Gene Gene information from NCBI Gene database.
Entrez ID 1373
Gene name Carbamoyl-phosphate synthase 1
Gene symbol CPS1
Synonyms (NCBI Gene)
CPSASE1GATD6PHN
Chromosome 2
Chromosome location 2q34
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 pr
SNPs SNP information provided by dbSNP.
78
SNP ID Visualize variation Clinical significance Consequence
rs28940283 A>G Pathogenic Coding sequence variant, missense variant, non coding transcript variant, upstream transcript variant, genic upstream transcript variant
rs41272669 C>T Likely-benign, uncertain-significance, conflicting-interpretations-of-pathogenicity Intron variant
rs114819130 G>A Conflicting-interpretations-of-pathogenicity, uncertain-significance Non coding transcript variant, genic upstream transcript variant, coding sequence variant, missense variant
rs121912592 C>A,T Pathogenic Non coding transcript variant, coding sequence variant, missense variant
rs121912593 C>T Pathogenic Non coding transcript variant, genic upstream transcript variant, stop gained, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
249
miRTarBase ID miRNA Experiments Reference
MIRT051022 hsa-miR-17-5p CLASH 23622248
MIRT688725 hsa-miR-548c-3p HITS-CLIP 23313552
MIRT688724 hsa-miR-548av-5p HITS-CLIP 23313552
MIRT688723 hsa-miR-548k HITS-CLIP 23313552
MIRT688722 hsa-miR-8054 HITS-CLIP 23313552
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
72
GO ID Ontology Definition Evidence Reference
GO:0000050 Process Urea cycle IEA
GO:0000050 Process Urea cycle NAS 1840546
GO:0000050 Process Urea cycle TAS
GO:0000166 Function Nucleotide binding IEA
GO:0001889 Process Liver development IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
608307 2323 ENSG00000021826
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P31327
Protein name Carbamoyl-phosphate synthase [ammonia], mitochondrial (EC 6.3.4.16) (Carbamoyl-phosphate synthetase I) (CPSase I)
Protein function Involved in the urea cycle of ureotelic animals where the enzyme plays an important role in removing excess ammonia from the cell.
PDB 2YVQ , 4UTR , 4UTV , 4UTX , 4UTZ , 4UU7 , 4UU8 , 4UUA , 4UUB , 5DOT , 5DOU , 5OJO , 6UEL , 6W2J
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00988 CPSase_sm_chain 45 183 Carbamoyl-phosphate synthase small chain, CPSase domain Domain
PF00117 GATase 221 397 Glutamine amidotransferase class-I Domain
PF02786 CPSase_L_D2 546 750 Carbamoyl-phosphate synthase L chain, ATP binding domain Domain
PF02787 CPSase_L_D3 841 920 Carbamoyl-phosphate synthetase large chain, oligomerisation domain Domain
PF02786 CPSase_L_D2 1088 1291 Carbamoyl-phosphate synthase L chain, ATP binding domain Domain
PF02142 MGS 1373 1465 MGS-like domain Domain
Tissue specificity TISSUE SPECIFICITY: Primarily in the liver and small intestine.
