Gene Gene information from NCBI Gene database. Download as csv Download as pdf
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

72 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

33 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
PF01938	TRAM	515 → 589	TRAM domain	Domain
PF04055	Radical_SAM	252 → 461	Radical SAM superfamily	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)

Phenotype Name	Clinical Significance	Source	Reference	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. Show/Hide Unknown Diseases (24)
BILIARY TRACT CANCER	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CANCER	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CERVICAL CARCINOMA	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLORECTAL CANCER	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ENDOMETRIAL CANCER	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ESOPHAGEAL CANCER	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ESTROGEN-RECEPTOR NEGATIVE BREAST CANCER	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTRIC CANCER	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEPATOCELLULAR CARCINOMA	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG ADENOCARCINOMA	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG CANCER	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG CARCINOMA	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-HODGKINS LYMPHOMA	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-MELANOMA SKIN CARCINOMA	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN CANCER	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN CARCINOMA	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN ENDOMETRIOID CARCINOMA	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN SEROUS CARCINOMA	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PANCREATIC CARCINOMA	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CARCINOMA	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	30019117	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SQUAMOUS CELL LUNG CARCINOMA	—	GWAS catalog	34290314	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	35393509	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining Show/Hide Text Mining Associations (8)
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

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
CLK1	11	["Biliary tract cancer","Cancer","Cervical cancer","Endometrial cancer","Esophageal cancer","Estrogen-receptor negative breast cancer","Pancreatic cancer","Gastric cancer","Non-hodgkins lymphoma","Non-melanoma skin carcinoma","Ovarian serous carcinoma"]	[]	12	["GWAS catalog (Biliary tract cancer)","GWAS catalog (Cancer)","GWAS catalog (Cervical cancer)","GWAS catalog (Endometrial cancer)","GWAS catalog (Esophageal cancer)","GWAS catalog (Estrogen-receptor negative breast cancer)","GWAS catalog (Pancreatic cancer)","GWAS catalog (Gastric cancer)","GWAS catalog (Hepatocellular carcinoma)","GWAS catalog (Non-hodgkins lymphoma)","GWAS catalog (Non-melanoma skin carcinoma)","GWAS catalog (Ovarian serous carcinoma)"]
FAM83C	11	["Biliary tract cancer","Cancer","Cervical cancer","Endometrial cancer","Esophageal cancer","Estrogen-receptor negative breast cancer","Pancreatic cancer","Gastric cancer","Non-hodgkins lymphoma","Non-melanoma skin carcinoma","Ovarian serous carcinoma"]	[]	12	["GWAS catalog (Biliary tract cancer)","GWAS catalog (Cancer)","GWAS catalog (Cervical cancer)","GWAS catalog (Endometrial cancer)","GWAS catalog (Esophageal cancer)","GWAS catalog (Estrogen-receptor negative breast cancer)","GWAS catalog (Pancreatic cancer)","GWAS catalog (Gastric cancer)","GWAS catalog (Hepatocellular carcinoma)","GWAS catalog (Non-hodgkins lymphoma)","GWAS catalog (Non-melanoma skin carcinoma)","GWAS catalog (Ovarian serous carcinoma)"]
TRAK2	11	["Biliary tract cancer","Cancer","Cervical cancer","Endometrial cancer","Esophageal cancer","Estrogen-receptor negative breast cancer","Pancreatic cancer","Gastric cancer","Non-hodgkins lymphoma","Non-melanoma skin carcinoma","Ovarian serous carcinoma"]	[]	12	["GWAS catalog (Biliary tract cancer)","GWAS catalog (Cancer)","GWAS catalog (Cervical cancer)","GWAS catalog (Endometrial cancer)","GWAS catalog (Esophageal cancer)","GWAS catalog (Estrogen-receptor negative breast cancer)","GWAS catalog (Pancreatic cancer)","GWAS catalog (Gastric cancer)","GWAS catalog (Hepatocellular carcinoma)","GWAS catalog (Non-hodgkins lymphoma)","GWAS catalog (Non-melanoma skin carcinoma)","GWAS catalog (Ovarian serous carcinoma)"]
RNF19A	11	["Biliary tract cancer","Cancer","Cervical cancer","Endometrial cancer","Esophageal cancer","Estrogen-receptor negative breast cancer","Pancreatic cancer","Gastric cancer","Non-hodgkins lymphoma","Non-melanoma skin carcinoma","Ovarian serous carcinoma"]	[]	12	["GWAS catalog (Biliary tract cancer)","GWAS catalog (Cancer)","GWAS catalog (Cervical cancer)","GWAS catalog (Endometrial cancer)","GWAS catalog (Esophageal cancer)","GWAS catalog (Estrogen-receptor negative breast cancer)","GWAS catalog (Pancreatic cancer)","GWAS catalog (Gastric cancer)","GWAS catalog (Hepatocellular carcinoma)","GWAS catalog (Non-hodgkins lymphoma)","GWAS catalog (Non-melanoma skin carcinoma)","GWAS catalog (Ovarian serous carcinoma)"]
BPIFA3	11	["Biliary tract cancer","Cancer","Cervical cancer","Endometrial cancer","Esophageal cancer","Estrogen-receptor negative breast cancer","Pancreatic cancer","Gastric cancer","Non-hodgkins lymphoma","Non-melanoma skin carcinoma","Ovarian serous carcinoma"]	[]	12	["GWAS catalog (Biliary tract cancer)","GWAS catalog (Cancer)","GWAS catalog (Cervical cancer)","GWAS catalog (Endometrial cancer)","GWAS catalog (Esophageal cancer)","GWAS catalog (Estrogen-receptor negative breast cancer)","GWAS catalog (Pancreatic cancer)","GWAS catalog (Gastric cancer)","GWAS catalog (Hepatocellular carcinoma)","GWAS catalog (Non-hodgkins lymphoma)","GWAS catalog (Non-melanoma skin carcinoma)","GWAS catalog (Ovarian serous carcinoma)"]

CDK5RAP1 (CDK5RAP1 mitochondrial tRNA methylthiotransferase)

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