UPB1D
MCID: BTR002
MIFTS: 38

Beta-Ureidopropionase Deficiency (UPB1D)

Categories: Genetic diseases, Metabolic diseases, Nephrological diseases, Neuronal diseases, Rare diseases

Aliases & Classifications for Beta-Ureidopropionase Deficiency

MalaCards integrated aliases for Beta-Ureidopropionase Deficiency:

Name: Beta-Ureidopropionase Deficiency 57 25 59 75 37 13 40 73
Deficiency of Beta-Ureidopropionase 25 29 6
Beta-Alanine Synthase Deficiency 25 59
Upb1d 57 75
Beta-Ureidopropionase 13

Characteristics:

Orphanet epidemiological data:

59
beta-ureidopropionase deficiency
Inheritance: Autosomal recessive; Prevalence: <1/1000000 (Worldwide); Age of onset: Infancy,Neonatal;

OMIM:

57
Inheritance:
autosomal recessive

Miscellaneous:
onset in infancy
six genetically confirmed patients have been reported (as of december 2009)
inborn error of the pyrimidine degradation pathway


HPO:

32
beta-ureidopropionase deficiency:
Onset and clinical course infantile onset
Inheritance autosomal recessive inheritance


Classifications:



External Ids:

OMIM 57 613161
Orphanet 59 ORPHA65287
UMLS via Orphanet 74 C1291512
ICD10 via Orphanet 34 E79.8
MedGen 42 C1291512
MeSH 44 D011686
KEGG 37 H00200
UMLS 73 C1291512

Summaries for Beta-Ureidopropionase Deficiency

UniProtKB/Swiss-Prot : 75 Beta-ureidopropionase deficiency: An inborn error of metabolism due to a defect in pyrimidine degradation. It is characterized by muscular hypotonia, dystonic movements, scoliosis, microcephaly and severe developmental delay. Patients show strongly elevated levels of N-carbamyl-beta-alanine and N-carbamyl-beta-aminoisobutyric acid in plasma, cerebrospinal fluid and urine.

MalaCards based summary : Beta-Ureidopropionase Deficiency, also known as deficiency of beta-ureidopropionase, is related to status epilepticus and dihydropyrimidinase deficiency. An important gene associated with Beta-Ureidopropionase Deficiency is UPB1 (Beta-Ureidopropionase 1), and among its related pathways/superpathways are Pyrimidine metabolism and Drug metabolism - other enzymes. Affiliated tissues include liver, colon and appendix, and related phenotypes are intellectual disability and neurological speech impairment

Genetics Home Reference : 25 Beta-ureidopropionase deficiency is a disorder that causes excessive amounts of molecules called N-carbamyl-beta-aminoisobutyric acid and N-carbamyl-beta-alanine to be released in the urine. Neurological problems ranging from mild to severe also occur in some affected individuals.

OMIM : 57 Beta-ureidopropionase deficiency is a rare autosomal recessive inborn error of metabolism due to a defect in pyrimidine degradation. Less than 10 patients have been reported, and the phenotype can range from severe neurologic involvement with mental retardation and seizures to normal neurologic development (Yaplito-Lee et al., 2008). (613161)

Related Diseases for Beta-Ureidopropionase Deficiency

Diseases related to Beta-Ureidopropionase Deficiency via text searches within MalaCards or GeneCards Suite gene sharing:

# Related Disease Score Top Affiliating Genes
1 status epilepticus 10.2
2 dihydropyrimidinase deficiency 9.8 DPYD DPYS
3 purine-pyrimidine metabolic disorder 9.8 DPYD DPYS
4 ornithine transcarbamylase deficiency, hyperammonemia due to 9.7 DPYD UPB1
5 dihydropyrimidine dehydrogenase deficiency 9.7 DPYD DPYS
6 pyrimidine metabolic disorder 9.6 DPYD DPYS UPB1

Graphical network of the top 20 diseases related to Beta-Ureidopropionase Deficiency:



Diseases related to Beta-Ureidopropionase Deficiency

Symptoms & Phenotypes for Beta-Ureidopropionase Deficiency

Symptoms via clinical synopsis from OMIM:

57
Neurologic Central Nervous System:
hypotonia, neonatal
delayed psychomotor development, severe (in 2 of 6 patients)
mental retardation (in 2 of 6 patients)
normal development (in 2 of 6 patients)
seizures (in 2 of 6 patients)
more
Abdomen Gastrointestinal:
anal atresia (in 1 of 6 patients)
duplicated appendix and distal colon (in 1 of 6 patients)

