CMPK2

cytidine/uridine monophosphate kinase 2

Basic information

Region (hg38): 2:6840570-6866635

Links

ENSG00000134326

∙ NCBI:129607 ∙ OMIM:611787 ∙ HGNC:27015 ∙ Uniprot:Q5EBM0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

basal ganglia calcification, idiopathic, 10, autosomal recessive (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Basal ganglia calcification, idiopathic, 10, autosomal recessive	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	36443312

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CMPK2 gene.

not_specified (87 variants)
CMPK2-related_disorder (4 variants)
Basal_ganglia_calcification,_idiopathic,_10,_autosomal_recessive (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CMPK2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000207315.4. 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	1 clinvar		85 clinvar	6 clinvar		92
nonsense						0
start loss	2					2
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	3	0	85	6	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CMPK2	protein_coding	protein_coding	ENST00000256722	5	26066

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000113	0.362	124763	1	35	124799	0.000144

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.274	170	180	0.943	0.00000943	2788
Missense in Polyphen		70	75.095	0.93215		986
Synonymous	0.171	75	76.9	0.975	0.00000398	985
Loss of Function	0.472	10	11.7	0.851	5.00e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000985	0.000984
Ashkenazi Jewish	0.00	0.00
East Asian	0.000389	0.000389
Finnish	0.00	0.00
European (Non-Finnish)	0.0000710	0.0000706
Middle Eastern	0.000389	0.000389
South Asian	0.000131	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: May participate in dUTP and dCTP synthesis in mitochondria. Is able to phosphorylate dUMP, dCMP, CMP, UMP and monophosphates of the pyrimidine nucleoside analogs ddC, dFdC, araC, BVDU and FdUrd with ATP as phosphate donor. Efficacy is highest for dUMP followed by dCMP; CMP and UMP are poor substrates. May be involved in mtDNA depletion caused by long term treatment with ddC or other pyrimidine analogs. Also displays broad nucleoside diphosphate kinase activity. {ECO:0000269|PubMed:17999954, ECO:0000269|PubMed:23416111}.;
Pathway: Pyrimidine metabolism - Homo sapiens (human);Pyrimidine Metabolism;UMP Synthase Deiciency (Orotic Aciduria);MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy);Beta Ureidopropionase Deficiency;Dihydropyrimidinase Deficiency;Pyrimidine metabolism;UTP and CTP de novo biosynthesis;superpathway of pyrimidine ribonucleotides de novo biosynthesis;superpathway of pyrimidine deoxyribonucleoside salvage;CMP phosphorylation;pyrimidine deoxyribonucleotide phosphorylation;superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (Consensus)

Recessive Scores

pRec: 0.111

Haploinsufficiency Scores

pHI: 0.0719
hipred: N
hipred_score: 0.180
ghis: 0.531

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.575

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cmpk2
Phenotype: homeostasis/metabolism phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process: nucleoside diphosphate phosphorylation;dUDP biosynthetic process;dTDP biosynthetic process;dTTP biosynthetic process;nucleoside triphosphate biosynthetic process;nucleoside monophosphate phosphorylation;cellular response to lipopolysaccharide
Cellular component: cytoplasm;mitochondrion
Molecular function: cytidylate kinase activity;nucleoside diphosphate kinase activity;thymidylate kinase activity;ATP binding;uridylate kinase activity;UMP kinase activity