CDK5RAP1

Summary

CDK5RAP1 (CDK5RAP1 mitochondrial tRNA methylthiotransferase, HGNC:15880) is a protein-coding gene on chromosome 20q11.21, encoding Mitochondrial tRNA methylthiotransferase CDK5RAP1 (Q96SZ6). 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 (Ser(UCN), Phe, Tyr and Trp).

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 kinase 5 activity. Alternative splicing results in multiple transcript variants that encode different isoforms.

Source: NCBI Gene 51654 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 92 total
• MANE Select transcript: NM_016408

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15880
Approved symbol	CDK5RAP1
Name	CDK5RAP1 mitochondrial tRNA methylthiotransferase
Location	20q11.21
Locus type	gene with protein product
Status	Approved
Aliases	CGI-05, HSPC167, C42
Ensembl gene	ENSG00000101391
Ensembl biotype	protein_coding
OMIM	608200
Entrez	51654

Gene structure

Transcript identifiers

Ensembl transcripts: 41 — 30 protein_coding, 9 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000339269, ENST00000346416, ENST00000357886, ENST00000427097, ENST00000460043, ENST00000461356, ENST00000461710, ENST00000471264, ENST00000473791, ENST00000473997, ENST00000477105, ENST00000481964, ENST00000482967, ENST00000488723, ENST00000496381, ENST00000498525, ENST00000874260, ENST00000874261, ENST00000874262, ENST00000874263, ENST00000874264, ENST00000874265, ENST00000874266, ENST00000874267, ENST00000874268, ENST00000912367, ENST00000912368, ENST00000912369, ENST00000912370, ENST00000912371, ENST00000912372, ENST00000912373, ENST00000912374, ENST00000945685, ENST00000945686, ENST00000945687, ENST00000945688, ENST00000945689, ENST00000945690, ENST00000945691, ENST00000945692

RefSeq mRNA: 6 — MANE Select: NM_016408 NM_001278167, NM_001278168, NM_001278169, NM_001365728, NM_016082, NM_016408

CCDS: CCDS13219, CCDS63255, CCDS93031

Canonical transcript exons

ENST00000346416 — 14 exons

Exon	Start	End
ENSE00002729245	33396761	33397084
ENSE00003702519	33379461	33379691
ENSE00003702850	33366859	33367008
ENSE00003703143	33387323	33387533
ENSE00003704569	33372642	33372697
ENSE00003704982	33392142	33392242
ENSE00003705860	33370499	33370629
ENSE00003706355	33395013	33395116
ENSE00003706683	33394032	33394066
ENSE00003708199	33374115	33374212
ENSE00003708834	33360351	33360491
ENSE00003708909	33385650	33385770
ENSE00003711394	33358839	33359123
ENSE00003850948	33401428	33401519

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 93.43.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.2647 / max 135.4164, expressed in 1815 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
186953	21.2647	1815

Top tissues by expression

288 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	93.43	gold quality
right lobe of thyroid gland	UBERON:0001119	93.17	gold quality
apex of heart	UBERON:0002098	93.01	gold quality
left lobe of thyroid gland	UBERON:0001120	92.62	gold quality
skin of leg	UBERON:0001511	92.47	gold quality
cerebellar hemisphere	UBERON:0002245	92.45	gold quality
cerebellar cortex	UBERON:0002129	92.39	gold quality
right hemisphere of cerebellum	UBERON:0014890	92.33	gold quality
skin of abdomen	UBERON:0001416	92.22	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	92.18	gold quality
thyroid gland	UBERON:0002046	92.00	gold quality
spleen	UBERON:0002106	91.75	gold quality
gastrocnemius	UBERON:0001388	91.72	gold quality
adenohypophysis	UBERON:0002196	91.71	gold quality
muscle of leg	UBERON:0001383	91.61	gold quality
tibial nerve	UBERON:0001323	91.43	gold quality
cerebellum	UBERON:0002037	91.43	gold quality
hindlimb stylopod muscle	UBERON:0004252	91.38	gold quality
small intestine Peyer’s patch	UBERON:0003454	91.36	gold quality
mucosa of transverse colon	UBERON:0004991	91.23	gold quality
tongue squamous epithelium	UBERON:0006919	90.92	gold quality
right ovary	UBERON:0002118	90.88	gold quality
lower esophagus mucosa	UBERON:0035834	90.87	gold quality
pituitary gland	UBERON:0000007	90.85	gold quality
zone of skin	UBERON:0000014	90.85	gold quality
endothelial cell	CL:0000115	90.80	gold quality
putamen	UBERON:0001874	90.73	gold quality
right frontal lobe	UBERON:0002810	90.70	gold quality
body of pancreas	UBERON:0001150	90.67	gold quality
muscle organ	UBERON:0001630	90.57	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.71