Genitourinary Kidneys:
pelvicalyceal dilatation (in 1 of 6 patients)

Genitourinary Bladder:
bladder exstrophy (in 1 of 6 patients)

Laboratory Abnormalities:
increased urinary dihydropyrimidines
increased urinary, plasma, and csf n-carbamyl-beta-alanine
increased urinary, plasma, and csf n-carbamyl-beta-aminoisobutyric acid
increased urinary, plasma, and csf dihydrouracil
increased urinary, plasma, and csf dihydrothymine
more
Head And Neck Head:
microcephaly (in 1 of 6 patients)

Genitourinary External Genitalia Male:
bifid phallus (in 1 of 6 patients)
bifid scrotum (in 1 of 6 patients)

Genitourinary Ureters:
ureteric dilatation (in 1 of 6 patients)

Skeletal Spine:
scoliosis (in 1 of 6 patients)


Clinical features from OMIM:

613161

Human phenotypes related to Beta-Ureidopropionase Deficiency:

32 (show all 13)
# Description HPO Frequency HPO Source Accession
1 intellectual disability 32 very rare (1%) HP:0001249
2 neurological speech impairment 32 HP:0002167
3 scoliosis 32 very rare (1%) HP:0002650
4 global developmental delay 32 HP:0001263
5 microcephaly 32 very rare (1%) HP:0000252
6 neonatal hypotonia 32 HP:0001319
7 dystonia 32 HP:0001332
8 status epilepticus 32 very rare (1%) HP:0002133
9 anal atresia 32 very rare (1%) HP:0002023
10 bifid scrotum 32 very rare (1%) HP:0000048
11 hypsarrhythmia 32 very rare (1%) HP:0002521
12 delayed cns myelination 32 HP:0002188
13 bladder exstrophy 32 HP:0002836

GenomeRNAi Phenotypes related to Beta-Ureidopropionase Deficiency according to GeneCards Suite gene sharing:

26 (show all 11)
# Description GenomeRNAi Source Accession Score Top Affiliating Genes
1 Decreased shRNA abundance (Z-score < -2) GR00366-A-139 9.4 DPYD
2 Decreased shRNA abundance (Z-score < -2) GR00366-A-148 9.4 DPYS
3 Decreased shRNA abundance (Z-score < -2) GR00366-A-17 9.4 DPYD
4 Decreased shRNA abundance (Z-score < -2) GR00366-A-184 9.4 DPYD
5 Decreased shRNA abundance (Z-score < -2) GR00366-A-203 9.4 DPYS
6 Decreased shRNA abundance (Z-score < -2) GR00366-A-204 9.4 DPYS
7 Decreased shRNA abundance (Z-score < -2) GR00366-A-213 9.4 DPYD
8 Decreased shRNA abundance (Z-score < -2) GR00366-A-59 9.4 DPYD
9 Decreased shRNA abundance (Z-score < -2) GR00366-A-61 9.4 DPYS
10 Decreased shRNA abundance (Z-score < -2) GR00366-A-84 9.4 DPYS
11 Decreased shRNA abundance (Z-score < -2) GR00366-A-91 9.4 DPYD DPYS

Drugs & Therapeutics for Beta-Ureidopropionase Deficiency

Search Clinical Trials , NIH Clinical Center for Beta-Ureidopropionase Deficiency

Genetic Tests for Beta-Ureidopropionase Deficiency

Genetic tests related to Beta-Ureidopropionase Deficiency:

# Genetic test Affiliating Genes
1 Deficiency of Beta-Ureidopropionase 29 UPB1

Anatomical Context for Beta-Ureidopropionase Deficiency

MalaCards organs/tissues related to Beta-Ureidopropionase Deficiency:

41
Liver, Colon, Appendix

Publications for Beta-Ureidopropionase Deficiency

Articles related to Beta-Ureidopropionase Deficiency:

