CKM

creatine kinase, M-type

Basic information

Region (hg38): 19:45306413-45322875

Previous symbols: [ "CKMM" ]

Links

ENSG00000104879 ∙ NCBI:1158 ∙ OMIM:123310 ∙ HGNC:1994 ∙ Uniprot:P06732 ∙ 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 CKM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CKM gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			35	1		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	35	2	1

Variants in CKM

This is a list of pathogenic ClinVar variants found in the CKM region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-45306752-A-G			Likely benign (Dec 31, 2019)
19-45306774-G-T		not specified	Uncertain significance (Aug 28, 2023)
19-45306806-C-G		not specified	Uncertain significance (Oct 06, 2021)
19-45306817-A-G		not specified	Uncertain significance (Nov 25, 2024)
19-45306829-C-T		not specified	Uncertain significance (Nov 10, 2021)
19-45306889-A-G		not specified	Uncertain significance (Feb 01, 2023)
19-45306899-C-A		not specified	Uncertain significance (May 26, 2024)
19-45306923-C-T		not specified	Uncertain significance (Oct 12, 2024)
19-45307487-C-A		not specified	Uncertain significance (Nov 26, 2024)
19-45307488-G-A		not specified	Uncertain significance (Oct 07, 2024)
19-45307602-G-A		not specified	Uncertain significance (Aug 19, 2024)
19-45307628-G-A		not specified	Uncertain significance (Dec 22, 2023)
19-45307628-G-T		not specified	Uncertain significance (Jul 25, 2023)
19-45308434-C-G			Likely benign (Mar 01, 2023)
19-45308455-C-T		not specified	Uncertain significance (Jan 18, 2022)
19-45311752-A-T		not specified	Uncertain significance (May 17, 2023)
19-45311758-C-T		not specified	Uncertain significance (Dec 12, 2023)
19-45311776-C-T		not specified	Uncertain significance (Aug 17, 2022)
19-45311819-C-T		not specified	Uncertain significance (Aug 26, 2024)
19-45311912-T-C		not specified	Uncertain significance (Jun 21, 2021)
19-45315477-G-A		not specified	Uncertain significance (Sep 14, 2023)
19-45315491-C-T		not specified	Uncertain significance (Sep 12, 2023)
19-45315503-C-A		not specified	Uncertain significance (Jan 24, 2023)
19-45315525-T-G		not specified	Uncertain significance (May 12, 2024)
19-45315542-C-T		not specified	Uncertain significance (May 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CKM	protein_coding	protein_coding	ENST00000221476	7	16564

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00782	0.979	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.661	217	246	0.881	0.0000159	2517
Missense in Polyphen		59	85.019	0.69396		875
Synonymous	0.110	102	103	0.986	0.00000738	722
Loss of Function	2.17	6	15.1	0.398	6.48e-7	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000447	0.000437
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000119	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.000106	0.0000980
Other	0.000163	0.000163

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);Abacavir Pathway, Pharmacokinetics/Pharmacodynamics;Urea cycle and metabolism of amino groups;creatine-phosphate biosynthesis;Metabolism of polyamines;Metabolism of amino acids and derivatives;Metabolism;Arginine Proline metabolism;Regulation of retinoblastoma protein;Creatine metabolism (Consensus)

Recessive Scores

• pRec: 0.795

Intolerance Scores

• loftool: 0.637
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.36

Haploinsufficiency Scores

• pHI: 0.294
• hipred: N
• hipred_score: 0.439
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.998

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ckm
• 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); homeostasis/metabolism phenotype; growth/size/body region phenotype; muscle phenotype; cellular phenotype

Gene ontology

• Biological process: creatine metabolic process;phosphorylation;phosphocreatine biosynthetic process
• Cellular component: extracellular space;cytosol
• Molecular function: creatine kinase activity;protein binding;ATP binding