CKMT2

gene
On this page

Also known as SMTCK

Summary

CKMT2 (creatine kinase, mitochondrial 2, HGNC:1996) is a protein-coding gene on chromosome 5q14.1, encoding Creatine kinase S-type, mitochondrial (P17540). Reversibly catalyzes the transfer of phosphate between ATP and various phosphogens (e.g. creatine phosphate).

Mitochondrial creatine kinase (MtCK) 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. Sarcomeric mitochondrial creatine kinase has 80% homology with the coding exons of ubiquitous mitochondrial creatine kinase. This gene contains sequences homologous to several motifs that are shared among some nuclear genes encoding mitochondrial proteins and thus may be essential for the coordinated activation of these genes during mitochondrial biogenesis. Three transcript variants encoding the same protein have been found for this gene.

Source: NCBI Gene 1160 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 69 total
  • MANE Select transcript: NM_001099735

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1996
Approved symbolCKMT2
Namecreatine kinase, mitochondrial 2
Location5q14.1
Locus typegene with protein product
StatusApproved
AliasesSMTCK
Ensembl geneENSG00000131730
Ensembl biotypeprotein_coding
OMIM123295
Entrez1160

Gene structure

Transcript identifiers

Ensembl transcripts: 32 — 25 protein_coding, 4 retained_intron, 3 protein_coding_CDS_not_defined

ENST00000254035, ENST00000424301, ENST00000437669, ENST00000505060, ENST00000505135, ENST00000505704, ENST00000505850, ENST00000511719, ENST00000513094, ENST00000514086, ENST00000515238, ENST00000515615, ENST00000865071, ENST00000865072, ENST00000865073, ENST00000865074, ENST00000865075, ENST00000865076, ENST00000865077, ENST00000865078, ENST00000865079, ENST00000865080, ENST00000865081, ENST00000865082, ENST00000928885, ENST00000953985, ENST00000953986, ENST00000953987, ENST00000953988, ENST00000953989, ENST00000953990, ENST00000953991

RefSeq mRNA: 3 — MANE Select: NM_001099735 NM_001099735, NM_001099736, NM_001825

CCDS: CCDS4053

Canonical transcript exons

ENST00000254035 — 10 exons

ExonStartEnd
ENSE000020845918123332281233377
ENSE000034674408125691581257000
ENSE000035175848125912081259254
ENSE000035667518126349181263616
ENSE000036203088125773381257856
ENSE000036268778125439681254491
ENSE000036853438125499381255214
ENSE000036893988125269581252893
ENSE000036925148125111381251284
ENSE000038439148126613981266398

Expression profiles

Bgee: expression breadth ubiquitous, 232 present calls, max score 99.77.

FANTOM5 (CAGE): breadth broad, TPM avg 13.4370 / max 1473.3802, expressed in 447 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
5734113.3283446
573400.108741

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
heart right ventricleUBERON:000208099.77gold quality
apex of heartUBERON:000209899.74gold quality
left ventricle myocardiumUBERON:000656699.68gold quality
cardiac ventricleUBERON:000208299.55gold quality
heart left ventricleUBERON:000208499.55gold quality
right atrium auricular regionUBERON:000663199.44gold quality
myocardiumUBERON:000234999.43gold quality
gastrocnemiusUBERON:000138899.42gold quality
cardiac atriumUBERON:000208199.41gold quality
biceps brachiiUBERON:000150799.40gold quality
diaphragmUBERON:000110399.39gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450299.39gold quality
vastus lateralisUBERON:000137999.37gold quality
hindlimb stylopod muscleUBERON:000425299.35gold quality
quadriceps femorisUBERON:000137799.31gold quality
triceps brachiiUBERON:000150999.27gold quality
skeletal muscle tissueUBERON:000113499.21gold quality
deltoidUBERON:000147699.17gold quality
gluteal muscleUBERON:000200099.12gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451199.12gold quality
body of tongueUBERON:001187699.07gold quality
cardiac muscle of right atriumUBERON:000337999.01gold quality
tibialis anteriorUBERON:000138598.77gold quality
muscle organUBERON:000163098.73gold quality
skeletal muscle organUBERON:001489298.73gold quality
muscle of legUBERON:000138398.52gold quality
heartUBERON:000094898.05gold quality
vena cavaUBERON:000408797.89gold quality
muscle tissueUBERON:000238597.70gold quality
right adrenal gland cortexUBERON:003582794.37gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.11

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MYOD1

miRNA regulators (miRDB)

