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

Gene ID: 1373, updated on 7-Jun-2020

Summary

Official Symbol
CPS1provided by HGNC
Official Full Name
carbamoyl-phosphate synthase 1provided by HGNC
Primary source
HGNC:HGNC:2323
See related
Ensembl:ENSG00000021826 MIM:608307
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]
Expression
Biased expression in liver (RPKM 281.3), duodenum (RPKM 102.6) and 1 other tissue See more
Orthologs

Genomic context

See CPS1 in Genome Data Viewer
Location:
2q34
Exon count:
43
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (210477685..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 LANCL1 antisense RNA 1 Neighboring gene myosin light chain 1 Neighboring gene LanC like 1 Neighboring gene CPS1 intron CAGE-defined high expression enhancer 1 Neighboring gene CPS1 intron CAGE-defined high expression enhancer 2 Neighboring gene CPS1 intronic transcript 1 Neighboring gene uncharacterized LOC107985978 Neighboring gene 5'-nucleotidase domain containing 2 pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Congenital hyperammonemia, type I
MedGen: C4082171 OMIM: 237300 GeneReviews: Urea Cycle Disorders Overview
Compare labs
Pulmonary hypertension, neonatal, susceptibility to
MedGen: C3714958 OMIM: 615371 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
An atlas of genetic influences on human blood metabolites.
NHGRI GWA Catalog
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 determinants influencing human serum metabolome among African Americans.
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
Genome-wide meta-analysis of homocysteine and methionine metabolism identifies five one carbon metabolism loci and a novel association of ALDH1L1 with ischemic stroke.
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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 EXP
Inferred from Experiment
more info
PubMed 
carbamoyl-phosphate synthase (ammonia) activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity IEA
Inferred from Electronic Annotation
more info
 
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
PubMed 
phospholipid binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
'de novo' pyrimidine nucleobase biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
anion homeostasis IEA
Inferred from Electronic Annotation
more info
 
carbamoyl phosphate biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to ammonia IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
hepatocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
homocysteine metabolic process IDA
Inferred from Direct Assay
more info
PubMed 
midgut development IEA
Inferred from Electronic Annotation
more info
 
nitric oxide metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
nitrogen compound metabolic process IBA
Inferred from Biological aspect of Ancestor
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 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 zinc ion IEA
Inferred from Electronic Annotation
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
 
vasodilation IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IDA
Inferred from Direct Assay
more info
 
protein-containing complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
carbamoyl-phosphate synthase [ammonia], mitochondrial
Names
carbamoyl-phosphate synthase (ammonia)
carbamoyl-phosphate synthase 1, mitochondrial
carbamoylphosphate synthetase I
NP_001116105.2
NP_001356185.1
NP_001356186.1
NP_001866.2

NCBI Reference Sequences (RefSeq)

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 RefSeqGene

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

mRNA and Protein(s)

  1. NM_001122633.3NP_001116105.2  carbamoyl-phosphate synthase [ammonia], mitochondrial isoform a precursor

    Status: REVIEWED

    Source sequence(s)
    AB208800, AC007970, N58033, Y15793
    Consensus CDS
    CCDS46505.1
    Related
    ENSP00000501022.1, ENST00000673711.1
    Conserved Domains (2) summary
    TIGR01368
    Location:46400
    CPSaseIIsmall; carbamoyl-phosphate synthase, small subunit
    TIGR01369
    Location:4191477
    CPSaseII_lrg; carbamoyl-phosphate synthase, large subunit
  2. NM_001369256.1NP_001356185.1  carbamoyl-phosphate synthase [ammonia], mitochondrial isoform d

    Status: REVIEWED

    Source sequence(s)
    AC007970, AC008172
    Conserved Domains (2) summary
    TIGR01368
    Location:57411
    CPSaseIIsmall; carbamoyl-phosphate synthase, small subunit
    TIGR01369
    Location:4301488
    CPSaseII_lrg; carbamoyl-phosphate synthase, large subunit
  3. NM_001369257.1NP_001356186.1  carbamoyl-phosphate synthase [ammonia], mitochondrial isoform b precursor

    Status: REVIEWED

    Source sequence(s)
    AC007970, AC008172
    Related
    ENSP00000500537.1, ENST00000673510.1
    Conserved Domains (2) summary
    TIGR01368
    Location:46400
    CPSaseIIsmall; carbamoyl-phosphate synthase, small subunit
    TIGR01369
    Location:4191477
    CPSaseII_lrg; carbamoyl-phosphate synthase, large subunit
  4. NM_001875.5NP_001866.2  carbamoyl-phosphate synthase [ammonia], mitochondrial isoform b precursor

    See identical proteins and their annotated locations for 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
    A0A024R454, Q6PEK7
    Related
    ENSP00000233072.5, ENST00000233072.10
    Conserved Domains (2) summary
    TIGR01368
    Location:46400
    CPSaseIIsmall; carbamoyl-phosphate synthase, small subunit
    TIGR01369
    Location:4191477
    CPSaseII_lrg; carbamoyl-phosphate synthase, large subunit

RNA

  1. NR_161225.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC008172
  2. NR_163592.1 RNA Sequence

    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)
    AB208800, AK302778, AK316425, AY317138, N58033
    Related
    ENST00000451903.3

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    210477685..210679107
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001122634.3: Suppressed sequence

    Description
    NM_001122634.3: This RefSeq was removed because currently there is support for the transcript but not for the protein.
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