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CPS1 (carbamoyl-phosphate synthase 1)

Gene

Carbamoyl-phosphate synthase 1

CPS1

CPSASE1, GATD6, PHN

2

2q34

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]

Show/Hide all(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
rs121912594	A>C	Benign, risk-factor	Non coding transcript variant, coding sequence variant, missense variant
rs121912595	G>A,C,T	Uncertain-significance, pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs121912596	C>T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs138392504	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Non coding transcript variant, coding sequence variant, missense variant, genic upstream transcript variant
rs138779023	T>C	Benign, conflicting-interpretations-of-pathogenicity, benign-likely-benign	Non coding transcript variant, coding sequence variant, synonymous variant, genic upstream transcript variant
rs141373204	A>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Non coding transcript variant, coding sequence variant, missense variant
rs192759073	C>T	Likely-benign, uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, non coding transcript variant, synonymous variant, genic upstream transcript variant
rs200214298	G>A,T	Pathogenic, likely-benign	Non coding transcript variant, stop gained, missense variant, coding sequence variant, genic upstream transcript variant
rs201716417	C>A,G,T	Likely-pathogenic, pathogenic, uncertain-significance	Coding sequence variant, non coding transcript variant, missense variant
rs202107577	C>A,T	Likely-benign, pathogenic-likely-pathogenic	Coding sequence variant, non coding transcript variant, stop gained, synonymous variant
rs369061090	T>A	Pathogenic, uncertain-significance	Coding sequence variant, non coding transcript variant, missense variant
rs727502824	GTG>-	Pathogenic	Inframe deletion, non coding transcript variant, coding sequence variant
rs755530984	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, non coding transcript variant
rs755882799	G>A,T	Likely-pathogenic	Splice acceptor variant
rs756021170	G>A,T	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant, non coding transcript variant, stop gained
rs757205958	G>A,C	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs758724746	G>A	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs759201450	C>T	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs761225695	C>T	Likely-pathogenic	Coding sequence variant, stop gained, non coding transcript variant, genic upstream transcript variant
rs764384490	G>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs766584384	A>G	Likely-pathogenic	Splice acceptor variant
rs767575696	T>C	Likely-pathogenic	Splice donor variant
rs767694281	G>A,T	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs772497399	G>A,C,T	Likely-pathogenic, uncertain-significance	Non coding transcript variant, coding sequence variant, missense variant
rs778346264	T>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, stop gained, genic upstream transcript variant
rs778766382	G>A	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs778958318	T>G	Conflicting-interpretations-of-pathogenicity	Missense variant, non coding transcript variant, coding sequence variant, genic upstream transcript variant
rs781088670	C>-	Likely-pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs961015305	C>A	Likely-pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs1015051007	C>A,G,T	Pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs1064794258	G>T	Likely-pathogenic	Genic upstream transcript variant, splice acceptor variant, upstream transcript variant
rs1275489342	G>A,C	Likely-pathogenic	Intron variant
rs1318756445	AT>-	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, frameshift variant, non coding transcript variant
rs1326644714	C>-	Pathogenic, likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1341782266	->T	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1374322297	T>C	Conflicting-interpretations-of-pathogenicity	Splice donor variant
rs1375304341	CTACAATGGTCAG>-	Likely-pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1392934477	C>T	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, missense variant
rs1414143303	C>T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1553507155	G>T	Likely-pathogenic	Coding sequence variant, missense variant, initiator codon variant, genic upstream transcript variant, non coding transcript variant
rs1553507167	A>T	Likely-pathogenic	Non coding transcript variant, genic upstream transcript variant, stop gained, coding sequence variant
rs1553507183	G>A	Likely-pathogenic	Splice donor variant, genic upstream transcript variant
rs1553509010	->AAGTGGTT	Likely-pathogenic	Non coding transcript variant, genic upstream transcript variant, coding sequence variant, frameshift variant
rs1553509023	G>T	Likely-pathogenic	Splice donor variant, genic upstream transcript variant
rs1553509303	A>-	Likely-pathogenic	Non coding transcript variant, genic upstream transcript variant, coding sequence variant, frameshift variant
rs1553509924	GA>-	Likely-pathogenic	Non coding transcript variant, genic upstream transcript variant, coding sequence variant, frameshift variant
rs1553510520	G>C	Likely-pathogenic	Splice donor variant, genic upstream transcript variant
rs1553510944	G>-	Likely-pathogenic	Non coding transcript variant, genic upstream transcript variant, coding sequence variant, frameshift variant
rs1553511326	G>A	Likely-pathogenic	Splice donor variant, upstream transcript variant, genic upstream transcript variant
rs1553511789	->T	Likely-pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1553512225	->C	Likely-pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1553512642	G>A	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1553513387	G>T	Likely-pathogenic	Splice acceptor variant
rs1553513429	G>C	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1553513433	G>A	Likely-pathogenic	Splice donor variant
rs1553513864	A>G	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1553516660	G>A	Likely-pathogenic	Splice donor variant
rs1553517122	A>-	Likely-pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1553517224	C>-	Likely-pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1553517670	->GG	Likely-pathogenic	Splice donor variant, non coding transcript variant, coding sequence variant
rs1553518389	G>A	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1553518395	T>A	Likely-pathogenic	Splice donor variant
rs1553518719	A>T	Likely-pathogenic	Splice acceptor variant
rs1553518720	G>C	Likely-pathogenic	Splice acceptor variant
rs1553518726	C>-	Likely-pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1559129372	G>C	Pathogenic	Splice donor variant
rs1574543988	T>C	Likely-pathogenic	Genic upstream transcript variant, splice donor variant
rs1574548003	T>C	Likely-pathogenic	Genic upstream transcript variant, splice donor variant
rs1574566578	G>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1574567901	C>G	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs1574577755	T>C	Likely-pathogenic	Splice donor variant
rs1574632659	A>C	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1574646079	G>C	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant

