UPB1 (beta-ureidopropionase 1)

Download as csv Download as pdf

Log in to bookmark this gene

Bookmark This Gene

Title Project / Tag (optional) Note (optional)

Cancel Save

On this page

Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases Related genes Diseases linked via similar genes

Gene

• Entrez ID: 51733
• Gene name: Beta-ureidopropionase 1
• Gene symbol: UPB1
• Synonyms (NCBI Gene): BUP1
• Chromosome: 22
• Chromosome location: 22q11.23
• 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

SNPs Show/Hide all (6)

SNP ID	Visualize variation	Clinical significance	Consequence
rs34035085	C>A,T	Likely-benign, benign, pathogenic	5 prime UTR variant, coding sequence variant, non coding transcript variant, missense variant
rs118163237	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Intron variant, non coding transcript variant, downstream transcript variant, genic downstream transcript variant, missense variant, coding sequence variant
rs138081800	A>G	Pathogenic-likely-pathogenic	Splice acceptor variant
rs143493067	G>A	Pathogenic	Genic downstream transcript variant, splice acceptor variant, intron variant
rs747539101	G>A	Pathogenic	Splice donor variant
rs876657373	A>G	Pathogenic	Splice acceptor variant, intron variant, genic downstream transcript variant

miRNA Show/Hide all (36)

miRTarBase ID	miRNA	Experiments	Reference
MIRT1476024	hsa-let-7a	CLIP-seq
MIRT1476025	hsa-let-7b	CLIP-seq
MIRT1476026	hsa-let-7c	CLIP-seq
MIRT1476027	hsa-let-7d	CLIP-seq
MIRT1476028	hsa-let-7e	CLIP-seq
MIRT1476029	hsa-let-7f	CLIP-seq
MIRT1476030	hsa-let-7g	CLIP-seq
MIRT1476031	hsa-let-7i	CLIP-seq
MIRT1476032	hsa-miR-1587	CLIP-seq
MIRT1476033	hsa-miR-202	CLIP-seq
MIRT1476034	hsa-miR-2110	CLIP-seq
MIRT1476035	hsa-miR-3150a-3p	CLIP-seq
MIRT1476036	hsa-miR-3175	CLIP-seq
MIRT1476037	hsa-miR-3690	CLIP-seq
MIRT1476038	hsa-miR-3909	CLIP-seq
MIRT1476039	hsa-miR-4269	CLIP-seq
MIRT1476040	hsa-miR-4282	CLIP-seq
MIRT1476041	hsa-miR-4458	CLIP-seq
MIRT1476042	hsa-miR-4492	CLIP-seq
MIRT1476043	hsa-miR-4498	CLIP-seq
MIRT1476044	hsa-miR-4500	CLIP-seq
MIRT1476045	hsa-miR-4514	CLIP-seq
MIRT1476046	hsa-miR-4638-3p	CLIP-seq
MIRT1476047	hsa-miR-4656	CLIP-seq
MIRT1476048	hsa-miR-4675	CLIP-seq
MIRT1476049	hsa-miR-4692	CLIP-seq
MIRT1476050	hsa-miR-4741	CLIP-seq
MIRT1476051	hsa-miR-4742-5p	CLIP-seq
MIRT1476052	hsa-miR-490-3p	CLIP-seq
MIRT1476053	hsa-miR-589	CLIP-seq
MIRT1476054	hsa-miR-619	CLIP-seq
MIRT1476055	hsa-miR-626	CLIP-seq
MIRT1476056	hsa-miR-762	CLIP-seq
MIRT1476057	hsa-miR-939	CLIP-seq
MIRT1476058	hsa-miR-98	CLIP-seq
MIRT1476054	hsa-miR-619	CLIP-seq

