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

No genCC data.

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.

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.

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			52	5		57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	5	0

Variants in CMPK2

This is a list of pathogenic ClinVar variants found in the CMPK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-6849890-G-A		not specified	Likely benign (May 24, 2024)
2-6849954-G-A		not specified	Uncertain significance (Mar 12, 2024)
2-6849959-T-C		BASAL GANGLIA CALCIFICATION, IDIOPATHIC, 10, AUTOSOMAL RECESSIVE	Pathogenic (Nov 22, 2024)
2-6849966-T-C		not specified	Likely benign (Oct 03, 2022)
2-6851456-C-T		not specified	Uncertain significance (Feb 14, 2023)
2-6851531-C-T		not specified	Uncertain significance (Jan 04, 2024)
2-6851540-G-A		not specified	Uncertain significance (Mar 06, 2023)
2-6851547-C-G		not specified	Uncertain significance (May 23, 2024)
2-6851605-G-T		CMPK2-related disorder	Uncertain significance (Jan 10, 2023)
2-6851655-T-C		not specified	Uncertain significance (Jun 30, 2024)
2-6861199-G-A		not specified	Uncertain significance (May 26, 2024)
2-6861226-T-G		not specified	Uncertain significance (Aug 04, 2023)
2-6861326-G-A		not specified	Uncertain significance (May 20, 2024)
2-6861370-G-A		not specified	Uncertain significance (Nov 17, 2022)
2-6861376-G-A		not specified	Uncertain significance (Jun 26, 2023)
2-6863466-G-A		not specified	Uncertain significance (Jan 20, 2023)
2-6863482-C-T		not specified	Uncertain significance (Dec 12, 2023)
2-6863484-A-G		not specified	Uncertain significance (Oct 26, 2022)
2-6863503-T-C		not specified	Uncertain significance (Mar 25, 2024)
2-6863553-C-T		not specified	Likely benign (Jan 16, 2024)
2-6865038-C-A		not specified	Uncertain significance (Jul 09, 2024)
2-6865051-G-A		not specified	Uncertain significance (Oct 30, 2024)
2-6865052-G-C		not specified	Uncertain significance (Oct 09, 2024)
2-6865053-T-C		not specified	Uncertain significance (Apr 15, 2024)
2-6865056-G-A		not specified	Uncertain significance (Jul 14, 2021)

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 <i>de novo</i> biosynthesis;superpathway of pyrimidine ribonucleotides <i>de novo</i> biosynthesis;superpathway of pyrimidine deoxyribonucleoside salvage;CMP phosphorylation;pyrimidine deoxyribonucleotide phosphorylation;superpathway of pyrimidine deoxyribonucleotides <i>de novo</i> 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