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CPS1 carbamoyl-phosphate synthase 1, mitochondrial [ Homo sapiens (human) ]

Gene ID: 1373, updated on 19-Jul-2014
Official Symbol
CPS1provided by HGNC
Official Full Name
carbamoyl-phosphate synthase 1, mitochondrialprovided by HGNC
Primary source
HGNC:2323
See related
Ensembl:ENSG00000021826; HPRD:01995; MIM:608307; Vega:OTTHUMG00000132994
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
PHN; CPSASE1
Summary
The mitochondrial enzyme encoded by this gene catalyzes synthesis of carbamoyl phosphate from ammonia and bicarbonate. This reaction is the first committed step of the urea cycle, which is important in the removal of excess urea from cells. The encoded protein may also represent a core mitochondrial nucleoid protein. Three transcript variants encoding different isoforms have been found for this gene. The shortest isoform may not be localized to the mitochondrion. Mutations in this gene have been associated with carbamoyl phosphate synthetase deficiency, susceptibility to persistent pulmonary hypertension, and susceptibility to venoocclusive disease after bone marrow transplantation.[provided by RefSeq, May 2010]
See CPS1 in Epigenomics, MapViewer
Location:
2q35
Exon count:
40
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 2 NC_000002.12 (210477682..210679107)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (211342406..211543831)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene myosin, light chain 1, alkali; skeletal, fast Neighboring gene LANCL1 antisense RNA 1 Neighboring gene LanC lantibiotic synthetase component C-like 1 (bacterial) Neighboring gene CPS1 intronic transcript 1 (non-protein coding) Neighboring gene 5'-nucleotidase domain containing 2 pseudogene Neighboring gene ribosomal protein S27 pseudogene 10

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Congenital hyperammonemia, type I
MedGen: C0751753 OMIM: 237300 GeneReviews: Not available
Compare labs
Pulmonary hypertension, neonatal, susceptibility to
MedGen: C0032768 OMIM: 615371 GeneReviews: Not available
not available

NHGRI GWAS Catalog

Description
Common genetic loci influencing plasma homocysteine concentrations and their effect on risk of coronary artery disease.
NHGRI GWA Catalog
Discovery and refinement of loci associated with lipid levels.
NHGRI GWA Catalog
Genetic variants associated with glycine metabolism and their role in insulin sensitivity and type 2 diabetes.
NHGRI GWA Catalog
Genome-wide association study of body mass index in 23 000 individuals with and without asthma.
NHGRI GWA Catalog
Genome-wide association study of homocysteine levels in Filipinos provides evidence for CPS1 in women and a stronger MTHFR effect in young adults.
NHGRI GWA Catalog
Human metabolic individuality in biomedical and pharmaceutical research.
NHGRI GWA Catalog
Multiethnic meta-analysis of genome-wide association studies in >100 000 subjects identifies 23 fibrinogen-associated Loci but no strong evidence of a causal association between circulating fibrinogen and cardiovascular disease.
NHGRI GWA Catalog
New loci associated with kidney function and chronic kidney disease.
NHGRI GWA Catalog
Novel loci, including those related to Crohn disease, psoriasis, and inflammation, identified in a genome-wide association study of fibrinogen in 17 686 women: the Women's Genome Health Study.
NHGRI GWA Catalog
Prognostic implications of genetic variants in advanced non-small cell lung cancer: a genome-wide association study.
NHGRI GWA Catalog
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
carbamoyl-phosphate synthase (ammonia) activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
endopeptidase activity IEA
Inferred from Electronic Annotation
more info
 
glutamate binding IEA
Inferred from Electronic Annotation
more info
 
modified amino acid binding IDA
Inferred from Direct Assay
more info
 
phospholipid binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein complex binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
anion homeostasis IEA
Inferred from Electronic Annotation
more info
 
carbamoyl phosphate biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular nitrogen compound metabolic process TAS
Traceable Author Statement
more info
 
cellular response to cAMP IEA
Inferred from Electronic Annotation
more info
 
cellular response to fibroblast growth factor stimulus IEA
Inferred from Electronic Annotation
more info
 
cellular response to glucagon stimulus IEA
Inferred from Electronic Annotation
more info
 
cellular response to oleic acid IEA
Inferred from Electronic Annotation
more info
 
citrulline biosynthetic process NAS
Non-traceable Author Statement
more info
PubMed 
glutamine catabolic process IEA
Inferred from Electronic Annotation
more info
 
glycogen catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
hepatocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
homocysteine metabolic process IDA
Inferred from Direct Assay
more info
 
midgut development IEA
Inferred from Electronic Annotation
more info
 
nitric oxide metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of vasodilation IMP
Inferred from Mutant Phenotype
more info
PubMed 
proteolysis IEA
Inferred from Electronic Annotation
more info
 
response to amine IEA
Inferred from Electronic Annotation
more info
 
response to amino acid IEA
Inferred from Electronic Annotation
more info
 
response to dexamethasone IEA
Inferred from Electronic Annotation
more info
 
response to drug IEA
Inferred from Electronic Annotation
more info
 
response to food IEA
Inferred from Electronic Annotation
more info
 
response to growth hormone IEA
Inferred from Electronic Annotation
more info
 
response to lipopolysaccharide IDA
Inferred from Direct Assay
more info
PubMed 
response to starvation IEA
Inferred from Electronic Annotation
more info
 
response to toxic substance IEA
Inferred from Electronic Annotation
more info
 
response to zinc ion IEA
Inferred from Electronic Annotation
more info
 
small molecule metabolic process TAS
Traceable Author Statement
more info
 
triglyceride catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
urea cycle NAS
Non-traceable Author Statement
more info
PubMed 
urea cycle TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
mitochondrial inner membrane IEA
Inferred from Electronic Annotation
more info
 
mitochondrial matrix TAS
Traceable Author Statement
more info
 
mitochondrial nucleoid IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IEA
Inferred from Electronic Annotation
more info
 
protein complex IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
carbamoyl-phosphate synthase [ammonia], mitochondrial
Names
carbamoyl-phosphate synthase [ammonia], mitochondrial
carbamoylphosphate synthetase I
NP_001116105.1
NP_001116106.1
NP_001866.2