Gene ontology (GO) Show/Hide all (24)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001701	Process	In utero embryonic development	IEA
GO:0001889	Process	Liver development	IEA
GO:0003837	Function	Beta-ureidopropionase activity	IBA
GO:0003837	Function	Beta-ureidopropionase activity	IDA	22525402, 29976570
GO:0003837	Function	Beta-ureidopropionase activity	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006248	Process	CMP catabolic process	IEA
GO:0006249	Process	DCMP catabolic process	IEA
GO:0008270	Function	Zinc ion binding	IDA	29976570
GO:0016787	Function	Hydrolase activity	IEA
GO:0019482	Process	Beta-alanine metabolic process	IEA
GO:0019483	Process	Beta-alanine biosynthetic process	IEA
GO:0033396	Process	Beta-alanine biosynthetic process via 3-ureidopropionate	IBA
GO:0033396	Process	Beta-alanine biosynthetic process via 3-ureidopropionate	IDA	22525402, 29976570
GO:0042803	Function	Protein homodimerization activity	IDA	29976570
GO:0044281	Process	Small molecule metabolic process	IEA
GO:0046050	Process	UMP catabolic process	IEA
GO:0046079	Process	DUMP catabolic process	IEA
GO:0046135	Process	Pyrimidine nucleoside catabolic process	IMP	22525402
GO:0051260	Process	Protein homooligomerization	IDA	22525402
GO:0051289	Process	Protein homotetramerization	IDA	29976570
GO:0070062	Component	Extracellular exosome	HDA	19056867

Other IDs

• MIM: 606673
• HGNC: 16297
• e!Ensembl: ENSG00000100024

Protein

• UniProt ID: Q9UBR1
• Protein name: Beta-ureidopropionase (EC 3.5.1.6) (BUP-1) (Beta-alanine synthase) (N-carbamoyl-beta-alanine amidohydrolase)
• Protein function: Catalyzes a late step in pyrimidine degradation (PubMed:22525402, PubMed:24526388). Converts N-carbamoyl-beta-alanine (3-ureidopropanoate) into beta-alanine, ammonia and carbon dioxide (PubMed:10415095, PubMed:10542323, PubMed:11508704, PubMed:2
• PDB: 6FTQ , 8PT4
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00795	CN_hydrolase	73 → 352	Carbon-nitrogen hydrolase	Family

• Tissue specificity: TISSUE SPECIFICITY: Detected in liver (at protein level). {ECO:0000269|PubMed:22525402}.
• Sequence:

  MAGAEWKSLEECLEKHLPLPDLQEVKRVLYGKELRKLDLPREAFEAASREDFELQGYAFE
  AAEEQLRRPRIVHVGLVQNRIPLPANAPVAEQVSALHRRIKAIVEVAAMCGVNIICFQEA
  WTMPFAFCTREKLPWTEFAESAEDGPTTRFCQKLAKNHDMVVVSPILERDSEHGDVLWNT
  AVVISNSGAVLGKTRKNHIPRVGDFNESTYYMEGNLGHPVFQTQFGRIAVNICYGRHHPL
  NWLMYSINGAEIIFNPSATIGALSESLWPIEARNAAIANHCFTCAINRVGTEHFPNEFTS
  GDGKKAHQDFGYFYGSSYVAAPDSSRTPGLSRSRDGLLVAKLDLNLCQQVNDVWNFKMTG
  RYEMYARELAEAVKSNYSPTIVKE

• Sequence length: 384

Pathways

KEGG Pathway	Reactome Pathway
Pyrimidine metabolism	Pyrimidine catabolism
beta-Alanine metabolism
Pantothenate and CoA biosynthesis
Drug metabolism - other enzymes
Metabolic pathways

