UPB1 beta-ureidopropionase 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: UPB1provided by HGNC
Official Full Name: beta-ureidopropionase 1provided by HGNC
Primary source: HGNC:HGNC:16297
See related: Ensembl:ENSG00000100024 MIM:606673; AllianceGenome:HGNC:16297
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: BUP1
Summary: This gene encodes a protein that belongs to the CN hydrolase family. Beta-ureidopropionase catalyzes the last step in the pyrimidine degradation pathway. The pyrimidine bases uracil and thymine are degraded via the consecutive action of dihydropyrimidine dehydrogenase (DHPDH), dihydropyrimidinase (DHP) and beta-ureidopropionase (UP) to beta-alanine and beta-aminoisobutyric acid, respectively. UP deficiencies are associated with N-carbamyl-beta-amino aciduria and may lead to abnormalities in neurological activity. [provided by RefSeq, Jul 2008]
Expression: Biased expression in liver (RPKM 34.8) and kidney (RPKM 13.3) See more
Orthologs: mouse all
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Genomic context

Location:: 22q11.23

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (24495332..24528390)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (24956949..24989995)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (24891300..24924358)

Chromosome 22 - NC_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Allosteric Regulation of Beta-Ureidopropionase Depends on Fine-Tuned Stability of Active-Site Loops and Subunit Interfaces.
Title: The Allosteric Regulation of Β-Ureidopropionase Depends on Fine-Tuned Stability of Active-Site Loops and Subunit Interfaces.
Low UPB1 Level Correlates With Poor Prognosis in Lung Adenocarcinoma.
Title: Low UPB1 Level Correlates With Poor Prognosis in Lung Adenocarcinoma.
The relationship between beta-ureidopropionase deficiency due to UPB1 variants and human phenotypes is uncertain.
Title: The relationship between beta-ureidopropionase deficiency due to UPB1 variants and human phenotypes is uncertain.
beta-Ureidopropionase deficiency due to novel and rare UPB1 mutations affecting pre-mRNA splicing and protein structural integrity and catalytic activity.
Title: β-Ureidopropionase deficiency due to novel and rare UPB1 mutations affecting pre-mRNA splicing and protein structural integrity and catalytic activity.
The compound heterozygous mutations of the UPB1 gene probably underlie the beta-ureidopropinoase deficiency in this fabily pedigree.
Title: [Identification of a novel mutation of UPB1 gene in a Chinese family affected with beta-ureidopropinoase deficiency].
Crystal structure and pH-dependent allosteric regulation of human beta-ureidopropionase, an enzyme involved in anticancer drug metabolism.
Title: Crystal structure and pH-dependent allosteric regulation of human β-ureidopropionase, an enzyme involved in anticancer drug metabolism.
The c.977G>A (p.R326Q) is the most common mutation of the UPB1 gene in Chinese. The predicted incidence indicates that beta-ureidopropionase deficiency is significantly underdiagnosed in the Chinese population.
Title: Genetic analysis of the UPB1 gene in two new Chinese families with β-ureidopropionase deficiency and the carrier frequency of the mutation c.977G>A in Northern China.
High prevalence of p.R326Q in the normal Japanese population indicates that betaUP deficiency is not as rare as generally considered
Title: Clinical, biochemical and molecular analysis of 13 Japanese patients with β-ureidopropionase deficiency demonstrates high prevalence of the c.977G > A (p.R326Q) mutation [corrected].
This study reports the clinical, biochemical, and molecular analysis of a newly identified patient with beta-ureidopropionase deficiency and the effect of the first synonymous mutation in UBP1 affecting pre-mRNA splicing, using the minigene approach.
Title: Identification of a novel synonymous mutation in the human β -Ureidopropionase Gene UPB1 affecting pre-mRNA splicing.
analysis of UPB1 variants on 5-FU-related toxicity in the population of all analyzed patients revealed an association between the c.-80C>G (rs2070474) variant and gastrointestinal toxicity
Title: Contribution of the β-ureidopropionase (UPB1) gene alterations to the development of fluoropyrimidine-related toxicity.

Submit: New GeneRIF Correction See all GeneRIFs (15)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Deficiency of beta-ureidopropionase MedGen: C1291512 OMIM: 613161 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D10S275 (e-PCR)
- UniSTS:147992

D8S2279 (e-PCR)
- UniSTS:473907

NoName (e-PCR)
- UniSTS:486221

STS-T67940 (e-PCR)
- UniSTS:73294

D1S1425 (e-PCR)
- UniSTS:149621

SGC33315 (e-PCR)
- UniSTS:81017

D1S1431 (e-PCR)
- UniSTS:149627

WIAF-2537 (e-PCR)
- UniSTS:90799

D22S156 (e-PCR), detects polymorphism
- UniSTS:13490

HSC1IC042 (e-PCR)
- UniSTS:14521

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables beta-ureidopropionase activity	IBA Inferred from Biological aspect of Ancestor more info
enables beta-ureidopropionase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
NOT enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in CMP catabolic process	IEA Inferred from Electronic Annotation more info
involved_in UMP catabolic process	IEA Inferred from Electronic Annotation more info
involved_in beta-alanine biosynthetic process via 3-ureidopropionate	IBA Inferred from Biological aspect of Ancestor more info
involved_in beta-alanine biosynthetic process via 3-ureidopropionate	IDA Inferred from Direct Assay more info	PubMed
involved_in dCMP catabolic process	IEA Inferred from Electronic Annotation more info
involved_in dUMP catabolic process	IEA Inferred from Electronic Annotation more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in liver development	IEA Inferred from Electronic Annotation more info
involved_in protein homooligomerization	IDA Inferred from Direct Assay more info	PubMed
involved_in protein homotetramerization	IDA Inferred from Direct Assay more info	PubMed
involved_in pyrimidine nucleoside catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed

General protein information

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Preferred Names: beta-ureidopropionase

Names: beta-alanine synthase; n-carbamoyl-beta-alanine amidohydrolase; ureidopropionase, beta

NP_057411.1

EC 3.5.1.6

XP_011528525.1

EC 3.5.1.6

XP_047297360.1

EC 3.5.1.6

XP_047297361.1

EC 3.5.1.6

XP_054181664.1

EC 3.5.1.6

XP_054181665.1

EC 3.5.1.6

XP_054181666.1

EC 3.5.1.6

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_012858.2 RefSeqGene

Range

5050..38108

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_016327.3 → NP_057411.1 beta-ureidopropionase

See identical proteins and their annotated locations for NP_057411.1

Status: REVIEWED

Source sequence(s)

AP000355, BC033388, CR456375

Consensus CDS

CCDS13827.1

UniProtKB/Swiss-Prot

A3KMF8, Q9UBR1, Q9UIR3

UniProtKB/TrEMBL

B2RBM2

Related

ENSP00000324343.5, ENST00000326010.10

Conserved Domains (1) summary

cd07587
Location:9 → 371

ML_beta-AS; mammalian-like beta-alanine synthase (beta-AS) and similar proteins (class 5 nitrilases)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000022.11 Reference GRCh38.p14 Primary Assembly

Range

24495332..24528390

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047441404.1 → XP_047297360.1 beta-ureidopropionase isoform X1
XM_047441405.1 → XP_047297361.1 beta-ureidopropionase isoform X3
XM_011530223.3 → XP_011528525.1 beta-ureidopropionase isoform X2

Conserved Domains (1) summary

cl11424
Location:9 → 318

nitrilase; Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes