CKMT1A

creatine kinase, mitochondrial 1A

Basic information

Region (hg38): 15:43692886-43699222

Previous symbols: [ "CKMT1" ]

Links

ENSG00000223572 ∙ NCBI:548596 ∙ OMIM:613415 ∙ HGNC:31736 ∙ Uniprot:P12532 ∙ 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 CKMT1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CKMT1A 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				2		2
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	2	0

Variants in CKMT1A

This is a list of pathogenic ClinVar variants found in the CKMT1A region.

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

Position	Type	Phenotype	Significance	ClinVar
15-43696283-G-T		not specified	Uncertain significance (Mar 15, 2024)
15-43698643-T-A		not specified	Uncertain significance (Mar 12, 2024)
15-43698648-G-A		not specified	Uncertain significance (Sep 17, 2021)
15-43698685-G-A			Likely benign (Aug 01, 2023)
15-43698687-G-T		not specified	Uncertain significance (Nov 08, 2022)
15-43698750-G-A		not specified	Uncertain significance (Mar 17, 2023)
15-43698765-A-G		not specified	Uncertain significance (Feb 27, 2024)
15-43699040-G-A		not specified	Uncertain significance (Apr 12, 2022)
15-43699044-C-G			Likely benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CKMT1A	protein_coding	protein_coding	ENST00000413453	9	6337

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.25e-7	0.221	125703	2	38	125743	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.631	94	113	0.833	0.00000678	2669
Missense in Polyphen		45	53.967	0.83384		1184
Synonymous	0.390	35	38.1	0.920	0.00000184	887
Loss of Function	0.131	10	10.5	0.956	6.54e-7	225

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000776	0.000768
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000462	0.000462
European (Non-Finnish)	0.000115	0.000105
Middle Eastern	0.00	0.00
South Asian	0.000197	0.000163
Other	0.00	0.00

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: 0.676

Haploinsufficiency Scores

• pHI: 0.352
• hipred: N
• hipred_score: 0.238
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.787

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ckmt1
• Phenotype: growth/size/body region phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

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