UCKL1

uridine-cytidine kinase 1 like 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 20:63939829-63956416

Previous symbols: [ "URKL1" ]

Links

ENSG00000198276 ∙ NCBI:54963 ∙ OMIM:610866 ∙ HGNC:15938 ∙ Uniprot:Q9NWZ5 ∙ 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 UCKL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UCKL1 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			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					4	4
Total	0	0	19	2	4

Variants in UCKL1

This is a list of pathogenic ClinVar variants found in the UCKL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-63939983-G-A		not specified	Uncertain significance (Oct 29, 2024)
20-63940064-AG-A			Benign (Dec 31, 2019)
20-63940064-AGG-A			Benign (Dec 31, 2019)
20-63940064-AGGG-A			Benign (Dec 31, 2019)
20-63940064-A-AG			Benign (Dec 31, 2019)
20-63940241-G-C		not specified	Uncertain significance (Nov 15, 2024)
20-63940466-G-A		not specified	Uncertain significance (Nov 26, 2024)
20-63940847-C-T		not specified	Uncertain significance (Apr 11, 2023)
20-63940850-C-T		not specified	Uncertain significance (Jul 10, 2024)
20-63941026-C-T		not specified	Uncertain significance (Sep 10, 2024)
20-63941125-A-G		not specified	Uncertain significance (Mar 19, 2024)
20-63944437-A-G		not specified	Uncertain significance (Dec 13, 2021)
20-63944653-C-T		not specified	Uncertain significance (Mar 20, 2023)
20-63944668-C-G		not specified	Uncertain significance (Feb 05, 2024)
20-63944698-C-T		not specified	Uncertain significance (Mar 21, 2023)
20-63945813-T-C		not specified	Uncertain significance (Jun 05, 2024)
20-63945818-C-T		not specified	Uncertain significance (May 11, 2022)
20-63945821-C-T		not specified	Uncertain significance (Jun 25, 2024)
20-63945900-C-T		not specified	Uncertain significance (May 03, 2023)
20-63945929-T-C		not specified	Uncertain significance (Apr 07, 2023)
20-63945966-C-G		not specified	Likely benign (Aug 20, 2023)
20-63946172-A-G		not specified	Uncertain significance (Sep 20, 2023)
20-63946228-G-A		not specified	Uncertain significance (May 03, 2023)
20-63946250-C-T		not specified	Uncertain significance (Aug 16, 2021)
20-63946256-C-T		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UCKL1	protein_coding	protein_coding	ENST00000354216	15	16584

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.36e-15	0.0239	125535	0	66	125601	0.000263

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.32	242	367	0.659	0.0000253	3544
Missense in Polyphen		82	144.89	0.56594		1325
Synonymous	-1.28	182	161	1.13	0.0000124	1098
Loss of Function	0.288	23	24.5	0.937	0.00000113	293

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00116	0.00105
Ashkenazi Jewish	0.0000996	0.0000993
East Asian	0.000277	0.000272
Finnish	0.0000473	0.0000462
European (Non-Finnish)	0.000227	0.000211
Middle Eastern	0.000277	0.000272
South Asian	0.000293	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May contribute to UTP accumulation needed for blast transformation and proliferation. {ECO:0000269|PubMed:12199906}.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Drug metabolism - other enzymes - Homo sapiens (human);Pyrimidine Metabolism;UMP Synthase Deiciency (Orotic Aciduria);MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy);Beta Ureidopropionase Deficiency;Dihydropyrimidinase Deficiency;Pyrimidine metabolism;Metabolism of nucleotides;Metabolism;Pyrimidine salvage;Nucleotide salvage;pyrimidine ribonucleosides salvage I (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.140
• rvis_EVS: -1.4
• rvis_percentile_EVS: 4.19

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.319
• ghis: 0.662

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.936

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Uckl1

Gene ontology

• Biological process: viral process;phosphorylation;pyrimidine nucleoside salvage;UMP salvage;CTP salvage
• Cellular component: nucleus;cytosol
• Molecular function: uridine kinase activity;protein binding;ATP binding;kinase activity