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal Show/Hide Causal Diseases (6)
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Cervical cancer	Likely pathogenic; Pathogenic	rs143493067	RCV005901092	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Clear cell carcinoma of kidney	Likely pathogenic; Pathogenic	rs143493067	RCV005901093	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Deficiency of beta-ureidopropionase	Pathogenic; Likely pathogenic	rs140157113, rs770644036, rs772212502, rs1012254852, rs2147041278, rs138081800, rs747539101, rs1296034492, rs1568979622, rs143493067, rs765062693	RCV005432699 RCV003989419 RCV002279889 RCV002279890 RCV002279891 RCV000004363 RCV001334907 RCV003388491 RCV004527177 RCV000763075 RCV004799346	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Hepatocellular carcinoma	Likely pathogenic; Pathogenic	rs747539101	RCV005895478	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Malignant tumor of esophagus	Likely pathogenic; Pathogenic	rs143493067	RCV005901091	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
UPB1-related disorder	Likely pathogenic; Pathogenic	rs1012254852, rs138081800, rs143493067	RCV004750721 RCV004751199 RCV003424067	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations Show/Hide Unknown Diseases (8)
Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
AUTISTIC DISORDER	—	CTD, Disgenet CTD, Disgenet	18853477	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BETA-UREIDOPROPIONASE DEFICIENCY	—	CTD, Disgenet, GenCC, HPO, Orphanet CTD, Disgenet, GenCC, HPO, Orphanet CTD, Disgenet, GenCC, HPO, Orphanet CTD, Disgenet, GenCC, HPO, Orphanet CTD, Disgenet, GenCC, HPO, Orphanet	15385443	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CELIAC DISEASE	—	CTD, Disgenet CTD, Disgenet	30097691	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRYPTOGENIC WEST SYNDROME	—	Disgenet	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC DISEASES	—	CTD, Disgenet CTD, Disgenet	18853477	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYOCARDIAL INFARCTION	—	GWAS catalog	38072966	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SALAAM SEIZURES	—	Disgenet	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WEST SYNDROME	—	Disgenet	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining Show/Hide Text Mining Associations (32)
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Autism Spectrum Disorder	Autism	Pubtator	23275889	Associate	★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	CTD_human_DG	18853477		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Autistic Disorder	Autism	Pubtator	24526388	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Beta-Ureidopropionase Deficiency	Beta-Ureidopropionase Deficiency	UNIPROT_DG	15385443, 22525402, 24526388		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Beta-Ureidopropionase Deficiency	Beta-Ureidopropionase Deficiency	ORPHANET_DG	15385443		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Beta-ureidopropionase deficiency	Beta-Ureidopropionase Deficiency	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Beta-Ureidopropionase Deficiency	Beta-Ureidopropionase Deficiency	BEFREE	17964839, 25236466		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Beta-Ureidopropionase Deficiency	Beta-Ureidopropionase Deficiency	GENOMICS_ENGLAND_DG	17964839, 25445412, 27604308		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Beta-Ureidopropionase Deficiency	Beta-Ureidopropionase Deficiency	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Beta-Ureidopropionase Deficiency	Beta-Ureidopropionase Deficiency	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bladder Exstrophy	Bladder Exstrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	26414287, 28717245	Associate	★☆☆☆☆ Found in Text Mining only
Celiac Disease	Celiac disease	CTD_human_DG	30097691		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal Carcinoma	Colorectal Cancer	BEFREE	27733154		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	27733154	Associate	★☆☆☆☆ Found in Text Mining only
Cryptogenic Infantile Spasms	Cryptogenic West syndrome	CTD_human_DG	18853477		★☆☆☆☆ Found in Text Mining only
Gastrointestinal Diseases	Gastrointestinal disease	Pubtator	23238479	Associate	★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	BEFREE	30608453		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Jackknife Seizures	Jackknife Seizures	CTD_human_DG	18853477		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	26414287		★☆☆☆☆ Found in Text Mining only
Metabolic Diseases	Metabolic Diseases	CTD_human_DG	18853477		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Mucositis	Mucositis	Pubtator	23238479	Associate	★☆☆☆☆ Found in Text Mining only
Neonatal Hypotonia	Hypotonia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nodding spasm	Spasmus nutans	CTD_human_DG	18853477		★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	37279148	Associate	★☆☆☆☆ Found in Text Mining only
Salaam Seizures	Salaam Seizures	CTD_human_DG	18853477		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
spasmus nutans	Spasmus nutans	CTD_human_DG	18853477		★☆☆☆☆ Found in Text Mining only
Speech Disorders	Speech Disorders	HPO_DG			★☆☆☆☆ Found in Text Mining only
Status Epilepticus	Status epilepticus	Pubtator	16417553	Associate	★☆☆☆☆ Found in Text Mining only
Symptomatic Infantile Spasms	Symptomatic West syndrome	CTD_human_DG	18853477		★☆☆☆☆ Found in Text Mining only
West Syndrome	West Syndrome	CTD_human_DG	18853477		★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Related Genes

