CMPK1

cytidine/uridine monophosphate kinase 1

Basic information

Region (hg38): 1:47333789-47394866

Previous symbols: [ "CMPK" ]

Links

ENSG00000162368 ∙ NCBI:51727 ∙ OMIM:191710 ∙ HGNC:18170 ∙ Uniprot:P30085 ∙ 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 CMPK1 gene.

• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CMPK1 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in CMPK1

This is a list of pathogenic ClinVar variants found in the CMPK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-47334072-G-T		not specified	Uncertain significance (Dec 17, 2021)
1-47373075-T-C		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CMPK1	protein_coding	protein_coding	ENST00000371873	6	45043

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.848	0.152	123814	0	1	123815	0.00000404

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.93	52	109	0.479	0.00000506	1486
Missense in Polyphen		9	30.887	0.29138		396
Synonymous	0.970	31	38.7	0.802	0.00000177	406
Loss of Function	2.73	1	10.6	0.0947	5.43e-7	141

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000167	0.000167

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the phosphorylation of pyrimidine nucleoside monophosphates at the expense of ATP. Plays an important role in de novo pyrimidine nucleotide biosynthesis. Has preference for UMP and CMP as phosphate acceptors. Also displays broad nucleoside diphosphate kinase activity. {ECO:0000255|HAMAP-Rule:MF_03172, ECO:0000269|PubMed:10462544, ECO:0000269|PubMed:11912132, ECO:0000269|PubMed:23416111}.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Drug metabolism - other enzymes - Homo sapiens (human);Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics;Gemcitabine Pathway, Pharmacodynamics;GLUT-1 deficiency syndrome;Congenital disorder of glycosylation CDG-IId;Lactose Synthesis;Gemcitabine Action Pathway;Lamivudine Metabolism Pathway;Gemcitabine Metabolism Pathway;Pyrimidine metabolism;UTP and CTP <i>de novo</i> biosynthesis;Metabolism of nucleotides;Interconversion of nucleotide di- and triphosphates;Metabolism;Pyrimidine metabolism;superpathway of pyrimidine ribonucleotides <i>de novo</i> biosynthesis;superpathway of pyrimidine deoxyribonucleoside salvage;CMP phosphorylation;Pyrimidine nucleotides nucleosides metabolism;pyrimidine deoxyribonucleotide phosphorylation;superpathway of pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis (Consensus)

Recessive Scores

• pRec: 0.200

Intolerance Scores

• loftool: 0.342
• rvis_EVS: 0.37
• rvis_percentile_EVS: 74.95

Haploinsufficiency Scores

• pHI: 0.203
• hipred: N
• hipred_score: 0.437
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.250

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cmpk1

Gene ontology

• Biological process: nucleoside diphosphate phosphorylation;'de novo' pyrimidine nucleobase biosynthetic process;UMP biosynthetic process;nucleoside triphosphate biosynthetic process;pyrimidine ribonucleotide biosynthetic process;nucleobase-containing small molecule interconversion;nucleoside monophosphate phosphorylation
• Cellular component: nucleus;nucleolus;cytoplasm;cytosol;extracellular exosome
• Molecular function: cytidylate kinase activity;nucleoside diphosphate kinase activity;uridine kinase activity;ATP binding;uridylate kinase activity;nucleoside monophosphate kinase activity