(show all 11)
# Title Authors Year
1
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]. ( 24526388 )
2014
2
Five cases of beta-ureidopropionase deficiency detected by GC/MS analysis of urine metabolome. ( 18853477 )
2009
3
Beta-ureidopropionase deficiency presenting with congenital anomalies of the urogenital and colorectal systems. ( 17964839 )
2008
4
Clinical findings and a therapeutic trial in the first patient with beta-ureidopropionase deficiency. ( 16541364 )
2006
5
Beta-ureidopropionase deficiency presenting with febrile status epilepticus. ( 16417553 )
2006
6
Genetic analysis of the first 4 patients with beta-ureidopropionase deficiency. ( 17065070 )
2006
7
Beta-ureidopropionase deficiency: an inborn error of pyrimidine degradation associated with neurological abnormalities. ( 15385443 )
2004
8
Screening and diagnosis of beta-ureidopropionase deficiency by gas chromatographic/mass spectrometric analysis of urine. ( 12271438 )
2002
9
Detection of beta-ureidopropionase deficiency with HPLC-electrospray tandem mass spectrometry and confirmation of the defect at the enzyme level. ( 11804209 )
2001
10
beta-Ureidopropionase deficiency: a novel inborn error of metabolism discovered using NMR spectroscopy on urine. ( 11675655 )
2001
11
Confirmation of the enzyme defect in the first case of beta-ureidopropionase deficiency. Beta-alanine deficiency. ( 11783492 )
2000

Variations for Beta-Ureidopropionase Deficiency

UniProtKB/Swiss-Prot genetic disease variations for Beta-Ureidopropionase Deficiency:

75
# Symbol AA change Variation ID SNP ID
1 UPB1 p.Ala85Glu VAR_026752 rs34035085

ClinVar genetic disease variations for Beta-Ureidopropionase Deficiency:

