UPP2

uridine phosphorylase 2

Basic information

Region (hg38): 2:157876679-158136154

Links

ENSG00000007001 ∙ NCBI:151531 ∙ OMIM:617340 ∙ HGNC:23061 ∙ Uniprot:O95045 ∙ 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 UPP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UPP2 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					1	1
missense			19	5	1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	20	5	2

Variants in UPP2

This is a list of pathogenic ClinVar variants found in the UPP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-158102053-T-C		not specified	Uncertain significance (Mar 20, 2023)
2-158102068-C-G		not specified	Uncertain significance (Nov 10, 2022)
2-158102071-C-T		not specified	Uncertain significance (Jan 19, 2024)
2-158102092-G-A		not specified	Likely benign (Dec 15, 2023)
2-158106115-G-A		not specified	Uncertain significance (Sep 25, 2023)
2-158115113-G-A		not specified	Uncertain significance (Apr 17, 2023)
2-158115152-A-C			Benign (Dec 31, 2019)
2-158115161-G-A		not specified	Uncertain significance (Feb 27, 2023)
2-158115162-A-G		not specified	Uncertain significance (Aug 28, 2023)
2-158115167-G-A		not specified	Likely benign (Jun 03, 2022)
2-158115173-G-C		not specified	Uncertain significance (Feb 05, 2024)
2-158115228-T-C		not specified	Uncertain significance (May 14, 2024)
2-158117890-C-T		not specified	Uncertain significance (Feb 10, 2022)
2-158117920-G-A		not specified	Uncertain significance (Mar 31, 2023)
2-158117921-G-C		not specified	Uncertain significance (Feb 28, 2024)
2-158121416-A-C			Benign (Jan 25, 2018)
2-158121469-G-A		not specified	Likely benign (Apr 17, 2023)
2-158121494-C-G		not specified	Uncertain significance (Sep 22, 2023)
2-158121548-C-A		not specified	Uncertain significance (Nov 15, 2021)
2-158121597-T-C		not specified	Uncertain significance (Jul 09, 2021)
2-158123758-G-T		not specified	Uncertain significance (Jul 27, 2021)
2-158123842-T-C		not specified	Uncertain significance (May 27, 2022)
2-158123893-A-G		not specified	Uncertain significance (Jun 17, 2022)
2-158134766-C-T		not specified	Uncertain significance (Dec 20, 2023)
2-158134805-C-T		not specified	Uncertain significance (Sep 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UPP2	protein_coding	protein_coding	ENST00000605860	9	259453

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00126	0.963	110916	1095	13730	125741	0.0608

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.378	193	208	0.926	0.0000109	2457
Missense in Polyphen		52	60.331	0.86192		760
Synonymous	0.465	70	75.1	0.932	0.00000402	723
Loss of Function	1.85	7	14.7	0.477	7.83e-7	200

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.298	0.294
Ashkenazi Jewish	0.0727	0.0723
East Asian	0.133	0.132
Finnish	0.0188	0.0188
European (Non-Finnish)	0.0304	0.0301
Middle Eastern	0.133	0.132
South Asian	0.109	0.105
Other	0.0506	0.0493

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1- phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis. Shows substrate specificity and accept uridine, deoxyuridine, and thymidine as well as the two pyrimidine nucleoside analogs 5-fluorouridine and 5-fluoro-2(')-deoxyuridine as substrates.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Drug metabolism - other enzymes - Homo sapiens (human);Fluoropyrimidine Pathway, Pharmacokinetics;Pyrimidine Metabolism;UMP Synthase Deiciency (Orotic Aciduria);MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy);Beta Ureidopropionase Deficiency;Dihydropyrimidinase Deficiency;Fluoropyrimidine Activity;pyrimidine ribonucleosides degradation;pyrimidine deoxyribonucleosides degradation;Pyrimidine catabolism;Nucleobase catabolism;Metabolism of nucleotides;Metabolism;Pyrimidine salvage;Nucleotide salvage;Pyrimidine metabolism;pyrimidine ribonucleosides degradation (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.408
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.26

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.219
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.935

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Upp2

Gene ontology

• Biological process: nucleoside metabolic process;nucleotide catabolic process;pyrimidine nucleoside salvage;UMP salvage;uridine metabolic process;pyrimidine nucleoside catabolic process
• Cellular component: cytosol;type III intermediate filament
• Molecular function: uridine phosphorylase activity;protein binding