CKMT1A

Summary

CKMT1A (creatine kinase, mitochondrial 1A, HGNC:31736) is a protein-coding gene on chromosome 15q15.3, encoding Creatine kinase U-type, mitochondrial (P12532). Reversibly catalyzes the transfer of phosphate between ATP and various phosphogens (e.g. creatine phosphate).

Mitochondrial creatine (MtCK) kinase is responsible for the transfer of high energy phosphate from mitochondria to the cytosolic carrier, creatine. It belongs to the creatine kinase isoenzyme family. It exists as two isoenzymes, sarcomeric MtCK and ubiquitous MtCK, encoded by separate genes. Mitochondrial creatine kinase occurs in two different oligomeric forms: dimers and octamers, in contrast to the exclusively dimeric cytosolic creatine kinase isoenzymes. Many malignant cancers with poor prognosis have shown overexpression of ubiquitous mitochondrial creatine kinase; this may be related to high energy turnover and failure to eliminate cancer cells via apoptosis. Ubiquitous mitochondrial creatine kinase has 80% homology with the coding exons of sarcomeric mitochondrial creatine kinase. Two genes located near each other on chromosome 15 have been identified which encode identical mitochondrial creatine kinase proteins.

Source: NCBI Gene 548596 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 36 total
• Druggable target: yes
• MANE Select transcript: NM_001321926

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31736
Approved symbol	CKMT1A
Name	creatine kinase, mitochondrial 1A
Location	15q15.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000223572
Ensembl biotype	protein_coding
OMIM	613415
Entrez	548596

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 21 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000411750, ENST00000413453, ENST00000415044, ENST00000434505, ENST00000457648, ENST00000479938, ENST00000483604, ENST00000626814, ENST00000909067, ENST00000909068, ENST00000909069, ENST00000909070, ENST00000909071, ENST00000909072, ENST00000909073, ENST00000909074, ENST00000909075, ENST00000909076, ENST00000932396, ENST00000932397, ENST00000932398, ENST00000932399, ENST00000945384, ENST00000945385

RefSeq mRNA: 5 — MANE Select: NM_001321926 NM_001015001, NM_001321926, NM_001321927, NM_001321928, NM_001321929

CCDS: CCDS32217

Canonical transcript exons

ENST00000413453 — 9 exons

Exon	Start	End
ENSE00001634760	43698641	43698766
ENSE00001687656	43694804	43695002
ENSE00001693317	43696240	43696363
ENSE00001702905	43698014	43698148
ENSE00001765312	43695688	43695909
ENSE00001823401	43693859	43694199
ENSE00003598934	43696039	43696124
ENSE00003784312	43695206	43695301
ENSE00003901984	43698973	43699222

Expression profiles

Bgee: expression breadth ubiquitous, 129 present calls, max score 99.18.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	99.18	gold quality
cerebellar cortex	UBERON:0002129	99.10	gold quality
cerebellar hemisphere	UBERON:0002245	99.10	gold quality
cerebellum	UBERON:0002037	99.08	gold quality
mucosa of transverse colon	UBERON:0004991	98.67	gold quality
superior frontal gyrus	UBERON:0002661	97.84	gold quality
duodenum	UBERON:0002114	97.81	gold quality
rectum	UBERON:0001052	97.69	gold quality
primary visual cortex	UBERON:0002436	97.34	gold quality
esophagus mucosa	UBERON:0002469	96.20	gold quality
Brodmann (1909) area 9	UBERON:0013540	96.13	gold quality
right frontal lobe	UBERON:0002810	96.03	gold quality
frontal cortex	UBERON:0001870	95.86	gold quality
prefrontal cortex	UBERON:0000451	95.56	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	95.42	gold quality
cerebral cortex	UBERON:0000956	93.79	gold quality
skin of abdomen	UBERON:0001416	93.36	gold quality
anterior cingulate cortex	UBERON:0009835	92.71	gold quality
minor salivary gland	UBERON:0001830	92.63	gold quality
zone of skin	UBERON:0000014	92.61	gold quality
lower esophagus mucosa	UBERON:0035834	92.58	gold quality
saliva-secreting gland	UBERON:0001044	92.37	gold quality
hypothalamus	UBERON:0001898	92.16	gold quality
skin of leg	UBERON:0001511	92.06	gold quality
brain	UBERON:0000955	91.89	gold quality
nucleus accumbens	UBERON:0001882	91.25	gold quality
transverse colon	UBERON:0001157	90.84	gold quality
putamen	UBERON:0001874	89.45	gold quality
small intestine Peyer’s patch	UBERON:0003454	89.43	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.26	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.60

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting CKMT1A, 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-4534	99.99	66.58	1907
HSA-MIR-3612	99.45	66.02	1333
HSA-MIR-650	99.45	65.77	1309
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-2392	99.43	67.50	708
HSA-MIR-5697	99.39	67.74	1249
HSA-MIR-1909-3P	99.03	66.56	1662
HSA-MIR-1207-3P	98.99	66.22	1532
HSA-MIR-4443	98.02	66.25	1928
HSA-MIR-4294	97.86	65.72	1110
HSA-MIR-924	97.78	66.21	681
HSA-MIR-526B-5P	97.41	67.99	1074
HSA-MIR-4529-5P	96.74	65.77	569
HSA-MIR-6508-3P	96.73	65.48	576

Literature-anchored findings (GeneRIF, showing 13)

• MtCK, but not NDPK-D, shows some specificity in the nature of the lipids transferred and it is not active with phosphatidylcholine alone (PMID:17028143)
• uMtCK in prostate neoplasm cells (LNCaP) contributes to overproduction of reactive oxygen species, activation of Akt signaling pathway and more aggressive phenotypes including androgen independence development. (PMID:19415690)
• ASB9 interacts with the creatine kinase system and negatively regulates cell growth. (PMID:20302626)
• the knock-down of the mitochondrial creatine kinase-1 (CKMT1) by RNA interference causes the dissipation of the mitochondrial membrane potential (PMID:23880370)
• CKMT1 is a key regulator of the permeability transition pore through a complex that is distinct from the classical permeability transition pore. (PMID:24522192)
• Mitochondrial creatine kinase CKMT1 is necessary for survival of EVI1-expressing cells in subjects with EVI1-positive AML. (PMID:28191887)
• These findings suggest that activation of the phosphocreatine energy shuttle by MtCK1 Y153 phosphorylation creates a druggable metabolic vulnerability in cancer. (PMID:30174304)
• Mitochondrial creatine kinase 1 in non-small cell lung cancer progression and hypoxia adaptation. (PMID:34210337)
• CKMT1A is a novel potential prognostic biomarker in patients with endometrial cancer. (PMID:35077462)
• An integrative pan-cancer analysis of molecular characteristics and oncogenic role of mitochondrial creatine kinase 1A (CKMT1A) in human tumors. (PMID:35705641)
• A Zeb1/MtCK1 metabolic axis controls osteoclast activation and skeletal remodeling. (PMID:36843552)
• Ckmt1 is Dispensable for Mitochondrial Bioenergetics Within White/Beige Adipose Tissue. (PMID:37954502)
• Context-dependent roles for ubiquitous mitochondrial creatine kinase CKMT1 in breast cancer progression. (PMID:38615320)

Cross-species orthologs

12 orthologs

Organism	Symbol	Gene ID
danio_rerio	ckmt1	ENSDARG00000016598
mus_musculus	Ckmt1	ENSMUSG00000000308
rattus_norvegicus	Ckmt1	ENSRNOG00000014573
drosophila_melanogaster	Argk1	FBGN0000116
drosophila_melanogaster	Argk2	FBGN0035957
drosophila_melanogaster	CG4546	FBGN0038373
drosophila_melanogaster	CG30274	FBGN0050274
caenorhabditis_elegans		WBGENE00009706
caenorhabditis_elegans	ZC434.8	WBGENE00013894
caenorhabditis_elegans	F32B5.1	WBGENE00017975
caenorhabditis_elegans		WBGENE00018519
caenorhabditis_elegans	W10C8.5	WBGENE00021128

