UPP1

uridine phosphorylase 1

Basic information

Region (hg38): 7:48088628-48108736

Previous symbols: [ "UP" ]

Links

ENSG00000183696

∙ NCBI:7378 ∙ OMIM:191730 ∙ HGNC:12576 ∙ Uniprot:Q16831 ∙ 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 UPP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UPP1 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 clinvar	1
missense			2 clinvar			2
nonsense						0
start loss						0
frameshift				1 clinvar		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	1	1

Variants in UPP1

This is a list of pathogenic ClinVar variants found in the UPP1 region.

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

Position	Phenotype	Significance	ClinVar
7-48101941-C-T	Long QT syndrome	Likely benign (-)	207939
7-48103390-A-T		Uncertain significance (Dec 11, 2019)	994201
7-48107042-A-G		Benign (Aug 08, 2018)	769712
7-48107077-A-T		Uncertain significance (Dec 11, 2019)	993830
7-48107397-CG-C		Likely benign (Dec 01, 2022)	2657465

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UPP1	protein_coding	protein_coding	ENST00000331803	7	20106

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000376	0.851	125635	2	111	125748	0.000449

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.344	185	199	0.931	0.0000123	2025
Missense in Polyphen		59	76.514	0.7711		754
Synonymous	-1.18	95	81.5	1.17	0.00000544	627
Loss of Function	1.29	7	11.8	0.595	4.96e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000123	0.000105
Middle Eastern	0.000163	0.000163
South Asian	0.00301	0.00294
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1- phosphate (PubMed:7488099). The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis. {ECO:0000269|PubMed:7488099, ECO:0000305}.;
Pathway: Pyrimidine metabolism - Homo sapiens (human);Drug metabolism - other enzymes - Homo sapiens (human);Fluoropyrimidine Pathway, Pharmacokinetics;Fluoropyrimidine Activity;pyrimidine ribonucleosides degradation;Pyrimidine metabolism;pyrimidine deoxyribonucleosides degradation;Pyrimidine catabolism;Nucleobase catabolism;Metabolism of nucleotides;Metabolism;Pyrimidine salvage;Nucleotide salvage;pyrimidine ribonucleosides degradation;Pyrimidine nucleotides nucleosides metabolism (Consensus)

Recessive Scores

pRec: 0.183

Intolerance Scores

loftool: 0.206
rvis_EVS: -0.2
rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

pHI: 0.173
hipred: N
hipred_score: 0.350
ghis: 0.541

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Upp1
Phenotype: homeostasis/metabolism phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; skeleton phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Gene ontology

Biological process: nucleobase-containing compound metabolic process;uridine catabolic process;nucleotide catabolic process;cellular response to glucose starvation;pyrimidine nucleoside salvage;UMP salvage;pyrimidine nucleoside catabolic process
Cellular component: nucleus;nucleoplasm;cytosol
Molecular function: uridine phosphorylase activity