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.

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.

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						0
missense			37			37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	37	0	0

Variants in CKMT2

This is a list of pathogenic ClinVar variants found in the CKMT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-81251166-C-T		not specified	Uncertain significance (Jan 18, 2023)
5-81251167-G-A		not specified	Uncertain significance (Aug 02, 2022)
5-81251173-C-T		not specified	Uncertain significance (Jun 02, 2024)
5-81251202-A-G		not specified	Uncertain significance (Feb 27, 2024)
5-81251217-G-A		not specified	Uncertain significance (Oct 06, 2024)
5-81251262-C-G		not specified	Uncertain significance (Dec 25, 2024)
5-81251266-C-T		not specified	Uncertain significance (Jan 23, 2025)
5-81251272-T-C		not specified	Uncertain significance (Mar 28, 2024)
5-81252714-C-T		not specified	Uncertain significance (Jan 25, 2023)
5-81252754-C-T		not specified	Uncertain significance (Feb 03, 2025)
5-81252771-C-T		not specified	Uncertain significance (Jun 18, 2024)
5-81252772-G-A		not specified	Uncertain significance (Aug 01, 2024)
5-81252810-T-C		not specified	Uncertain significance (Mar 11, 2025)
5-81252833-C-A		not specified	Uncertain significance (Jan 23, 2023)
5-81252859-T-C		not specified	Uncertain significance (Oct 25, 2022)
5-81252889-A-G		not specified	Uncertain significance (Feb 12, 2024)
5-81254393-C-T			Uncertain significance (Mar 30, 2021)
5-81255014-G-A		not specified	Uncertain significance (Dec 11, 2023)
5-81255020-T-C		not specified	Uncertain significance (Sep 03, 2024)
5-81255051-G-A		not specified	Uncertain significance (May 03, 2023)
5-81255059-C-T		not specified	Uncertain significance (Aug 08, 2023)
5-81255089-C-T		not specified	Uncertain significance (Jan 10, 2023)
5-81255099-G-A		not specified	Uncertain significance (Sep 01, 2024)
5-81255116-G-A		not specified	Uncertain significance (Feb 28, 2024)
5-81255186-C-T		not specified	Uncertain significance (Oct 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CKMT2	protein_coding	protein_coding	ENST00000424301	9	33113

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.62e-17	0.00331	125634	0	114	125748	0.000453

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	212	272	0.778	0.0000173	2728
Missense in Polyphen		92	119.06	0.77273		1219
Synonymous	-0.206	109	106	1.03	0.00000679	856
Loss of Function	-0.251	25	23.7	1.06	0.00000153	232

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00102	0.00102
Ashkenazi Jewish	0.00	0.00
East Asian	0.000708	0.000707
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000600	0.000528
Middle Eastern	0.000708	0.000707
South Asian	0.000458	0.000457
Other	0.000164	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);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

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

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