Paralogs (4): CKM (ENSG00000104879), CKMT2 (ENSG00000131730), CKB (ENSG00000166165), CKMT1B (ENSG00000237289)

Protein

Protein identifiers

Creatine kinase U-type, mitochondrial — P12532 (reviewed: P12532)

Alternative names: Acidic-type mitochondrial creatine kinase, Ubiquitous mitochondrial creatine kinase

All UniProt accessions (5): C9J8F6, C9JT96, P12532, F8WCN3, F8WDP9

UniProt curated annotations — full annotation on UniProt →

Function. Reversibly catalyzes the transfer of phosphate between ATP and various phosphogens (e.g. creatine phosphate). Creatine kinase isoenzymes play a central role in energy transduction in tissues with large, fluctuating energy demands, such as skeletal muscle, heart, brain and spermatozoa.

Subunit / interactions. Exists as an octamer composed of four MTCK homodimers.

Subcellular location. Mitochondrion inner membrane.

Miscellaneous. Mitochondrial creatine kinase binds cardiolipin.

Similarity. Belongs to the ATP:guanido phosphotransferase family.

Isoforms (2)

UniProt ID	Names	Canonical?
P12532-1	1	yes
P12532-2	2

RefSeq proteins (5): NP_001015001, NP_001308855, NP_001308856, NP_001308857, NP_001308858 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000749	ATP-guanido_PTrfase	Family
IPR014746	Gln_synth/guanido_kin_cat_dom	Homologous_superfamily
IPR022413	ATP-guanido_PTrfase_N	Domain
IPR022414	ATP-guanido_PTrfase_cat	Domain
IPR022415	ATP-guanido_PTrfase_AS	Active_site
IPR036802	ATP-guanido_PTrfase_N_sf	Homologous_superfamily

Pfam: PF00217, PF02807

Enzyme classification (BRENDA):

• EC 2.7.3.2 — creatine kinase (BRENDA: 45 organisms, 67 substrates, 117 inhibitors, 317 Km, 122 kcat entries)

Substrate kinetics (BRENDA)

10 substrates with measured Km, best-characterized 10. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
ATP	0.042–20	133
CREATINE	0.35–167	102
PHOSPHOCREATINE	0.51–8.97	23
ADP	0.015–1.2	22
CREATINE PHOSPHATE	0.23–50	11
ALPHA-(RP)-BORANO SUBSTITUTED ADP	1	1
ALPHA-(SP)-BORANO SUBSTITUTED ADP	0.008	1
GLYCOCYAMINE	6.7	1
CYCLOCREATINE	—	0
N-ETHYLGLYCOCYAMINE	—	0

Catalyzed reactions (Rhea), 1 shown:

• creatine + ATP = N-phosphocreatine + ADP + H(+) (RHEA:17157)

UniProt features (55 total): helix 17, strand 13, binding site 6, turn 6, modified residue 5, sequence conflict 2, domain 2, transit peptide 1, chain 1, splice variant 1, region of interest 1

Structure

Experimental structures (PDB)

9 structures.

PDB	Method	Resolution (Å)
9B14	ELECTRON MICROSCOPY	2.2
9B0T	ELECTRON MICROSCOPY	2.3
9B05	ELECTRON MICROSCOPY	2.4
9B0U	ELECTRON MICROSCOPY	2.44
9B04	ELECTRON MICROSCOPY	2.52
9Z2F	ELECTRON MICROSCOPY	2.59
9Z2D	ELECTRON MICROSCOPY	2.6
1QK1	X-RAY DIFFRACTION	2.7
9B16	ELECTRON MICROSCOPY	2.89

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P12532-F1	89.88	0.80

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): 368; 161–165; 224; 269; 325; 353–358

Post-translational modifications (5): 151, 196, 213, 232, 355

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-71288	Creatine metabolism
R-HSA-1430728	Metabolism
R-HSA-71291	Metabolism of amino acids and derivatives

