miR-142-5p	CLIP-seq
MIRT2501057	hsa-miR-205	CLIP-seq
MIRT2197785	hsa-miR-21	CLIP-seq
MIRT2446709	hsa-miR-2110	CLIP-seq
MIRT2446710	hsa-miR-3127-3p	CLIP-seq
MIRT2446711	hsa-miR-3147	CLIP-seq
MIRT2446712	hsa-miR-3150a-3p	CLIP-seq
MIRT2446713	hsa-miR-3175	CLIP-seq
MIRT2501058	hsa-miR-3661	CLIP-seq
MIRT2446714	hsa-miR-3667-3p	CLIP-seq
MIRT2501059	hsa-miR-3691-3p	CLIP-seq
MIRT2501060	hsa-miR-3921	CLIP-seq
MIRT2501061	hsa-miR-3977	CLIP-seq
MIRT2501062	hsa-miR-433	CLIP-seq
MIRT2446715	hsa-miR-4425	CLIP-seq
MIRT2501063	hsa-miR-4653-5p	CLIP-seq
MIRT2501064	hsa-miR-4660	CLIP-seq
MIRT2501065	hsa-miR-4736	CLIP-seq
MIRT2501066	hsa-miR-4742-5p	CLIP-seq
MIRT2501067	hsa-miR-4763-3p	CLIP-seq
MIRT2501068	hsa-miR-5047	CLIP-seq
MIRT2197786	hsa-miR-561	CLIP-seq
MIRT2197787	hsa-miR-590-5p	CLIP-seq
MIRT2501069	hsa-miR-631	CLIP-seq
MIRT2446716	hsa-miR-939	CLIP-seq
MIRT2501054	hsa-miR-1207-5p	CLIP-seq
MIRT2501055	hsa-miR-1238	CLIP-seq
MIRT2501056	hsa-miR-1301	CLIP-seq
MIRT2197784	hsa-miR-142-5p	CLIP-seq
MIRT2501057	hsa-miR-205	CLIP-seq
MIRT2197785	hsa-miR-21	CLIP-seq
MIRT2446709	hsa-miR-2110	CLIP-seq
MIRT2446710	hsa-miR-3127-3p	CLIP-seq
MIRT2446711	hsa-miR-3147	CLIP-seq
MIRT2446712	hsa-miR-3150a-3p	CLIP-seq
MIRT2446713	hsa-miR-3175	CLIP-seq
MIRT2501058	hsa-miR-3661	CLIP-seq
MIRT2446714	hsa-miR-3667-3p	CLIP-seq
MIRT2501059	hsa-miR-3691-3p	CLIP-seq
MIRT2501060	hsa-miR-3921	CLIP-seq
MIRT2501061	hsa-miR-3977	CLIP-seq
MIRT2501062	hsa-miR-433	CLIP-seq
MIRT2446715	hsa-miR-4425	CLIP-seq
MIRT2677902	hsa-miR-4529-5p	CLIP-seq
MIRT2677903	hsa-miR-4649-3p	CLIP-seq
MIRT2501063	hsa-miR-4653-5p	CLIP-seq
MIRT2501064	hsa-miR-4660	CLIP-seq
MIRT2501065	hsa-miR-4736	CLIP-seq
MIRT2501066	hsa-miR-4742-5p	CLIP-seq
MIRT2501067	hsa-miR-4763-3p	CLIP-seq
MIRT2501068	hsa-miR-5047	CLIP-seq
MIRT2197786	hsa-miR-561	CLIP-seq
MIRT2197787	hsa-miR-590-5p	CLIP-seq
MIRT2501069	hsa-miR-631	CLIP-seq
MIRT2446716	hsa-miR-939	CLIP-seq

Show/Hide all (33)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003824	Function	Catalytic activity	IEA
GO:0005654	Component	Nucleoplasm	IDA	22422838
GO:0005654	Component	Nucleoplasm	IDA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	IDA	22422838
GO:0005829	Component	Cytosol	IBA
GO:0005829	Component	Cytosol	IDA	22422838
GO:0005829	Component	Cytosol	IDA
GO:0006400	Process	TRNA modification	IEA
GO:0007420	Process	Brain development	NAS	10915792
GO:0008033	Process	TRNA processing	IEA
GO:0009451	Process	RNA modification	IMP	22422838
GO:0016740	Function	Transferase activity	IEA
GO:0019901	Function	Protein kinase binding	NAS	10721722
GO:0035596	Function	Methylthiotransferase activity	IEA
GO:0035597	Function	TRNA-2-methylthio-N(6)-dimethylallyladenosine(37) synthase activity	IBA
GO:0035597	Function	TRNA-2-methylthio-N(6)-dimethylallyladenosine(37) synthase activity	IEA
GO:0035597	Function	TRNA-2-methylthio-N(6)-dimethylallyladenosine(37) synthase activity	IMP	22422838
GO:0035600	Process	TRNA methylthiolation	IEA
GO:0045664	Process	Regulation of neuron differentiation	NAS	10721722
GO:0045736	Process	Negative regulation of cyclin-dependent protein serine/threonine kinase activity	IDA	11882646
GO:0045786	Process	Negative regulation of cell cycle	TAS	17491008
GO:0045903	Process	Positive regulation of translational fidelity	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0051246	Process	Regulation of protein metabolic process	IEA
GO:0051536	Function	Iron-sulfur cluster binding	IEA
GO:0051539	Function	4 iron, 4 sulfur cluster binding	IEA
GO:0070131	Process	Positive regulation of mitochondrial translation	IEA
GO:0070900	Process	Mitochondrial tRNA modification	IBA
GO:0070900	Process	Mitochondrial tRNA modification	IEA