Show/Hide all(57)

miRTarBase ID	miRNA	Experiments	Reference
MIRT051022	hsa-miR-17-5p	CLASH	23622248
MIRT051022	hsa-miR-17-5p	HITS-CLIP	23313552
MIRT205178	hsa-miR-3121-3p	HITS-CLIP	23313552
MIRT205179	hsa-miR-4255	HITS-CLIP	23313552
MIRT478912	hsa-miR-4709-3p	PAR-CLIP	23592263
MIRT478913	hsa-miR-7154-5p	PAR-CLIP	23592263
MIRT478914	hsa-miR-101-3p	PAR-CLIP	23592263
MIRT478915	hsa-miR-1255b-5p	PAR-CLIP	23592263
MIRT478916	hsa-miR-1255a	PAR-CLIP	23592263
MIRT478917	hsa-miR-6744-5p	PAR-CLIP	23592263
MIRT478918	hsa-miR-8060	PAR-CLIP	23592263
MIRT478919	hsa-miR-16-1-3p	PAR-CLIP	23592263
MIRT478920	hsa-miR-144-3p	PAR-CLIP	23592263
MIRT478921	hsa-miR-216a-5p	PAR-CLIP	23592263
MIRT478922	hsa-miR-522-3p	PAR-CLIP	23592263
MIRT478923	hsa-miR-224-3p	PAR-CLIP	23592263
MIRT478924	hsa-miR-4694-3p	PAR-CLIP	23592263
MIRT688686	hsa-miR-6516-5p	HITS-CLIP	23313552
MIRT688687	hsa-miR-6738-3p	HITS-CLIP	23313552
MIRT688688	hsa-miR-1303	HITS-CLIP	23313552
MIRT688689	hsa-miR-3678-3p	HITS-CLIP	23313552
MIRT688690	hsa-miR-1273h-3p	HITS-CLIP	23313552
MIRT688691	hsa-miR-5001-3p	HITS-CLIP	23313552
MIRT688692	hsa-miR-4727-5p	HITS-CLIP	23313552
MIRT688693	hsa-miR-1200	HITS-CLIP	23313552
MIRT688694	hsa-miR-142-3p	HITS-CLIP	23313552
MIRT688695	hsa-miR-630	HITS-CLIP	23313552
MIRT688696	hsa-miR-146b-3p	HITS-CLIP	23313552
MIRT688697	hsa-miR-6799-3p	HITS-CLIP	23313552
MIRT688698	hsa-miR-3173-5p	HITS-CLIP	23313552
MIRT688699	hsa-miR-7976	HITS-CLIP	23313552
MIRT688700	hsa-miR-496	HITS-CLIP	23313552
MIRT688701	hsa-miR-302a-5p	HITS-CLIP	23313552
MIRT688702	hsa-miR-18a-3p	HITS-CLIP	23313552
MIRT688703	hsa-miR-324-3p	HITS-CLIP	23313552
MIRT688704	hsa-miR-1913	HITS-CLIP	23313552
MIRT688705	hsa-miR-4682	HITS-CLIP	23313552
MIRT688706	hsa-miR-544b	HITS-CLIP	23313552
MIRT688707	hsa-miR-4324	HITS-CLIP	23313552
MIRT688708	hsa-miR-4778-5p	HITS-CLIP	23313552
MIRT688709	hsa-miR-200b-5p	HITS-CLIP	23313552
MIRT688710	hsa-miR-200a-5p	HITS-CLIP	23313552
MIRT688711	hsa-miR-4796-3p	HITS-CLIP	23313552
MIRT688712	hsa-miR-93-5p	HITS-CLIP	23313552
MIRT688713	hsa-miR-526b-3p	HITS-CLIP	23313552
MIRT688714	hsa-miR-519d-3p	HITS-CLIP	23313552
MIRT688715	hsa-miR-20b-5p	HITS-CLIP	23313552
MIRT688716	hsa-miR-20a-5p	HITS-CLIP	23313552
MIRT688717	hsa-miR-106b-5p	HITS-CLIP	23313552
MIRT688718	hsa-miR-106a-5p	HITS-CLIP	23313552
MIRT688719	hsa-miR-548ah-5p	HITS-CLIP	23313552
MIRT688720	hsa-miR-3609	HITS-CLIP	23313552
MIRT688721	hsa-miR-548l	HITS-CLIP	23313552
MIRT688722	hsa-miR-8054	HITS-CLIP	23313552
MIRT688723	hsa-miR-548k	HITS-CLIP	23313552
MIRT688724	hsa-miR-548av-5p	HITS-CLIP	23313552
MIRT688725	hsa-miR-548c-3p	HITS-CLIP	23313552

