CKMT1B

creatine kinase, mitochondrial 1B

Basic information

Region (hg38): 15:43593054-43604901

Previous symbols: [ "CKMT", "CKMT1" ]

Links

ENSG00000237289

∙ NCBI:1159 ∙ OMIM:123290 ∙ HGNC:1995 ∙ 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 CKMT1B gene.

not_specified (23 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CKMT1B gene is commonly pathogenic or not. These statistics are base on transcript: NM_001375484.1. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			22 clinvar	1 clinvar	1 clinvar	24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	22	1	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CKMT1B	protein_coding	protein_coding	ENST00000300283	9	11848

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000323	0.588	125698	2	32	125732	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.534	96	112	0.858	0.00000667	2672
Missense in Polyphen		44	52.987	0.8304		1183
Synonymous	0.588	33	37.6	0.878	0.00000182	883
Loss of Function	0.740	8	10.6	0.755	6.57e-7	225

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000235
Ashkenazi Jewish	0.000893	0.000893
East Asian	0.0000564	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000132
Middle Eastern	0.0000564	0.0000544
South Asian	0.00	0.00
Other	0.000490	0.000489

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: 0.665

Haploinsufficiency Scores

pHI: 0.0983
hipred: N
hipred_score: 0.341
ghis: 0.540

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.965

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);