UCK2

uridine-cytidine kinase 2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 1:165827613-165911618

Previous symbols: [ "UMPK" ]

Links

ENSG00000143179 ∙ NCBI:7371 ∙ OMIM:609329 ∙ HGNC:12562 ∙ Uniprot:Q9BZX2 ∙ 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 UCK2 gene.

• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UCK2 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in UCK2

This is a list of pathogenic ClinVar variants found in the UCK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-165890313-C-T		not specified	Uncertain significance (Aug 03, 2022)
1-165891293-C-G		not specified	Uncertain significance (Apr 25, 2023)
1-165907689-A-G		not specified	Uncertain significance (Jul 19, 2023)
1-165907764-A-G		not specified	Uncertain significance (Aug 30, 2022)
1-165907794-G-A		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UCK2	protein_coding	protein_coding	ENST00000367879	7	84088

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.721	0.278	125745	0	3	125748	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.81	56	154	0.363	0.00000922	1712
Missense in Polyphen		14	71.539	0.1957		786
Synonymous	-0.243	65	62.6	1.04	0.00000392	490
Loss of Function	2.81	2	12.9	0.155	6.48e-7	150

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.000198	0.000198
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	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphorylates uridine and cytidine to uridine monophosphate and cytidine monophosphate. Does not phosphorylate deoxyribonucleosides or purine ribonucleosides. Can use ATP or GTP as a phosphate donor. Can also phosphorylate cytidine and uridine nucleoside analogs such as 6-azauridine, 5-fluorouridine, 4- thiouridine, 5-bromouridine, N(4)-acetylcytidine, N(4)- benzoylcytidine, 5-fluorocytidine, 2-thiocytidine, 5- methylcytidine, and N(4)-anisoylcytidine.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Drug metabolism - other enzymes - Homo sapiens (human);Fluoropyrimidine Pathway, Pharmacokinetics;Fluoropyrimidine Activity;Pyrimidine metabolism;Metabolism of nucleotides;Metabolism;Pyrimidine salvage;Nucleotide salvage;Pyrimidine nucleotides nucleosides metabolism;pyrimidine ribonucleosides salvage I (Consensus)

Recessive Scores

• pRec: 0.186

Intolerance Scores

• loftool: 0.155
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.379
• hipred: Y
• hipred_score: 0.728
• ghis: 0.666

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.982

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Uck2

Gene ontology

• Biological process: CMP salvage;phosphorylation;pyrimidine nucleoside salvage;UMP salvage;CTP salvage
• Cellular component: cellular_component;cytosol
• Molecular function: ATP binding;kinase activity;nucleoside kinase activity