Sequence
MTRILTAFKVVRTLKTGFGFTNVTAHQKWKFSRPGIRLLSVKAQTAHIVLEDGTKMKGYS
FGHPSSVAGEVVFNTGLGGYPEAITDPAYKGQILTMANPIIGNGGAPDTTALDELGLSKY
LESNGIKVSGLLVLDYSKDYNHWLATKSLGQWLQEEKVPAIYGVDTRMLTKIIRDKGTML
GKI
EFEGQPVDFVDPNKQNLIAEVSTKDVKVYGKGNPTKVVAVDCGIKNNVIRLLVKRGA
EVHLVPWNHDFTKMEYDGILIAGGPGNPALAEPLIQNVRKILESDRKEPLFGISTGNLIT
GLAAGAKTYKMSMANRGQNQPVLNITNKQAFITAQNHGYALDNTLPAGWKPLFVNVNDQT
NEGIMHESKPFFAVQFHPEVTPGPIDTEYLFDSFFSL
IKKGKATTITSVLPKPALVASRV
EVSKVLILGSGGLSIGQAGEFDYSGSQAVKAMKEENVKTVLMNPNIASVQTNEVGLKQAD
TVYFLPITPQFVTEVIKAEQPDGLILGMGGQTALNCGVELFKRGVLKEYGVKVLGTSVES
IMATEDRQLFSDKLNEINEKIAPSFAVESIEDALKAADTIGYPVMIRSAYALGGLGSGIC
PNRETLMDLSTKAFAMTNQILVEKSVTGWKEIEYEVVRDADDNCVTVCNMENVDAMGVHT
GDSVVVAPAQTLSNAEFQMLRRTSINVVRHLGIVGECNIQFALHPTSMEYCIIEVNARLS
RSSALASKATGYPLAFIAAKIALGIPLPEI
KNVVSGKTSACFEPSLDYMVTKIPRWDLDR
FHGTSSRIGSSMKSVGEVMAIGRTFEESFQKALRMCHPSIEGFTPRLPMNKEWPSNLDLR
KELSEPSSTRIYAIAKAIDDNMSLDEIEKLTYIDKWFLYKMRDILNMEKTLKGLNSESMT
EETLKRAKEIGFSDKQISKC
LGLTEAQTRELRLKKNIHPWVKQIDTLAAEYPSVTNYLYV
TYNGQEHDVNFDDHGMMVLGCGPYHIGSSVEFDWCAVSSIRTLRQLGKKTVVVNCNPETV
STDFDECDKLYFEELSLERILDIYHQEACGGCIISVGGQIPNNLAVPLYKNGVKIMGTSP
LQIDRAEDRSIFSAVLDELKVAQAPWKAVNTLNEALEFAKSVDYPCLLRPSYVLSGSAMN
VVFSEDEMKKFLEEATRVSQEHPVVLTKFVEGAREVEMDAVGKDGRVISHAISEHVEDAG
VHSGDATLMLPTQTISQGAIEKVKDATRKIAKAFAISGPFNVQFLVKGNDVLVIECNLRA
SRSFPFVSKTLGVDFIDVATKVMIGENVDEK
HLPTLDHPIIPADYVAIKAPMFSWPRLRD
ADPILRCEMASTGEVACFGEGIHTAFLKAMLSTGFKIPQKGILIGIQQSFRPRFLGVAEQ
LHNEGFKLFATEATSDWLNANNVPATPVAWPSQEGQNPSLSSIRKLIRDGSIDLVINLPN
NNTKFVHDNYVIRRTAVDSGIPLLT
NFQVTKLFAEAVQKSRKVDSKSLFHYRQYSAGKAA
Sequence length 1500
Interactions View interactions
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
2083
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Congenital hyperammonemia, type I Likely pathogenic; Pathogenic rs2106109125, rs2105840261, rs1206168005, rs1553513433, rs2105910926, rs1319489001, rs2105922845, rs2106113137, rs1375157321, rs2106126181, rs774484322, rs1698929326, rs2105850258, rs2105859138, rs756337473
View all (260 more)
RCV001375866
RCV001375867
RCV001379633
RCV001377851
RCV001378378
RCV001378075
RCV001379407
RCV001390724
RCV001382268
RCV001380978
RCV001380979
RCV001380479
RCV001384350
RCV001385247
RCV001390612
RCV001390872
RCV001381094
RCV001647339
RCV001553672
RCV001779494
RCV001844568
RCV001897177
RCV001984316
RCV001907227
RCV001968968
RCV002021997
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RCV001946749
RCV001865140
RCV001981780
RCV002003812
RCV001990006
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RCV001999712
RCV001918009
RCV002020754
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RCV001946627
RCV001949466
RCV001956334
RCV002026249
RCV001972722
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RCV001938120
RCV001974483
RCV002249835
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RCV002289044
RCV000149915
RCV000002519
RCV000002520
RCV000002521
RCV000002522
RCV000002526
RCV000002528
RCV002306498
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RCV002306809
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RCV002309879
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RCV002470032
RCV003087104
RCV002651590
RCV002651591
RCV002651594
RCV002651595
RCV002614393
RCV002657851
RCV002671333
RCV002658510
RCV002720739
RCV002727210
RCV002842530
RCV002861760
RCV002880878
RCV002898785
RCV002875882
RCV002885434
RCV002881873
RCV002963200
RCV002976506
RCV002999778
RCV003017320
RCV003057765
RCV003036627
RCV003056366
RCV003603134