Sort by: Blended Diseases Pathways Evidence source

DPYD 5 shared pathwaysPyrimidine metabolism, beta-Alanine metabolism, Pantothenate and CoA biosynthesis, Drug metabolism - other enzymes, Pyrimidine catabolism Related via 5 shared pathways including Pyrimidine metabolism, beta-Alanine metabolism. DPYS 5 shared pathwaysPyrimidine metabolism, beta-Alanine metabolism, Pantothenate and CoA biosynthesis, Drug metabolism - other enzymes, Pyrimidine catabolism Related via 5 shared pathways including Pyrimidine metabolism, beta-Alanine metabolism. MC2R 3 shared diseasesCryptogenic west syndrome, Infantile spasms, West syndrome 3 shared evidence sourcesDisgenet (Cryptogenic west syndrome), Disgenet (Infantile spasms), Disgenet (West syndrome) Related via 3 shared diseases including Cryptogenic west syndrome, Infantile spasms — evidence mostly Disgenet. HSD17B4 3 shared diseasesCryptogenic west syndrome, Infantile spasms, West syndrome 3 shared evidence sourcesDisgenet (Cryptogenic west syndrome), Disgenet (Infantile spasms), Disgenet (West syndrome) Related via 3 shared diseases including Cryptogenic west syndrome, Infantile spasms — evidence mostly Disgenet. TSC1 3 shared diseasesCryptogenic west syndrome, Infantile spasms, West syndrome 3 shared evidence sourcesDisgenet (Cryptogenic west syndrome), Disgenet (Infantile spasms), Disgenet (West syndrome) Related via 3 shared diseases including Cryptogenic west syndrome, Infantile spasms — evidence mostly Disgenet.

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
DPYD	0	[]	5	["Pyrimidine metabolism","beta-Alanine metabolism","Pantothenate and CoA biosynthesis","Drug metabolism - other enzymes","Pyrimidine catabolism"]	0	[]
DPYS	0	[]	5	["Pyrimidine metabolism","beta-Alanine metabolism","Pantothenate and CoA biosynthesis","Drug metabolism - other enzymes","Pyrimidine catabolism"]	0	[]
MC2R	3	["Cryptogenic west syndrome","Infantile spasms","West syndrome"]	0	[]	3	["Disgenet (Cryptogenic west syndrome)","Disgenet (Infantile spasms)","Disgenet (West syndrome)"]
HSD17B4	3	["Cryptogenic west syndrome","Infantile spasms","West syndrome"]	0	[]	3	["Disgenet (Cryptogenic west syndrome)","Disgenet (Infantile spasms)","Disgenet (West syndrome)"]
TSC1	3	["Cryptogenic west syndrome","Infantile spasms","West syndrome"]	0	[]	3	["Disgenet (Cryptogenic west syndrome)","Disgenet (Infantile spasms)","Disgenet (West syndrome)"]

Diseases Linked via Similar Genes

Hepatocellular carcinoma Linked via 2 of 5 related genesDPYD, TSC1 Dihydropyrimidine metabolism disorder Linked via 2 of 5 related genesDPYD, DPYS Diabetes mellitus type 2 Linked via 2 of 5 related genesDPYD, DPYS 1p21.3 microdeletion syndrome Linked via 1 of 5 related genesDPYD Anal polyp Linked via 1 of 5 related genesDPYD

Disease	Linked Via (Gene Count)	Linked Via (Gene Names)
Hepatocellular carcinoma	2	["DPYD","TSC1"]
Dihydropyrimidine metabolism disorder	2	["DPYD","DPYS"]
Diabetes mellitus type 2	2	["DPYD","DPYS"]
1p21.3 microdeletion syndrome	1	["DPYD"]
Anal polyp	1	["DPYD"]