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

  1. NG_008285.1 

    Range
    4998..206423
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_336

mRNA and Protein(s)

  1. NM_001122633.2NP_001116105.1  carbamoyl-phosphate synthase [ammonia], mitochondrial isoform a precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AB208800, BC058010, DA804480, Y15793
    Consensus CDS
    CCDS46505.1
    UniProtKB/Swiss-Prot
    P31327
    UniProtKB/TrEMBL
    Q6PEK7
    Related
    ENSP00000402608, OTTHUMP00000232820, ENST00000430249, OTTHUMT00000389617
    Conserved Domains (9) summary
    cd01744
    Location:226401
    Blast Score: 791
    GATase1_CPSase; Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II
    pfam02786
    Location:552756
    Blast Score: 853
    CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain
    smart01096
    Location:845968
    Blast Score: 477
    CPSase_L_D3; Carbamoyl-phosphate synthetase large chain, oligomerisation domain
    smart01097
    Location:50189
    Blast Score: 538
    CPSase_sm_chain; Carbamoyl-phosphate synthase small chain, CPSase domain
    TIGR01368
    Location:52406
    Blast Score: 1363
    CPSaseIIsmall; carbamoyl-phosphate synthase, small subunit
    TIGR01369
    Location:4251483
    Blast Score: 3960
    CPSaseII_lrg; carbamoyl-phosphate synthase, large subunit
    cd01423
    Location:13661481
    Blast Score: 434
    MGS_CPS_I_III; Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain.
    pfam00289
    Location:9831086
    Blast Score: 246
    CPSase_L_chain; Carbamoyl-phosphate synthase L chain, N-terminal domain
    cl17255
    Location:10941297
    Blast Score: 288
    ATP-grasp_4; ATP-grasp domain
  2. NM_001122634.2NP_001116106.1  carbamoyl-phosphate synthase [ammonia], mitochondrial isoform c

    See proteins identical to NP_001116106.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a and may not be localized to the mitochondrion.
    Source sequence(s)
    AK316425, AY317138, BC058010
    Consensus CDS
    CCDS46506.1
    UniProtKB/TrEMBL
    B7ZAW0
    UniProtKB/Swiss-Prot
    P31327
    UniProtKB/TrEMBL
    Q6PEK7
    Related
    ENSP00000406136, OTTHUMP00000206561, ENST00000451903, OTTHUMT00000336827
    Conserved Domains (6) summary
    pfam02786
    Location:95299
    Blast Score: 849
    CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain
    smart01096
    Location:388511
    Blast Score: 475
    CPSase_L_D3; Carbamoyl-phosphate synthetase large chain, oligomerisation domain
    TIGR01369
    Location:11026
    Blast Score: 3787
    CPSaseII_lrg; carbamoyl-phosphate synthase, large subunit
    cd01423
    Location:9091024
    Blast Score: 434
    MGS_CPS_I_III; Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain.
    pfam00289
    Location:526629
    Blast Score: 245
    CPSase_L_chain; Carbamoyl-phosphate synthase L chain, N-terminal domain
    cl17255
    Location:637840
    Blast Score: 286
    ATP-grasp_4; ATP-grasp domain
  3. NM_001875.4NP_001866.2  carbamoyl-phosphate synthase [ammonia], mitochondrial isoform b precursor

    See proteins identical to NP_001866.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a.
    Source sequence(s)
    BC058010, BC140943, BJ995129
    Consensus CDS
    CCDS2393.1
    UniProtKB/Swiss-Prot
    P31327
    UniProtKB/TrEMBL
    Q6PEK7
    Related
    ENSP00000233072, OTTHUMP00000163944, ENST00000233072, OTTHUMT00000256569
    Conserved Domains (9) summary
    cd01744
    Location:220395
    Blast Score: 791
    GATase1_CPSase; Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II
    pfam02786
    Location:546750
    Blast Score: 853
    CPSase_L_D2; Carbamoyl-phosphate synthase L chain, ATP binding domain
    smart01096
    Location:839962
    Blast Score: 477
    CPSase_L_D3; Carbamoyl-phosphate synthetase large chain, oligomerisation domain
    smart01097
    Location:44183
    Blast Score: 539
    CPSase_sm_chain; Carbamoyl-phosphate synthase small chain, CPSase domain
    TIGR01368
    Location:46400
    Blast Score: 1363
    CPSaseIIsmall; carbamoyl-phosphate synthase, small subunit
    TIGR01369
    Location:4191477
    Blast Score: 3960
    CPSaseII_lrg; carbamoyl-phosphate synthase, large subunit
    cd01423
    Location:13601475
    Blast Score: 434
    MGS_CPS_I_III; Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain.
    pfam00289
    Location:9771080
    Blast Score: 246
    CPSase_L_chain; Carbamoyl-phosphate synthase L chain, N-terminal domain
    cl17255
    Location:10881291
    Blast Score: 288
    ATP-grasp_4; ATP-grasp domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000002.12 

    Range
    210477682..210679107
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000134.1 

    Range
    203188451..203390097
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018913.2 

    Range
    211348531..211549854
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)