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting CDK5RAP1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-646	99.68	67.84	1645
HSA-MIR-4524A-5P	99.57	71.73	1193
HSA-MIR-4524B-5P	99.57	71.68	1195
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-6719-3P	99.29	67.78	1387
HSA-MIR-5693	99.24	66.67	1106
HSA-MIR-670-3P	99.03	68.88	2404
HSA-MIR-181A-2-3P	98.91	67.60	1168
HSA-MIR-1301-3P	98.64	68.27	1071
HSA-MIR-5047	98.64	68.62	1035
HSA-MIR-6509-3P	98.32	67.33	1343
HSA-MIR-943	97.81	64.42	694
HSA-MIR-6509-5P	97.39	68.27	969
HSA-MIR-4436B-5P	96.71	68.37	1346
HSA-MIR-331-5P	96.59	67.94	705

Literature-anchored findings (GeneRIF, showing 5)

• CDK5RAP1 is a radical SAM enzyme, which postsynthetically converts the RNA modification N6-isopentenyladenosine into 2-methylthio-N6-isopentenyladenosine. (PMID:22422838)
• CDK5RAP1 may be a risk factor of vitiligo in the Korean population (PMID:22534366)
• data indicated that CDK5RAP1 deficiency induced cell cycle arrest and apoptosis in human breast cancer (PMID:25607831)
• Which resulted in respiratory defects in Cdk5rap1 knockout (KO) mice. (PMID:25738458)
• The mitochondrial localization of ms2i6A modification was diminished in HeLa cells when transfected with siRNA against Cdk5 regulatory subunit-associated protein 1 (Cdk5rap1), suggesting that the modification occurs in tRNAs in mitochondria. (PMID:28981754)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cdk5rap1	ENSMUSG00000027487
rattus_norvegicus	Cdk5rap1	ENSRNOG00000015696

Paralogs (1): CDKAL1 (ENSG00000145996)

Protein

Protein identifiers

Mitochondrial tRNA methylthiotransferase CDK5RAP1 — Q96SZ6 (reviewed: Q96SZ6)

Alternative names: CDK5 activator-binding protein C42, CDK5 regulatory subunit-associated protein 1, mt-tRNA-2-methylthio-N6-dimethylallyladenosine synthase, mt-tRNA-N6-(dimethylallyl)adenosine(37) methylthiotransferase

All UniProt accessions (5): Q96SZ6, A0A0S2Z592, A0A0S2Z5J9, H0Y721, Q53H36

UniProt curated annotations — full annotation on UniProt →

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 (Ser(UCN), Phe, Tyr and Trp). Essential for efficient and highly accurate protein translation by the ribosome. Specifically inhibits CDK5 activation by CDK5R1. Essential for efficient mitochondrial protein synthesis and respiratory chain; shows pathological consequences in mitochondrial disease.

Subunit / interactions. Interacts with CDK5R1 (p35 form). CDK5RAP1, CDK5RAP2 and CDK5RAP3 show competitive binding to CDK5R1. Forms a complex with CDK5R1 and CDK5.

Subcellular location. Mitochondrion.

Tissue specificity. Expressed in heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas. Expressed in neurons of central nervous tissue. Mainly expressed in brain, placenta and testis. High expression in placenta and lung.