RCV003110198
RCV003110199
RCV003110200
RCV003110203
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RCV003110205
RCV003110206
RCV003143804
RCV003141665
RCV003141674
RCV003143810
RCV000667844
RCV002519139
RCV003335983
RCV003498012
RCV004574048
RCV005030054
RCV003603171
RCV005030055
RCV003603172
RCV003603173
RCV003603174
RCV003486524
RCV003498218
RCV003498266
RCV003498802
RCV003499192
RCV003499202
RCV003499240
RCV003499136
RCV003498963
RCV003499917
RCV003499918
RCV003497392
RCV003497468
RCV003497645
RCV003498448
RCV003498378
RCV003498775
RCV003499500
RCV003603490
RCV003604183
RCV003604485
RCV003604505
RCV003604848
RCV003604940
RCV003602633
RCV003603682
RCV003603963
RCV003825366
RCV003827617
RCV003858359
RCV003870827
RCV003989169
RCV003990557
RCV003990641
RCV005618360
RCV004577419
RCV001380980
RCV000023698
RCV000477877
RCV005632418
RCV000702328
RCV000690237
RCV000539406
RCV000529677
RCV000578300
RCV000589986
RCV000655213
RCV000655211
RCV000672330
RCV000664568
RCV000668963
RCV000664516
RCV000673757
RCV000674444
RCV000664614
RCV000674031
RCV000671406
RCV000669628
RCV000671809
RCV000672320
RCV000674394
RCV000669529
RCV000672757
RCV000674202
RCV000669578
RCV000673682
RCV000671803
RCV000671123
RCV000669673
RCV000666827
RCV000672677
RCV000665437
RCV000667858
RCV000669266
RCV000665850
RCV000674800
RCV000668711
RCV000674758
RCV000671041
RCV000673929
RCV000667346
RCV000674114
RCV000673303
RCV000674756
RCV000674980
RCV000674344
RCV000672818
RCV000667061
RCV000668329
RCV000667803
RCV000670805
RCV000668983
RCV000672280
RCV000781315
RCV000813104
RCV000816596
RCV000818676
RCV000812446
RCV000800633
RCV000792675
RCV000986993
RCV000986995
RCV000986996
RCV000986998
RCV001045342
RCV001059094
RCV001043431
RCV001039493
RCV001057661
RCV001069987
RCV001174969
RCV001193021
RCV001201653
RCV001205119
RCV001234058
RCV001241984
RCV001264191
RCV001264192
RCV001264193
RCV001264194
RCV001264195
RCV001264196
RCV001264197
RCV001264198
RCV001263623
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RCV001263625
RCV001263626
RCV001263627
RCV001263628
RCV001263629
RCV001263630
RCV001263914
RCV001263915
RCV001263916
RCV001263917
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RCV001263919
RCV001263920
RCV001263921
RCV001264081
RCV001264082
RCV001293465
RCV001298254
CPS1-related disorder Likely pathogenic; Pathogenic rs1375157321, rs369061090 RCV004731144
RCV003409396
Hereditary breast ovarian cancer syndrome Likely pathogenic; Pathogenic rs1015051007 RCV004540597
Lung cancer Likely pathogenic rs1700129715 RCV005925636
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Acute myeloid leukemia Benign; Likely benign rs147937942 RCV005896095
CARBAMOYL PHOSPHATE SYNTHETASE I POLYMORPHISM Benign rs1047891 RCV003334453
Cervical cancer Benign; Likely benign rs147937942 RCV005896097
Cholangiocarcinoma Benign rs41272671 RCV005925015
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Adenocarcinoma of Lung Associate 28376202, 30808730, 33493519, 34996932, 37047726, 37709932, 37938151
Adenoma Associate 37565794
Adenomatous Polyposis Coli Associate 37565794
Azoospermia Associate 36945018
Carbamoyl Phosphate Synthase I Deficiency Disease Associate 28444906, 29314318, 31749211, 33090410
Carcinogenesis Associate 18026163, 21281797
Carcinoma Hepatocellular Inhibit 21281797
Carcinoma Hepatocellular Associate 25526364, 25780289, 28622513
Carcinoma Non Small Cell Lung Associate 30808730
Carcinoma Ovarian Epithelial Inhibit 28770969