18 targeting CKMT2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-12118100.0065.881270
HSA-MIR-6891-5P99.9866.531372
HSA-MIR-3173-3P99.9866.491217
HSA-MIR-590-3P99.9674.346478
HSA-MIR-442899.7366.411733
HSA-MIR-453099.6966.471509
HSA-MIR-7849-3P99.4768.171224
HSA-MIR-132499.4666.571302
HSA-MIR-94099.3766.142064
HSA-MIR-6808-5P99.3166.232150
HSA-MIR-6893-5P99.3166.252119
HSA-MIR-4477B99.2370.491733
HSA-MIR-4477A98.8369.752952
HSA-MIR-654-3P98.3867.61905
HSA-MIR-316698.2466.631223
HSA-MIR-63497.7467.11818
HSA-MIR-519296.8963.35879
HSA-MIR-433095.4466.39993

Literature-anchored findings (GeneRIF, showing 6)

  • three C-terminal lysines determine high affinity sMtCK/cardiolipin interaction and its effects on MtCK structure, whereas low level binding and some effect on membrane fluidity depend on other structural components (PMID:15044463)
  • After the training period, intracellular energetic units had a higher control of mitochondrial respiration by creatine linked to a more efficient functional coupling adenine nucleotide translocase-mitochondrial creatine kinase. (PMID:16020522)
  • CK2alpha has a role in progression of acute myeloid leukemia (PMID:17289898)
  • These findings support increased CK activity as protection against ischaemia-reperfusion injury, in particular, protection via CKMT2 in a cardiac-relevant cell line, which merits further investigation in vivo. (PMID:28806770)
  • Prognostic value of mitochondrial CKMT2 in Pan-cancer and its tumor immune correlation analysis. (PMID:38172162)
  • Decreased mitochondrial creatine kinase 2 impairs skeletal muscle mitochondrial function independently of insulin in type 2 diabetes. (PMID:39383244)

Cross-species orthologs

13 orthologs

OrganismSymbolGene ID
danio_reriockmt2bENSDARG00000039929
danio_reriockmt2aENSDARG00000069615
mus_musculusCkmt2ENSMUSG00000021622
rattus_norvegicusCkmt2ENSRNOG00000055450
drosophila_melanogasterArgk1FBGN0000116
drosophila_melanogasterArgk2FBGN0035957
drosophila_melanogasterCG4546FBGN0038373
drosophila_melanogasterCG30274FBGN0050274
caenorhabditis_elegansWBGENE00009706
caenorhabditis_elegansZC434.8WBGENE00013894
caenorhabditis_elegansF32B5.1WBGENE00017975
caenorhabditis_elegansWBGENE00018519
caenorhabditis_elegansW10C8.5WBGENE00021128

Paralogs (4): CKM (ENSG00000104879), CKB (ENSG00000166165), CKMT1A (ENSG00000223572), CKMT1B (ENSG00000237289)

Protein

Protein identifiers

Creatine kinase S-type, mitochondrialP17540 (reviewed: P17540)

Alternative names: Basic-type mitochondrial creatine kinase, Sarcomeric mitochondrial creatine kinase

All UniProt accessions (3): D6R998, D6RHV3, P17540

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 CKMT2 homodimers.

Subcellular location. Mitochondrion inner membrane.

Tissue specificity. Sarcomere-specific. Found only in heart and skeletal muscles.

Miscellaneous. Mitochondrial creatine kinase binds cardiolipin.

Similarity. Belongs to the ATP:guanido phosphotransferase family.

RefSeq proteins (3): NP_001093205, NP_001093206, NP_001816 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000749ATP-guanido_PTrfaseFamily
IPR014746Gln_synth/guanido_kin_cat_domHomologous_superfamily
IPR022413ATP-guanido_PTrfase_NDomain
IPR022414ATP-guanido_PTrfase_catDomain
IPR022415ATP-guanido_PTrfase_ASActive_site
IPR036802ATP-guanido_PTrfase_N_sfHomologous_superfamily

Pfam: PF00217, PF02807

Catalyzed reactions (Rhea), 1 shown:

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

UniProt features (47 total): helix 18, strand 9, binding site 6, turn 6, modified residue 2, domain 2, transit peptide 1, chain 1, sequence conflict 1, region of interest 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
4Z9MX-RAY DIFFRACTION2.1

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P17540-F189.800.78

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): 369; 162–166; 225; 270; 326; 354–359

Post-translational modifications (2): 255, 356

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

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

MSigDB gene sets: 132 (showing top): MODULE_493, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, MEF2_02, MODULE_329, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GNF2_MYL3, GOBP_MUSCLE_CONTRACTION, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4, GOCC_MITOCHONDRIAL_ENVELOPE, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, MODULE_284, LEE_LIVER_CANCER_ACOX1_DN, GOBP_MUSCLE_SYSTEM_PROCESS, VECCHI_GASTRIC_CANCER_EARLY_DN, MODULE_387

GO Biological Process (2): muscle contraction (GO:0006936), 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:

CategoryPathways
Metabolism of amino acids and derivatives1
Metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
muscle system process1
phosphocreatine metabolic process1
phosphagen biosynthetic process1
kinase activity1
phosphotransferase activity, nitrogenous group as acceptor1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
nucleoside phosphate binding1
heterocyclic compound binding1
molecular_function1
binding1
transferase activity, transferring phosphorus-containing groups1
catalytic activity1
transferase activity1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
cellular anatomical structure1

Protein interactions and networks

STRING

1216 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CKMT2LDHAL6AQ6ZMR3733
CKMT2LDHAL6BQ9BYZ2732
CKMT2LDHCP07864686
CKMT2GOT1L1Q8NHS2618
CKMT2LDHAP00338565
CKMT2GAMTQ14353530
CKMT2GOT1P17174528
CKMT2SLC6A8P48029511
CKMT2GATMP50440471
CKMT2AK1P00568463
CKMT2GGT6Q6P531447
CKMT2GOT2P00505435
CKMT2ALPGP10696435
CKMT2TNNI1P19237426
CKMT2SDHAP31040424

IntAct

34 interactions, top by confidence:

ABTypeScore
RCAN1PPP3CBpsi-mi:“MI:0914”(association)0.660
CETN3CKMT2psi-mi:“MI:0915”(physical association)0.560
CKMT2NRF1psi-mi:“MI:0915”(physical association)0.560
CKMT2P4HA3psi-mi:“MI:0915”(physical association)0.560
CKMT2KLHL42psi-mi:“MI:0915”(physical association)0.560
CKMT2NME2P1psi-mi:“MI:0914”(association)0.530
AKR1D1DIRAS1psi-mi:“MI:0914”(association)0.530
CKMT1ACKMT2psi-mi:“MI:0915”(physical association)0.500
CKMT2CKMT1Apsi-mi:“MI:0914”(association)0.500
FER1L6CKMT2psi-mi:“MI:0915”(physical association)0.400
CKMT1ACKMT2psi-mi:“MI:0915”(physical association)0.400
ELNCKMT2psi-mi:“MI:0915”(physical association)0.370
CKMT2TMED9psi-mi:“MI:0915”(physical association)0.370
ABHD6CKMT2psi-mi:“MI:0915”(physical association)0.370
HSCBRBP5psi-mi:“MI:0914”(association)0.350
IKZF5PEX14psi-mi:“MI:0914”(association)0.350
LATS1ATP2A1psi-mi:“MI:0914”(association)0.350
TSPAN33ATP2A1psi-mi:“MI:0914”(association)0.350
AP5M1HSPA12Apsi-mi:“MI:0914”(association)0.350
ASB9A2ML1psi-mi:“MI:0914”(association)0.350
MRPS23MYH7Bpsi-mi:“MI:0914”(association)0.350
CETN3CKMT2psi-mi:“MI:0915”(physical association)0.000
NRF1CKMT2psi-mi:“MI:0915”(physical association)0.000
P4HA3CKMT2psi-mi:“MI:0915”(physical association)0.000
KLHL42CKMT2psi-mi:“MI:0915”(physical association)0.000

BioGRID (58): CKMT2 (Co-fractionation), CKMT2 (Co-fractionation), HSPE1 (Co-fractionation), CKMT2 (Affinity Capture-MS), CKM (Affinity Capture-MS), NME2P1 (Affinity Capture-MS), CKMT2 (Affinity Capture-MS), CKMT2 (Affinity Capture-MS), OLFML3 (Two-hybrid), CKMT2 (Two-hybrid), LRIF1 (Two-hybrid), UNC119 (Two-hybrid), CKMT2 (Two-hybrid), P4HA3 (Two-hybrid), CETN3 (Two-hybrid)

ESM2 similar proteins: A0A286R7K5, A0A976YI25, A1W3F2, B0FRF9, B1PVZ9, B8I2Z6, B9MCM3, C7E3T4, C9EIP1, G1ESZ9, H6VGI2, H6VGI3, O15989, O15990, O15991, O15992, O61367, O77814, O96507, P00564, P00566, P04414, P05123, P07310, P09605, P11009, P14208, P17540, P18294, P24722, P51541, P51544, P51545, P70079, P91798, Q004B5, Q10454, Q27535, Q39230, Q3ZBP1

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

2 interactions.