Cofactor. Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.

Miscellaneous. May be due to intron retention. Absence of the mitochondrial target sequence which may lead to miss-localization.

Similarity. Belongs to the methylthiotransferase family. MiaB subfamily.

Isoforms (6)

UniProt ID	Names	Canonical?
Q96SZ6-1	1	yes
Q96SZ6-2	2
Q96SZ6-3	3, CDK5RAP1_v1, isoform a
Q96SZ6-4	4, isoform d
Q96SZ6-5	5, CDK5RAP1_v4
Q96SZ6-6	6, CDK5RAP1_v3

RefSeq proteins (6): NP_001265096, NP_001265097, NP_001265098, NP_001352657, NP_057166, NP_057492* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002792	TRAM_dom	Domain
IPR005839	Methylthiotransferase	Family
IPR006463	MiaB_methiolase	Family
IPR006638	Elp3/MiaA/NifB-like_rSAM	Domain
IPR007197	rSAM	Domain
IPR013848	Methylthiotransferase_N	Domain
IPR020612	Methylthiotransferase_CS	Conserved_site
IPR023404	rSAM_horseshoe	Homologous_superfamily
IPR038135	Methylthiotransferase_N_sf	Homologous_superfamily
IPR058240	rSAM_sf	Homologous_superfamily

Pfam: PF00919, PF01938, PF04055

Catalyzed reactions (Rhea), 1 shown:

• N(6)-dimethylallyladenosine(37) in tRNA + (sulfur carrier)-SH + AH2 + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + (sulfur carrier)-H + 5’-deoxyadenosine + L-methionine + A + S-adenosyl-L-homocysteine + 2 H(+) (RHEA:37067)

UniProt features (30 total): sequence conflict 9, splice variant 7, binding site 6, mutagenesis site 3, domain 3, transit peptide 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96SZ6-F1	83.24	0.61

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (6): 265; 109; 145; 183; 258; 262

Mutagenesis-validated functional residues (3):

Position	Phenotype
258	loss of mitochondrial trnas methylthiotransferase activity; when associated with a-262 and a-265.
262	loss of mitochondrial trnas methylthiotransferase activity; when associated with a-258 and a-265.
265	loss of mitochondrial trnas methylthiotransferase activity; when associated with a-258 and a-262.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 190 (showing top): GOBP_REGULATION_OF_PHOSPHORYLATION, GOBP_NEGATIVE_REGULATION_OF_KINASE_ACTIVITY, GOBP_TRNA_METABOLIC_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_MITOCHONDRIAL_TRANSLATION, GOBP_REGULATION_OF_TRANSFERASE_ACTIVITY, GOBP_NEUROGENESIS, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_RNA_MODIFICATION, GOBP_REGULATION_OF_NEURON_DIFFERENTIATION, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE, GOBP_REGULATION_OF_CELL_CYCLE, GOBP_NEGATIVE_REGULATION_OF_PHOSPHORUS_METABOLIC_PROCESS

GO Biological Process (12): brain development (GO:0007420), RNA modification (GO:0009451), regulation of neuron differentiation (GO:0045664), negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736), negative regulation of cell cycle (GO:0045786), positive regulation of translational fidelity (GO:0045903), positive regulation of mitochondrial translation (GO:0070131), mitochondrial tRNA modification (GO:0070900), tRNA modification (GO:0006400), tRNA processing (GO:0008033), tRNA methylthiolation (GO:0035600), regulation of protein metabolic process (GO:0051246)

GO Molecular Function (8): protein kinase binding (GO:0019901), tRNA-2-methylthio-N(6)-dimethylallyladenosine(37) synthase activity (GO:0035597), metal ion binding (GO:0046872), 4 iron, 4 sulfur cluster binding (GO:0051539), catalytic activity (GO:0003824), transferase activity (GO:0016740), methylthiotransferase activity (GO:0035596), iron-sulfur cluster binding (GO:0051536)