Show/Hide all(47)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000050	Process	Urea cycle	NAS	1840546
GO:0000050	Process	Urea cycle	TAS
GO:0004087	Function	Carbamoyl-phosphate synthase (ammonia) activity	EXP	6249820
GO:0004087	Function	Carbamoyl-phosphate synthase (ammonia) activity	IMP	8486760, 9711878
GO:0004088	Function	Carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity	IEA
GO:0004175	Function	Endopeptidase activity	IEA
GO:0005509	Function	Calcium ion binding	IEA
GO:0005515	Function	Protein binding	IPI	12620389, 15161933, 20618440
GO:0005524	Function	ATP binding	IEA
GO:0005543	Function	Phospholipid binding	IEA
GO:0005730	Component	Nucleolus	IDA
GO:0005737	Component	Cytoplasm	IBA	21873635
GO:0005743	Component	Mitochondrial inner membrane	IEA
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0006207	Process	'de novo' pyrimidine nucleobase biosynthetic process	IEA
GO:0006508	Process	Proteolysis	IEA
GO:0006541	Process	Glutamine metabolic process	IBA	21873635
GO:0006807	Process	Nitrogen compound metabolic process	IBA	21873635
GO:0007494	Process	Midgut development	IEA
GO:0009636	Process	Response to toxic substance	IEA
GO:0010043	Process	Response to zinc ion	IEA
GO:0014075	Process	Response to amine	IEA
GO:0016595	Function	Glutamate binding	IEA
GO:0019240	Process	Citrulline biosynthetic process	NAS	14718356
GO:0019433	Process	Triglyceride catabolic process	IMP	9711878
GO:0032094	Process	Response to food	IEA
GO:0032496	Process	Response to lipopolysaccharide	IDA	15897806
GO:0032991	Component	Protein-containing complex	IEA
GO:0042311	Process	Vasodilation	IMP	14718356
GO:0042493	Process	Response to drug	IEA
GO:0042594	Process	Response to starvation	IEA
GO:0042645	Component	Mitochondrial nucleoid	IDA	18063578
GO:0043200	Process	Response to amino acid	IEA
GO:0044344	Process	Cellular response to fibroblast growth factor stimulus	IEA
GO:0044877	Function	Protein-containing complex binding	IEA
GO:0046209	Process	Nitric oxide metabolic process	IMP	14718356
GO:0050667	Process	Homocysteine metabolic process	IDA	20031578
GO:0055081	Process	Anion homeostasis	IEA
GO:0060416	Process	Response to growth hormone	IEA
GO:0070365	Process	Hepatocyte differentiation	IEA
GO:0070409	Process	Carbamoyl phosphate biosynthetic process	IMP	7416778, 21120950
GO:0071242	Process	Cellular response to ammonium ion	IMP	21120950
GO:0071320	Process	Cellular response to cAMP	IEA
GO:0071377	Process	Cellular response to glucagon stimulus	IEA
GO:0071400	Process	Cellular response to oleic acid	IEA
GO:0071548	Process	Response to dexamethasone	IEA
GO:0072341	Function	Modified amino acid binding	IDA	20031578