AEffectBMechanism
creatine“up-regulates activity”CKMT2“chemical activation”
CKMT2“up-regulates quantity”N-phosphocreatine“chemical modification”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance67
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1540 predictions. Top by Δscore:

VariantEffectΔscore
5:81251111:A:AGacceptor_gain1.0000
5:81251112:G:GGacceptor_gain1.0000
5:81251112:GAC:Gacceptor_gain1.0000
5:81251281:CAAGG:Cdonor_loss1.0000
5:81251282:AAGGT:Adonor_loss1.0000
5:81251283:AGGTA:Adonor_loss1.0000
5:81251284:GGTAA:Gdonor_loss1.0000
5:81251285:G:Adonor_loss1.0000
5:81252689:A:AGacceptor_gain1.0000
5:81252690:C:Gacceptor_gain1.0000
5:81252690:CACA:Cacceptor_loss1.0000
5:81252691:A:AGacceptor_gain1.0000
5:81252691:ACAGC:Aacceptor_gain1.0000
5:81252692:C:Gacceptor_gain1.0000
5:81252693:A:AGacceptor_gain1.0000
5:81252693:A:Cacceptor_loss1.0000
5:81252693:AGC:Aacceptor_gain1.0000
5:81252694:G:GGacceptor_gain1.0000
5:81252694:GC:Gacceptor_gain1.0000
5:81252694:GCG:Gacceptor_gain1.0000
5:81252694:GCGC:Gacceptor_gain1.0000
5:81252694:GCGCA:Gacceptor_gain1.0000
5:81252891:GAG:Gdonor_gain1.0000
5:81252894:GTAA:Gdonor_loss1.0000
5:81252895:T:Adonor_loss1.0000
5:81254393:CAGGT:Cacceptor_loss1.0000
5:81254395:GGT:Gacceptor_gain1.0000
5:81254487:CAAAG:Cdonor_loss1.0000
5:81254488:AAAG:Adonor_loss1.0000
5:81254489:AAGG:Adonor_loss1.0000

AlphaMissense

2733 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:81252823:G:AG94E1.000
5:81252861:G:CG107R1.000
5:81252862:G:AG107D1.000
5:81252871:C:AA110D1.000
5:81255048:G:AG168D1.000
5:81255050:C:AR169S1.000
5:81255053:A:CS170R1.000
5:81255055:C:AS170R1.000
5:81255055:C:GS170R1.000
5:81255099:G:CR185P1.000
5:81256927:T:CF228L1.000
5:81256928:T:GF228C1.000
5:81256929:T:AF228L1.000
5:81256929:T:GF228L1.000
5:81256978:T:AW245R1.000
5:81256978:T:CW245R1.000
5:81256980:G:CW245C1.000
5:81256980:G:TW245C1.000
5:81256991:G:CR249T1.000
5:81256991:G:TR249M1.000
5:81256992:G:CR249S1.000
5:81256992:G:TR249S1.000
5:81256993:G:AG250R1.000
5:81256993:G:CG250R1.000
5:81256994:G:AG250E1.000
5:81257761:T:AW262R1.000
5:81257761:T:CW262R1.000
5:81257769:T:AN264K1.000
5:81257769:T:GN264K1.000
5:81257771:A:TE265V1.000

dbSNP variants (sampled 300 via entrez): RS1000056836 (5:81233483 C>A,T), RS1000191461 (5:81235354 G>A), RS1000196565 (5:81237511 A>C), RS1000351430 (5:81253721 A>C), RS1000525897 (5:81236778 G>A,C), RS1000641679 (5:81236373 A>G), RS1000663812 (5:81243683 A>C), RS1000709745 (5:81242183 T>C), RS1000757882 (5:81231751 G>A), RS1000906862 (5:81259319 G>A), RS1000973339 (5:81265481 G>A,C), RS1001026198 (5:81248624 A>C,G), RS1001255950 (5:81266533 C>T), RS1001267230 (5:81242008 C>A,T), RS1001419805 (5:81236681 T>C)

Disease associations

OMIM: gene MIM:123295 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects cotreatment, decreases methylation, increases expression, decreases expression4
bisphenol Faffects cotreatment, decreases expression, increases expression2
Doxorubicinaffects expression, decreases expression2
Nickeldecreases expression2
triphenyl phosphateaffects expression1
terbufosincreases methylation1
arseniteincreases methylation1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
CGP 52608affects binding, increases reaction1
Resveratrolaffects cotreatment, decreases expression1
Sunitinibdecreases expression1
Fulvestrantincreases methylation, affects cotreatment, decreases methylation1
Acetaminophendecreases expression1
Benzo(a)pyreneincreases expression1
Cadmiumincreases expression, increases abundance1
Dexamethasonedecreases expression, affects cotreatment1
Fonofosincreases methylation1
Indomethacinaffects cotreatment, decreases expression1
Ivermectindecreases expression1
Nicotinedecreases expression1
Parathionincreases methylation1
Plant Extractsaffects cotreatment, decreases expression1
Tetrachlorodibenzodioxinincreases expression1
Valproic Acidincreases expression1
1-Methyl-3-isobutylxanthinedecreases expression, affects cotreatment1
8-Bromo Cyclic Adenosine Monophosphatedecreases expression1
Cyclosporineincreases expression1
Cadmium Chlorideincreases abundance, increases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.