GO Cellular Component (4): nucleoplasm (GO:0005654), mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
positive regulation of translation	2
mitochondrion	2
tRNA modification	2
cellular anatomical structure	2
cytoplasm	2
central nervous system development	1
animal organ development	1
head development	1
RNA metabolic process	1
macromolecule modification	1
neuron differentiation	1
regulation of cell differentiation	1
regulation of cyclin-dependent protein serine/threonine kinase activity	1
cyclin-dependent protein serine/threonine kinase activity	1
negative regulation of cell cycle	1
negative regulation of protein serine/threonine kinase activity	1
negative regulation of cyclin-dependent protein kinase activity	1
cell cycle	1
negative regulation of cellular process	1
regulation of cell cycle	1
regulation of translational fidelity	1
mitochondrial translation	1
regulation of mitochondrial translation	1
mitochondrial tRNA processing	1
mitochondrial RNA modification	1
tRNA processing	1
RNA modification	1
RNA processing	1
tRNA metabolic process	1
protein metabolic process	1
regulation of macromolecule metabolic process	1
regulation of primary metabolic process	1
kinase binding	1
methylthiotransferase activity	1
tRNA methylthiolation	1
catalytic activity, acting on a tRNA	1
cation binding	1
iron-sulfur cluster binding	1
molecular_function	1
catalytic activity	1

Protein interactions and networks

STRING

1882 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CDK5RAP1	CDK5	Q00535	910
CDK5RAP1	TRIT1	Q9H3H1	717
CDK5RAP1	CDK5R1	Q15078	660
CDK5RAP1	GTPBP3	Q969Y2	613
CDK5RAP1	YRDC	Q86U90	560
CDK5RAP1	OSGEPL1	Q9H4B0	555
CDK5RAP1	TRMU	O75648	544
CDK5RAP1	MOCS1	Q9NZB8	538
CDK5RAP1	TYW1	Q9NV66	520
CDK5RAP1	CNOT11	Q9UKZ1	507
CDK5RAP1	CDK5RAP3	Q96JB5	488
CDK5RAP1	QTRT2	Q9H974	485
CDK5RAP1	POLR3H	Q9Y535	479
CDK5RAP1	POLR3F	Q9H1D9	475
CDK5RAP1	RSAD1	Q9HA92	475

IntAct

63 interactions, top by confidence:

A	B	Type	Score
HEXIM2	AHCYL1	psi-mi:“MI:0914”(association)	0.740
NDUFS6	NDUFS8	psi-mi:“MI:0914”(association)	0.640
CARNMT1	NUP42	psi-mi:“MI:0914”(association)	0.640
CCT6A	TXNDC9	psi-mi:“MI:0914”(association)	0.530
YBX1	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
PLA2G10	CHEK1	psi-mi:“MI:0914”(association)	0.530
KIAA0930	ATG7	psi-mi:“MI:0914”(association)	0.530
FAM174A	BLTP3B	psi-mi:“MI:0914”(association)	0.530
CLEC11A	VWA8	psi-mi:“MI:0914”(association)	0.530
VASP	GTPBP1	psi-mi:“MI:0914”(association)	0.530
UQCRFS1	NDUFAB1	psi-mi:“MI:0914”(association)	0.530
GPSM3	ATE1	psi-mi:“MI:0914”(association)	0.530
KCTD17	CBX4	psi-mi:“MI:0914”(association)	0.530
RIPK4	VWA8	psi-mi:“MI:0914”(association)	0.350
ATAD3A	TMEM223	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
IMMP2L	ANKHD1-EIF4EBP3	psi-mi:“MI:0914”(association)	0.350
FKBP5	IFT56	psi-mi:“MI:0914”(association)	0.350
SFTPA2	PRPSAP2	psi-mi:“MI:0914”(association)	0.350
CARNMT1	LENG9	psi-mi:“MI:0914”(association)	0.350
PDZK1	ZBTB5	psi-mi:“MI:0914”(association)	0.350
GPSM3	PHF1	psi-mi:“MI:0914”(association)	0.350
HS1BP3	TAF5L	psi-mi:“MI:0914”(association)	0.350
CDK5RAP1	XRCC6	psi-mi:“MI:0914”(association)	0.350
KCTD17	PXDNL	psi-mi:“MI:0914”(association)	0.350
MRM2	VWA8	psi-mi:“MI:0914”(association)	0.350
TRIM43	VWA8	psi-mi:“MI:0914”(association)	0.350
YARS2	VWA8	psi-mi:“MI:0914”(association)	0.350
MRPS24	VWA8	psi-mi:“MI:0914”(association)	0.350

