GeneBe

CKMT2

creatine kinase, mitochondrial 2

Basic information

Region (hg38): 5:81233320-81266398

Links

ENSG00000131730 ∙ NCBI:1160 ∙ OMIM:123295 ∙ HGNC:1996 ∙ Uniprot:P17540 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CKMT2 gene.

  • not_specified (56 variants)
  • not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CKMT2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001099735.2. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
0
missense
56
clinvar
 56
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 56 0 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CKMT2protein_codingprotein_codingENST00000424301 933113
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.62e-170.0033112563401141257480.000453
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.302122720.7780.00001732728
Missense in Polyphen92119.060.772731219
Synonymous-0.2061091061.030.00000679856
Loss of Function-0.2512523.71.060.00000153232

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001020.00102
Ashkenazi Jewish0.000.00
East Asian0.0007080.000707
Finnish0.0001390.000139
European (Non-Finnish)0.0006000.000528
Middle Eastern0.0007080.000707
South Asian0.0004580.000457
Other0.0001640.000163

dbNSFP

Source: dbNSFP

Function
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.;
Pathway
Arginine and proline metabolism - Homo sapiens (human);creatine-phosphate biosynthesis;Metabolism of polyamines;Metabolism of amino acids and derivatives;Metabolism;Arginine Proline metabolism;Glycine, serine, alanine and threonine metabolism;Creatine metabolism (Consensus)

Recessive Scores

pRec
0.615

Intolerance Scores

loftool
0.945
rvis_EVS
-0.62
rvis_percentile_EVS
17.16

Haploinsufficiency Scores

pHI
0.158
hipred
N
hipred_score
0.335
ghis
0.549

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.979

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ckmt2
Phenotype
cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region phenotype; muscle phenotype;

Gene ontology

Biological process
creatine metabolic process;muscle contraction;phosphorylation
Cellular component
mitochondrion;mitochondrial inner membrane
Molecular function
creatine kinase activity;ATP binding