MSigDB gene sets: 36 (showing top): GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, KOYAMA_SEMA3B_TARGETS_UP, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_MODIFIED_AMINO_ACID_METABOLIC_PROCESS, GOCC_ORGANELLE_INNER_MEMBRANE, GOMF_KINASE_ACTIVITY, BENPORATH_ES_1, GOMF_PHOSPHOTRANSFERASE_ACTIVITY_NITROGENOUS_GROUP_AS_ACCEPTOR, GOMF_ADENYL_NUCLEOTIDE_BINDING, GOMF_TRANSFERASE_ACTIVITY_TRANSFERRING_PHOSPHORUS_CONTAINING_GROUPS, GOCC_ORGANELLE_ENVELOPE, PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_DN, KEGG_ARGININE_AND_PROLINE_METABOLISM, CAMP_UP.V1_UP

GO Biological Process (1): phosphocreatine biosynthetic process (GO:0046314)

GO Molecular Function (8): creatine kinase activity (GO:0004111), ATP binding (GO:0005524), nucleotide binding (GO:0000166), catalytic activity (GO:0003824), protein binding (GO:0005515), kinase activity (GO:0016301), transferase activity (GO:0016740), transferase activity, transferring phosphorus-containing groups (GO:0016772)

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Metabolism of amino acids and derivatives	1
Metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
phosphocreatine metabolic process	1
phosphagen biosynthetic process	1
kinase activity	1
phosphotransferase activity, nitrogenous group as acceptor	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
molecular_function	1
binding	1
transferase activity, transferring phosphorus-containing groups	1
catalytic activity	1
transferase activity	1
cytoplasm	1
intracellular membrane-bounded organelle	1
organelle inner membrane	1
mitochondrial membrane	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1354 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CKMT1A	CATSPER2	Q96P56	948
CKMT1A	STRC	Q7RTU9	943
CKMT1A	SLC6A8	P48029	917
CKMT1A	PPIP5K1	Q6PFW1	867
CKMT1A	NME4	O00746	840
CKMT1A	GATM	P50440	800
CKMT1A	LDHAL6A	Q6ZMR3	734
CKMT1A	LDHAL6B	Q9BYZ2	732
CKMT1A	LDHC	P07864	707
CKMT1A	ASB9	Q96DX5	678
CKMT1A	GOT1L1	Q8NHS2	619
CKMT1A	GAMT	Q14353	604
CKMT1A	VDAC1	P21796	571
CKMT1A	LDHA	P00338	538
CKMT1A	GOT1	P17174	527

IntAct

127 interactions, top by confidence:

A	B	Type	Score
ASB9	CKM	psi-mi:“MI:0914”(association)	0.870
CKMT1A	ASB9	psi-mi:“MI:0915”(physical association)	0.740
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
CFTR	HAX1	psi-mi:“MI:0914”(association)	0.610
OCM	CKMT1A	psi-mi:“MI:0915”(physical association)	0.600
HPCA	CKMT1A	psi-mi:“MI:0915”(physical association)	0.560
CTNNA3	CKMT1A	psi-mi:“MI:0915”(physical association)	0.560
CKMT1A	NUTF2	psi-mi:“MI:0915”(physical association)	0.560
CKMT1A	RXRG	psi-mi:“MI:0915”(physical association)	0.560
CKMT1A	HPCA	psi-mi:“MI:0915”(physical association)	0.560
CKM	CKMT1A	psi-mi:“MI:0915”(physical association)	0.560
CKMT1A	PPP1R16A	psi-mi:“MI:0915”(physical association)	0.560
CKMT1A	PSMC3	psi-mi:“MI:0915”(physical association)	0.560
CKMT1A	CTNNA3	psi-mi:“MI:0915”(physical association)	0.560
CKMT1A	WFS1	psi-mi:“MI:0915”(physical association)	0.560
CKMT1A	JPH3	psi-mi:“MI:0915”(physical association)	0.560
ASB9	ARIH2	psi-mi:“MI:0914”(association)	0.530
CKMT1A	CKMT2	psi-mi:“MI:0915”(physical association)	0.500
CKMT2	CKMT1A	psi-mi:“MI:0914”(association)	0.500
	CAND2	psi-mi:“MI:0914”(association)	0.460
HTRA2	HAX1	psi-mi:“MI:2364”(proximity)	0.420