BioGRID (127): CDK5RAP1 (Affinity Capture-MS), CDK5RAP1 (Affinity Capture-MS), CDK5RAP1 (Affinity Capture-MS), CDK5RAP1 (Affinity Capture-MS), CDK5RAP1 (Affinity Capture-MS), ZMYND19 (Affinity Capture-MS), NDUFAF5 (Affinity Capture-MS), XRCC6 (Affinity Capture-MS), XRCC5 (Affinity Capture-MS), CDK5RAP1 (Affinity Capture-MS), CDK5RAP1 (Affinity Capture-MS), ZZEF1 (Affinity Capture-MS), ARMC8 (Affinity Capture-MS), MATR3 (Affinity Capture-MS), CDK5RAP1 (Affinity Capture-RNA)

ESM2 similar proteins: A0A7J6F8C5, A0FKE6, A2Y3Q5, A4GNA8, A6QLU1, A7DZP8, F4JHA2, F4KAK5, O04921, O22436, O42479, O57478, O59786, P0DKG8, P11605, P15719, P16622, P17569, P22315, P22600, P22830, P35571, P39865, P39867, P39868, P42043, P42044, P42045, P43304, P52426, Q05145, Q0DIV0, Q2R1U4, Q3YA36, Q42606, Q4R755, Q5JN42, Q64521, Q69TB1, Q6AVG6

Diamond homologs: A0M7D3, A0Q0M5, A0RHE4, A1BIX2, A3DDI9, A4IMH7, A4J5Q8, A4SCW6, A5D2K1, A5FIU2, A5G670, A5I2S3, A5IJD4, A6H119, A6KZJ2, A6LEM6, A6LWI1, A7FUL1, A7GE46, A7GRA2, A7MQS5, A7Z4X2, A8FDH0, A8LSE7, A8Z642, A9VS16, B0K1A1, B0K9L4, B0S9E2, B0SS31, B0UUU9, B1HR59, B1IM69, B1KSA4, B1L8F3, B2RKG6, B2TIA8, B2V276, B2V930, B3EGT4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

92 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	68
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2867 predictions. Top by Δscore:

Variant	Effect	Δscore
20:33360487:CTGAG:C	acceptor_gain	1.0000
20:33360489:GAGCT:G	acceptor_loss	1.0000
20:33360490:AGC:A	acceptor_loss	1.0000
20:33360491:GC:G	acceptor_loss	1.0000
20:33360492:C:CC	acceptor_gain	1.0000
20:33360493:T:A	acceptor_loss	1.0000
20:33366849:ATGG:A	donor_gain	1.0000
20:33366857:ACC:A	donor_gain	1.0000
20:33366858:CCC:C	donor_gain	1.0000
20:33366876:A:AC	donor_gain	1.0000
20:33366877:C:CC	donor_gain	1.0000
20:33367012:T:TC	acceptor_gain	1.0000
20:33370498:CCTGT:C	donor_gain	1.0000
20:33370626:ACACC:A	acceptor_loss	1.0000
20:33370630:C:CG	acceptor_loss	1.0000
20:33374094:C:CA	donor_gain	1.0000
20:33374116:C:CA	donor_gain	1.0000
20:33374139:CGG:C	donor_gain	1.0000
20:33385644:CTTCA:C	donor_loss	1.0000
20:33385645:TTCAC:T	donor_loss	1.0000
20:33385646:TCA:T	donor_loss	1.0000
20:33385647:CAC:C	donor_loss	1.0000
20:33385648:A:AT	donor_loss	1.0000
20:33385649:CC:C	donor_loss	1.0000
20:33385672:T:TA	donor_gain	1.0000
20:33387318:CTCA:C	donor_loss	1.0000
20:33387320:CA:C	donor_loss	1.0000
20:33387321:A:AC	donor_gain	1.0000
20:33387321:ACAC:A	donor_loss	1.0000
20:33387322:C:CA	donor_gain	1.0000