6 (show top 50) (show all 76)
# Gene Variation Type Significance SNP ID Assembly Location
1 UPB1 NM_016327.2(UPB1): c.105-2A> G single nucleotide variant Pathogenic/Likely pathogenic rs138081800 GRCh37 Chromosome 22, 24896073: 24896073
2 UPB1 NM_016327.2(UPB1): c.105-2A> G single nucleotide variant Pathogenic/Likely pathogenic rs138081800 GRCh38 Chromosome 22, 24500105: 24500105
3 UPB1 NM_016327.2(UPB1): c.917-2A> G single nucleotide variant Pathogenic rs876657373 GRCh38 Chromosome 22, 24523617: 24523617
4 UPB1 NM_016327.2(UPB1): c.917-2A> G single nucleotide variant Pathogenic rs876657373 GRCh37 Chromosome 22, 24919585: 24919585
5 UPB1 NM_016327.2(UPB1): c.254C> A (p.Ala85Glu) single nucleotide variant Likely benign rs34035085 GRCh37 Chromosome 22, 24896224: 24896224
6 UPB1 NM_016327.2(UPB1): c.254C> A (p.Ala85Glu) single nucleotide variant Likely benign rs34035085 GRCh38 Chromosome 22, 24500256: 24500256
7 UPB1 NM_016327.2(UPB1): c.254C> A (p.Ala85Glu) single nucleotide variant Likely benign rs34035085 NCBI36 Chromosome 22, 23226224: 23226224
8 UPB1 NM_016327.2(UPB1): c.209G> C (p.Arg70Pro) single nucleotide variant Pathogenic rs121908066 GRCh37 Chromosome 22, 24896179: 24896179
9 UPB1 NM_016327.2(UPB1): c.209G> C (p.Arg70Pro) single nucleotide variant Pathogenic rs121908066 GRCh38 Chromosome 22, 24500211: 24500211
10 UPB1 NM_016327.2(UPB1): c.-80C> G single nucleotide variant Benign rs2070474 GRCh37 Chromosome 22, 24891292: 24891292
11 UPB1 NM_016327.2(UPB1): c.-80C> G single nucleotide variant Benign rs2070474 GRCh38 Chromosome 22, 24495324: 24495324
12 UPB1 NM_016327.2(UPB1): c.-80C> G single nucleotide variant Benign rs2070474 NCBI36 Chromosome 22, 23221292: 23221292
13 UPB1 NM_016327.2(UPB1): c.-17A> T single nucleotide variant Benign rs2070475 GRCh37 Chromosome 22, 24891355: 24891355
14 UPB1 NM_016327.2(UPB1): c.-17A> T single nucleotide variant Benign rs2070475 GRCh38 Chromosome 22, 24495387: 24495387
15 UPB1 NM_016327.2(UPB1): c.-17A> T single nucleotide variant Benign rs2070475 NCBI36 Chromosome 22, 23221355: 23221355
16 UPB1 NM_016327.2(UPB1): c.846C> T (p.Phe282=) single nucleotide variant Uncertain significance rs2232867 GRCh37 Chromosome 22, 24916409: 24916409
17 UPB1 NM_016327.2(UPB1): c.846C> T (p.Phe282=) single nucleotide variant Uncertain significance rs2232867 GRCh38 Chromosome 22, 24520441: 24520441
18 UPB1 NM_016327.2(UPB1): c.846C> T (p.Phe282=) single nucleotide variant Uncertain significance rs2232867 NCBI36 Chromosome 22, 23246409: 23246409
19 UPB1 NM_016327.2(UPB1): c.873+9C> T single nucleotide variant Uncertain significance rs111674727 GRCh37 Chromosome 22, 24916445: 24916445
20 UPB1 NM_016327.2(UPB1): c.873+9C> T single nucleotide variant Uncertain significance rs111674727 GRCh38 Chromosome 22, 24520477: 24520477
21 UPB1 NM_016327.2(UPB1): c.873+9C> T single nucleotide variant Uncertain significance rs111674727 NCBI36 Chromosome 22, 23246445: 23246445
22 UPB1 NM_016327.2(UPB1): c.976C> A (p.Arg326=) single nucleotide variant Uncertain significance rs113975342 GRCh37 Chromosome 22, 24919646: 24919646
23 UPB1 NM_016327.2(UPB1): c.976C> A (p.Arg326=) single nucleotide variant Uncertain significance rs113975342 GRCh38 Chromosome 22, 24523678: 24523678
24 UPB1 NM_016327.2(UPB1): c.976C> A (p.Arg326=) single nucleotide variant Uncertain significance rs113975342 NCBI36 Chromosome 22, 23249646: 23249646
25 UPB1 NM_016327.2(UPB1): c.977G> A (p.Arg326Gln) single nucleotide variant Uncertain significance rs118163237 GRCh37 Chromosome 22, 24919647: 24919647
26 UPB1 NM_016327.2(UPB1): c.977G> A (p.Arg326Gln) single nucleotide variant Uncertain significance rs118163237 GRCh38 Chromosome 22, 24523679: 24523679
27 UPB1 NM_016327.2(UPB1): c.-27G> C single nucleotide variant Uncertain significance rs780314131 GRCh37 Chromosome 22, 24891345: 24891345
28 UPB1 NM_016327.2(UPB1): c.-27G> C single nucleotide variant Uncertain significance rs780314131 GRCh38 Chromosome 22, 24495377: 24495377
29 UPB1 NM_016327.2(UPB1): c.-11G> A single nucleotide variant Uncertain significance rs541169952 GRCh37 Chromosome 22, 24891361: 24891361
30 UPB1 NM_016327.2(UPB1): c.-11G> A single nucleotide variant Uncertain significance rs541169952 GRCh38 Chromosome 22, 24495393: 24495393
31 UPB1 NM_016327.2(UPB1): c.514G> A (p.Glu172Lys) single nucleotide variant Uncertain significance rs145749836 GRCh37 Chromosome 22, 24909346: 24909346
32 UPB1 NM_016327.2(UPB1): c.514G> A (p.Glu172Lys) single nucleotide variant Uncertain significance rs145749836 GRCh38 Chromosome 22, 24513378: 24513378
33 UPB1 NM_016327.2(UPB1): c.899C> T (p.Ser300Leu) single nucleotide variant Uncertain significance rs762081192 GRCh37 Chromosome 22, 24917979: 24917979
34 UPB1 NM_016327.2(UPB1): c.899C> T (p.Ser300Leu) single nucleotide variant Uncertain significance rs762081192 GRCh38 Chromosome 22, 24522011: 24522011
35 UPB1 NM_016327.2(UPB1): c.*23G> A single nucleotide variant Uncertain significance rs201029672 GRCh37 Chromosome 22, 24921785: 24921785
36 UPB1 NM_016327.2(UPB1): c.*23G> A single nucleotide variant Uncertain significance rs201029672 GRCh38 Chromosome 22, 24525817: 24525817
37 UPB1 NM_016327.2(UPB1): c.-7C> G single nucleotide variant Uncertain significance rs200677387 GRCh37 Chromosome 22, 24891365: 24891365
38 UPB1 NM_016327.2(UPB1): c.-7C> G single nucleotide variant Uncertain significance rs200677387 GRCh38 Chromosome 22, 24495397: 24495397
39 UPB1 NM_016327.2(UPB1): c.384T> C (p.Cys128=) single nucleotide variant Uncertain significance rs200161281 GRCh37 Chromosome 22, 24906736: 24906736
40 UPB1 NM_016327.2(UPB1): c.384T> C (p.Cys128=) single nucleotide variant Uncertain significance rs200161281 GRCh38 Chromosome 22, 24510768: 24510768
41 UPB1 NM_016327.2(UPB1): c.464C> T (p.Ala155Val) single nucleotide variant Uncertain significance rs199788632 GRCh37 Chromosome 22, 24909296: 24909296
42 UPB1 NM_016327.2(UPB1): c.464C> T (p.Ala155Val) single nucleotide variant Uncertain significance rs199788632 GRCh38 Chromosome 22, 24513328: 24513328
43 UPB1 NM_016327.2(UPB1): c.1122G> A (p.Lys374=) single nucleotide variant Uncertain significance rs35916595 GRCh37 Chromosome 22, 24921729: 24921729
44 UPB1 NM_016327.2(UPB1): c.1122G> A (p.Lys374=) single nucleotide variant Uncertain significance rs35916595 GRCh38 Chromosome 22, 24525761: 24525761
45 UPB1 NM_016327.2(UPB1): c.-65T> C single nucleotide variant Uncertain significance rs886057288 GRCh37 Chromosome 22, 24891307: 24891307
46 UPB1 NM_016327.2(UPB1): c.-65T> C single nucleotide variant Uncertain significance rs886057288 GRCh38 Chromosome 22, 24495339: 24495339
47 UPB1 NM_016327.2(UPB1): c.-63C> T single nucleotide variant Uncertain significance rs116629687 GRCh37 Chromosome 22, 24891309: 24891309
48 UPB1 NM_016327.2(UPB1): c.-63C> T single nucleotide variant Uncertain significance rs116629687 GRCh38 Chromosome 22, 24495341: 24495341
49 UPB1 NM_016327.2(UPB1): c.26T> C (p.Leu9Pro) single nucleotide variant Uncertain significance rs755104394 GRCh37 Chromosome 22, 24891397: 24891397
50 UPB1 NM_016327.2(UPB1): c.26T> C (p.Leu9Pro) single nucleotide variant Uncertain significance rs755104394 GRCh38 Chromosome 22, 24495429: 24495429