BioGRID (206): CKMT1A (Affinity Capture-MS), CKMT1B (Affinity Capture-MS), CKMT1A (Affinity Capture-MS), CKMT1A (Affinity Capture-MS), CKMT1B (Co-fractionation), CKMT1A (Co-fractionation), CKMT1B (Co-fractionation), CKMT1A (Co-fractionation), CKMT1B (Co-fractionation), CKMT1A (Co-fractionation), CKMT1B (Co-fractionation), CKMT1A (Co-fractionation), CKMT1B (Co-fractionation), CKMT1A (Co-fractionation), CKMT1B (Co-fractionation)

ESM2 similar proteins: A0A286R7K5, A0A976YI25, B0FRF9, B1PVZ9, C7E3T4, C9EIP1, H6VGI2, H6VGI3, O61367, O77814, O96507, P00563, P00564, P00565, P00566, P04414, P05123, P05124, P06732, P07310, P07335, P09605, P11009, P12532, P14208, P17540, P24722, P25809, P30275, P48610, P51541, P51545, P70079, P91798, Q004B5, Q04447, Q29577, Q29594, Q3ZBP1, Q5EA61

Diamond homologs: A0A286R7K5, A0A976YI25, A4J0X5, A5D5K7, A8F953, B0FRF9, B1PVZ9, C1KYG4, C7E3T4, C9EIP1, G1ESZ9, H6VGI2, H6VGI3, O15989, O15990, O15991, O15992, O61367, O77814, O96507, P00563, P00564, P00565, P00566, P00567, P04414, P05122, P05123, P05124, P06732, P07310, P07335, P09605, P11009, P12277, P12532, P14208, P16641, P17540, P18294

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
creatine	“up-regulates activity”	CKMT1A	“chemical activation”
CKMT1A	“up-regulates quantity”	N-phosphocreatine	“chemical modification”
ABL1	“up-regulates quantity by stabilization”	CKMT1A	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 113 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
SRP-dependent cotranslational protein targeting to membrane	7	8.8×	7e-03

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	6	10.6×	9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	26
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1621 predictions. Top by Δscore:

Variant	Effect	Δscore
15:43695194:A:AG	acceptor_gain	1.0000
15:43695195:A:G	acceptor_gain	1.0000
15:43695201:CTTA:C	acceptor_loss	1.0000
15:43695202:TTAGG:T	acceptor_loss	1.0000
15:43695203:TAGGT:T	acceptor_loss	1.0000
15:43695204:A:AG	acceptor_gain	1.0000
15:43695204:AG:A	acceptor_gain	1.0000
15:43695205:G:A	acceptor_gain	1.0000
15:43695205:G:GA	acceptor_gain	1.0000
15:43695205:GGT:G	acceptor_gain	1.0000
15:43695205:GGTA:G	acceptor_gain	1.0000
15:43695205:GGTAT:G	acceptor_gain	1.0000
15:43695297:G:GG	donor_gain	1.0000
15:43695297:GTAAA:G	donor_loss	1.0000
15:43695298:TAAA:T	donor_gain	1.0000
15:43695299:AAA:A	donor_gain	1.0000
15:43695302:G:GG	donor_gain	1.0000
15:43695910:G:GG	donor_gain	1.0000
15:43695915:GGCCT:G	donor_gain	1.0000
15:43696034:CCCA:C	acceptor_loss	1.0000
15:43696035:CCAG:C	acceptor_loss	1.0000
15:43696036:CA:C	acceptor_loss	1.0000
15:43696037:A:AG	acceptor_gain	1.0000
15:43696038:G:GG	acceptor_gain	1.0000
15:43696122:TTGGT:T	donor_loss	1.0000
15:43696123:TGGT:T	donor_loss	1.0000
15:43696125:G:GA	donor_loss	1.0000
15:43696126:T:A	donor_loss	1.0000
15:43696235:CTCA:C	acceptor_loss	1.0000
15:43696236:TCA:T	acceptor_loss	1.0000