MIM	HGNC	e!Ensembl
608200	15880	ENSG00000101391

Q96SZ6

Protein name

Mitochondrial tRNA methylthiotransferase CDK5RAP1 (EC 2.8.4.3) (CDK5 activator-binding protein C42) (CDK5 regulatory subunit-associated protein 1) (mt-tRNA-2-methylthio-N6-dimethylallyladenosine synthase) (mt-tRNA-N6-(dimethylallyl)adenosine(37) methylthi

Protein function

Methylthiotransferase that catalyzes the conversion of N6-(dimethylallyl)adenosine (i(6)A) to 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 (adjacent to the 3'-end of the anticodon) of four mitochondrial DNA-encoded tRNAs

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00919	UPF0004	101 → 204	Uncharacterized protein family UPF0004	Family
PF04055	Radical_SAM	252 → 461	Radical SAM superfamily	Domain
PF01938	TRAM	515 → 589	TRAM domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas (PubMed:10721722). Expressed in neurons of central nervous tissue (PubMed:10721722, PubMed:11882646). {ECO:0000269|PubMed:10721722, ECO:0000269|PubM

Sequence

MHPLQCVLQVQRSLGWGPLASVSWLSLRMCRAHSSLSSTMCPSPERQEDGARKDFSSRLA
AGPTFQHFLKSASAPQEKLSSEVEDPPPYLMMDELLGRQRKVYLETYGCQMNVNDTEIAW
SILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKALKTRRPRSRVPLRIGI
LGCMAERLKEEILNREKMVDILAGPDAYRDLPRLLAVAESGQQAANVLLSLDETYADVMP
VQTSASATSAFVSIMRGCDNMCSYCIVPFTRGRERSRPIASILEEVKKLSEQVFLPPRPP
KVLGLQGLKEVTLLGQNVNSFRDNSEVQFNSAVPTNLSRGFTTNYKTKQGGLRFAHLLDQ
VSRVDPEMRIRFTSPHPKDFPDEVLQLIHERDNICKQIHLPAQSGSSRVLEAMRRGYSRE
AYVELVHHIRESIPGVSLSSDFIAGFCGETEEDHVQTVSLLREVQYNMGFLFAYSMRQKT
RAYHRLKDDVPEEVKLRRLEELITIFREEATKANQTSVGCTQLVLVEGLSKRSATDLCGR
NDGNLKVIFPDAEMEDVNNPGLRVRAQPGDYVLVKITSASSQTLRGHVLCRTTLRDSSAY
C

Sequence length

601

Interactions

View interactions

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (24)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
BILIARY TRACT CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CERVICAL CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ENDOMETRIAL CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ESOPHAGEAL CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ESTROGEN-RECEPTOR NEGATIVE BREAST CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTRIC CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEPATOCELLULAR CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG ADENOCARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-HODGKINS LYMPHOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-MELANOMA SKIN CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN CANCER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN ENDOMETRIOID CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN SEROUS CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PANCREATIC CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SQUAMOUS CELL LUNG CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (8)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
B-Cell Lymphomas	B-Cell Lymphoma	BEFREE	29552116		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	9460986	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	29552116		★★★★★ ★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	GWASDB_DG	18488026		★★★★★ ★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	29552116		★★★★★ ★☆☆☆☆ Found in Text Mining only
Myopathy	Myopathy	BEFREE	25738458		★★★★★ ★☆☆☆☆ Found in Text Mining only
Vitiligo	Vitiligo	BEFREE	22534366		★★★★★ ★☆☆☆☆ Found in Text Mining only
VITILIGO-ASSOCIATED MULTIPLE AUTOIMMUNE DISEASE SUSCEPTIBILITY 1 (finding)	Vitiligo-associated SYSTEMIC LUPUS ERYTHEMATOSUS	BEFREE	22534366		★★★★★ ★☆☆☆☆ Found in Text Mining only

CDK5RAP1 (CDK5RAP1 mitochondrial tRNA methylthiotransferase)