Expression for Beta-Ureidopropionase Deficiency

Search GEO for disease gene expression data for Beta-Ureidopropionase Deficiency.

Pathways for Beta-Ureidopropionase Deficiency

Pathways related to Beta-Ureidopropionase Deficiency according to KEGG:

37
# Name Kegg Source Accession
1 Pyrimidine metabolism hsa00240
2 Drug metabolism - other enzymes hsa00983

Pathways related to Beta-Ureidopropionase Deficiency according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1
Show member pathways
12.28 DPYD DPYS UPB1
2
Show member pathways
12.11 DPYD DPYS UPB1
3
Show member pathways
11.84 DPYD DPYS UPB1
4
Show member pathways
11.56 DPYD DPYS UPB1
5
Show member pathways
10.86 DPYD DPYS UPB1
6 10.41 DPYD DPYS UPB1
7
Show member pathways
10.05 DPYD DPYS UPB1

GO Terms for Beta-Ureidopropionase Deficiency

Biological processes related to Beta-Ureidopropionase Deficiency according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 beta-alanine metabolic process GO:0019482 9.37 DPYS UPB1
2 thymine catabolic process GO:0006210 9.32 DPYD DPYS
3 beta-alanine biosynthetic process GO:0019483 9.26 DPYD UPB1
4 pyrimidine nucleobase catabolic process GO:0006208 9.16 DPYD DPYS
5 uracil catabolic process GO:0006212 8.96 DPYD DPYS
6 pyrimidine nucleoside catabolic process GO:0046135 8.8 DPYD DPYS UPB1

Molecular functions related to Beta-Ureidopropionase Deficiency according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 uracil binding GO:0002058 8.62 DPYD DPYS

Sources for Beta-Ureidopropionase Deficiency

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 ExPASy
19 FMA
28 GO
29 GTR
30 HGMD
31 HMDB
32 HPO
33 ICD10
34 ICD10 via Orphanet
35 ICD9CM
36 IUPHAR
37 KEGG
38 LifeMap
40 LOVD
42 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
54 NINDS
55 Novoseek
57 OMIM
58 OMIM via Orphanet
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 SNOMED-CT via Orphanet
71 TGDB
72 Tocris
73 UMLS
74 UMLS via Orphanet
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