AlphaMissense

2687 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:43696051:T:C	F227L	1.000
15:43696053:T:A	F227L	1.000
15:43696053:T:G	F227L	1.000
15:43696102:T:A	W244R	1.000
15:43696102:T:C	W244R	1.000
15:43696268:T:A	W261R	1.000
15:43696268:T:C	W261R	1.000
15:43696279:G:C	E264D	1.000
15:43696279:G:T	E264D	1.000
15:43696283:G:C	D266H	1.000
15:43696284:A:C	D266A	1.000
15:43698069:G:A	G311E	1.000
15:43698083:T:C	C316R	1.000
15:43698094:C:A	N319K	1.000
15:43698094:C:G	N319K	1.000
15:43698099:G:A	G321D	1.000
15:43698105:G:A	G323E	1.000
15:43698742:T:A	N371K	1.000
15:43698742:T:G	N371K	1.000
15:43694837:C:A	N61K	0.999
15:43694837:C:G	N61K	0.999
15:43694931:G:C	G93R	0.999
15:43694932:G:A	G93D	0.999
15:43694950:A:G	H99R	0.999
15:43694951:C:A	H99Q	0.999
15:43694951:C:G	H99Q	0.999
15:43694970:G:C	G106R	0.999
15:43694971:G:A	G106D	0.999
15:43694971:G:T	G106V	0.999
15:43694980:C:A	A109D	0.999

dbSNP variants (sampled 300 via entrez): RS1002632822 (15:43693064 T>A,C), RS1006029270 (15:43696469 T>C), RS1006222105 (15:43696798 T>C), RS1009117140 (15:43698884 A>C), RS1009917968 (15:43696952 C>G,T), RS1010117121 (15:43697333 G>A,T), RS1012211225 (15:43698524 G>A,T), RS1013585986 (15:43696002 T>C,G), RS1015012344 (15:43698230 G>A), RS1015146448 (15:43697780 C>T), RS1015485245 (15:43699459 C>T), RS1018925738 (15:43698717 C>A), RS1019206495 (15:43698901 C>G,T), RS1020211646 (15:43697380 T>C), RS1023461351 (15:43699350 G>A)

Disease associations

OMIM: gene MIM:613415 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST007094_7	Diastolic blood pressure	1.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006336	diastolic blood pressure

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066961 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
8.00	Kd	9.912	nM	CHEMBL5653589
7.76	ED50	17.2	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2148076: Binding affinity to human CKMT1A incubated for 45 mins by Kinobead based pull down assay	kd	0.0099	uM

CTD chemical–gene interactions

37 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	3
Cadmium Chloride	decreases expression, increases expression	3
Benzo(a)pyrene	affects methylation, decreases expression	2
Tobacco Smoke Pollution	affects expression, decreases expression	2
Particulate Matter	decreases expression, increases abundance, affects cotreatment, increases expression	2
3,19-(2-bromobenzylidene)andrographolide	decreases expression, decreases response to substance	1
propionaldehyde	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	increases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
pentanal	increases expression	1
CGP 52608	affects binding, increases reaction	1
ICG 001	increases expression	1
abrine	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Ethanol	affects cotreatment, increases abundance, increases expression	1
Aldehydes	increases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Dibutyl Phthalate	increases expression	1
Diethylhexyl Phthalate	decreases expression, affects cotreatment, affects expression	1
Folic Acid	decreases expression	1
Colforsin	affects cotreatment, affects expression	1
Gasoline	increases abundance, increases expression, affects cotreatment	1
Indomethacin	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Plant Extracts	affects cotreatment, decreases expression	1
Polycyclic Aromatic Hydrocarbons	increases abundance, increases expression, affects cotreatment	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5651118	Binding	Binding affinity to human CKMT1A incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2UG	Abcam HEK293T CKMT1A KO	Transformed cell line	Female

Clinical trials (associated diseases)

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