MIM	HGNC	e!Ensembl
608307	2323	ENSG00000021826

Protein

UniProt ID

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

Sequence

MTRILTAFKVVRTLKTGFGFTNVTAHQKWKFSRPGIRLLSVKAQTAHIVLEDGTKMKGYS
FGHPSSVAGEVVFNTGLGGYPEAITDPAYKGQILTMANPIIGNGGAPDTTALDELGLSKY
LESNGIKVSGLLVLDYSKDYNHWLATKSLGQWLQEEKVPAIYGVDTRMLTKIIRDKGTML
GKIEFEGQPVDFVDPNKQNLIAEVSTKDVKVYGKGNPTKVVAVDCGIKNNVIRLLVKRGA
EVHLVPWNHDFTKMEYDGILIAGGPGNPALAEPLIQNVRKILESDRKEPLFGISTGNLIT
GLAAGAKTYKMSMANRGQNQPVLNITNKQAFITAQNHGYALDNTLPAGWKPLFVNVNDQT
NEGIMHESKPFFAVQFHPEVTPGPIDTEYLFDSFFSLIKKGKATTITSVLPKPALVASRV
EVSKVLILGSGGLSIGQAGEFDYSGSQAVKAMKEENVKTVLMNPNIASVQTNEVGLKQAD
TVYFLPITPQFVTEVIKAEQPDGLILGMGGQTALNCGVELFKRGVLKEYGVKVLGTSVES
IMATEDRQLFSDKLNEINEKIAPSFAVESIEDALKAADTIGYPVMIRSAYALGGLGSGIC
PNRETLMDLSTKAFAMTNQILVEKSVTGWKEIEYEVVRDADDNCVTVCNMENVDAMGVHT
GDSVVVAPAQTLSNAEFQMLRRTSINVVRHLGIVGECNIQFALHPTSMEYCIIEVNARLS
RSSALASKATGYPLAFIAAKIALGIPLPEIKNVVSGKTSACFEPSLDYMVTKIPRWDLDR
FHGTSSRIGSSMKSVGEVMAIGRTFEESFQKALRMCHPSIEGFTPRLPMNKEWPSNLDLR
KELSEPSSTRIYAIAKAIDDNMSLDEIEKLTYIDKWFLYKMRDILNMEKTLKGLNSESMT
EETLKRAKEIGFSDKQISKCLGLTEAQTRELRLKKNIHPWVKQIDTLAAEYPSVTNYLYV
TYNGQEHDVNFDDHGMMVLGCGPYHIGSSVEFDWCAVSSIRTLRQLGKKTVVVNCNPETV
STDFDECDKLYFEELSLERILDIYHQEACGGCIISVGGQIPNNLAVPLYKNGVKIMGTSP
LQIDRAEDRSIFSAVLDELKVAQAPWKAVNTLNEALEFAKSVDYPCLLRPSYVLSGSAMN
VVFSEDEMKKFLEEATRVSQEHPVVLTKFVEGAREVEMDAVGKDGRVISHAISEHVEDAG
VHSGDATLMLPTQTISQGAIEKVKDATRKIAKAFAISGPFNVQFLVKGNDVLVIECNLRA
SRSFPFVSKTLGVDFIDVATKVMIGENVDEKHLPTLDHPIIPADYVAIKAPMFSWPRLRD
ADPILRCEMASTGEVACFGEGIHTAFLKAMLSTGFKIPQKGILIGIQQSFRPRFLGVAEQ
LHNEGFKLFATEATSDWLNANNVPATPVAWPSQEGQNPSLSSIRKLIRDGSIDLVINLPN
NNTKFVHDNYVIRRTAVDSGIPLLTNFQVTKLFAEAVQKSRKVDSKSLFHYRQYSAGKAA

Sequence length

1500

Interactions

View interactions

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