AlphaMissense

3857 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:33370613:G:C	S440R	0.999
20:33370613:G:T	S440R	0.999
20:33370615:T:G	S440R	0.999
20:33385726:A:T	V267D	0.999
20:33385731:G:C	C265W	0.999
20:33385732:C:T	C265Y	0.999
20:33385733:A:G	C265R	0.999
20:33395085:A:C	N112K	0.999
20:33395085:A:T	N112K	0.999
20:33379494:A:C	F372L	0.998
20:33379494:A:T	F372L	0.998
20:33379496:A:G	F372L	0.998
20:33379498:C:G	R371P	0.998
20:33379540:A:G	L357P	0.998
20:33379653:A:C	N319K	0.998
20:33379653:A:T	N319K	0.998
20:33379659:A:C	N317K	0.998
20:33379659:A:T	N317K	0.998
20:33379662:C:A	Q316H	0.998
20:33379662:C:G	Q316H	0.998
20:33385714:C:G	R271P	0.998
20:33385732:C:A	C265F	0.998
20:33385732:C:G	C265S	0.998
20:33385733:A:T	C265S	0.998
20:33385753:C:T	C258Y	0.998
20:33385754:A:G	C258R	0.998
20:33385756:C:T	G257D	0.998
20:33385757:C:G	G257R	0.998
20:33387531:A:G	C183R	0.998
20:33392142:C:G	G182R	0.998

dbSNP variants (sampled 300 via entrez): RS1000048479 (20:33391842 T>G), RS1000101845 (20:33392115 T>C), RS1000148161 (20:33389316 C>T), RS1000298505 (20:33367083 G>A,C), RS1000349972 (20:33398082 T>C), RS1000384503 (20:33360760 A>C), RS1000427974 (20:33402903 C>A), RS1000516576 (20:33389002 G>A), RS1000527032 (20:33372516 A>G), RS1000628725 (20:33365619 A>C), RS1000635433 (20:33394340 T>C), RS1000730236 (20:33403563 C>T), RS1000794929 (20:33401656 A>C), RS1000841508 (20:33369230 T>A,C), RS1000862466 (20:33403348 A>G)

Disease associations

OMIM: gene MIM:608200 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST004067_169	Hip circumference adjusted for BMI	2.000000e-07
GCST004067_63	Hip circumference adjusted for BMI	1.000000e-09
GCST006627_36	Diastolic blood pressure	7.000000e-12
GCST012227_1366	Hip circumference adjusted for BMI	3.000000e-10
GCST90002392_102	Mean corpuscular volume	1.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0008039	BMI-adjusted hip circumference
EFO:0006336	diastolic blood pressure

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	increases abundance, increases oxidation, affects expression, affects cotreatment	2
Ozone	increases abundance, affects expression, affects cotreatment, increases oxidation	2
Cadmium Chloride	decreases expression	2
TAK-243	increases sumoylation	1
bufotalin	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
beta-lapachone	increases expression	1
sodium arsenite	decreases expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
abrine	increases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Arsenic	affects methylation	1
Benzo(a)pyrene	affects methylation	1
Cannabidiol	decreases expression	1
Dimethyl Sulfoxide	increases expression	1
Doxorubicin	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Valproic Acid	increases expression	1
Isotretinoin	decreases expression	1
Cyclosporine	increases expression	1
Volatile Organic Compounds	affects cotreatment, increases oxidation	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_SI40	HAP1 CDK5RAP1 (-) 1	Cancer cell line	Male
CVCL_SI41	HAP1 CDK5RAP1 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.