CleftGeneDB-Search

Gene: CBS

Basic information

Tag	Content
Uniprot ID	P35520; B2R993; D3DSK4; Q99425; Q9BWC5;
Entrez ID	875
Genbank protein ID	AAC64683.1; AAH10242.1; EAX09515.1; CAA61252.1; AAH07257.1; BAG36440.1; EAX09509.1; AAH11381.1; AAA98524.1; AAC64684.1; AAH00440.1; EAX09508.1; AAP35818.1; AAA19874.1; EAX09510.1; EAX09511.1; CAA57656.1;
Genbank nucleotide ID	XM_017028214.1; XM_011529777.1; NM_001178009.2; XM_011546095.2; XM_017028217.1; XM_017028490.1; NM_001178008.2; XM_011546094.1; XM_011546099.1; XM_017028218.1; XM_017028211.1; NM_000071.2; XM_017028213.1; XM_011529782.1; XM_017028216.1; XM_017028212.1; XM_017028489.1; XM_017028492.1; XM_017028215.1; NM_001320298.1; NM_001321073.1; XM_011546098.1; XM_011546097.2; XM_017028491.1; XM_011529781.1;
Ensembl protein ID	ENSP00000381231; ENSP00000352643; ENSP00000344460; ENSP00000381225;
Ensembl nucleotide ID	ENSG00000160200
Gene name	Cystathionine beta-synthase
Gene symbol	CBS
Organism	Homo sapiens
NCBI taxa ID	9606
Cleft type	CPO,CL/P
Developmental stage
Data sources	Manually collected
Reference	21564312; 24437588; 18203168; 16007597;
Functional description	Hydro-lyase catalyzing the first step of the transsulfuration pathway, where the hydroxyl group of L-serine is displaced by L-homocysteine in a beta-replacement reaction to form L-cystathionine, the precursor of L-cysteine. This catabolic route allows the elimination of L-methionine and the toxic metabolite L-homocysteine (PubMed:23981774, PubMed:20506325, PubMed:23974653). Also involved in the production of hydrogen sulfide, a gasotransmitter with signaling and cytoprotective effects on neurons (By similarity).
Sequence	MPSETPQAEV GPTGCPHRSG PHSAKGSLEK GSPEDKEAKE PLWIRPDAPS RCTWQLGRPA 60 SESPHHHTAP AKSPKILPDI LKKIGDTPMV RINKIGKKFG LKCELLAKCE FFNAGGSVKD 120 RISLRMIEDA ERDGTLKPGD TIIEPTSGNT GIGLALAAAV RGYRCIIVMP EKMSSEKVDV 180 LRALGAEIVR TPTNARFDSP ESHVGVAWRL KNEIPNSHIL DQYRNASNPL AHYDTTADEI 240 LQQCDGKLDM LVASVGTGGT ITGIARKLKE KCPGCRIIGV DPEGSILAEP EELNQTEQTT 300 YEVEGIGYDF IPTVLDRTVV DKWFKSNDEE AFTFARMLIA QEGLLCGGSA GSTVAVAVKA 360 AQELQEGQRC VVILPDSVRN YMTKFLSDRW MLQKGFLKEE DLTEKKPWWW HLRVQELGLS 420 APLTVLPTIT CGHTIEILRE KGFDQAPVVD EAGVILGMVT LGNMLSSLLA GKVQPSDQVG 480 KVIYKQFKQI RLTDTLGRLS HILEMDHFAL VVHEQIQYHS TGKSSQRQMV FGVVTAIDLL 540 NFVAAQERDQ K 551

Abbreviation :
CLO : cleft lip only. CPO : cleft palate only. CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.
For humans: CL/P, CLO, CPO, and CLP. For mice: CLO, CLP, and CPO.

Gene expression in different tissues (ENCODE)

Protein structural annotations

3D structure in PDB database

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PDB ID
1JBQ
1M54
1M54
4COO
4COO

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Protein disorder information

Orthologous information

There is no orthologous record for this gene !

Identified variants/mutations related to cleft phenotype

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Gene symbol	Significant Variants/SNPS	Methods	PubMed ID
CBS	c.844ins68	TDT	16007597
CBS	rs4920037	Genotyping	21564312
CBS	c.844ins68	Genotyping	24437588
CBS	rs234706; c.699C>T	Genotyping	18203168

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Other genetic variants/mutations

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ID	Variant	Type	Disease	Chromosome\Coordinate	Evidence
rs201827340	p.Arg18Cys	missense variant	-	NC_000021.9:g.43072142G>A	UniProt,dbSNP
rs555959266	p.Arg58Trp	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43072022G>A	UniProt,dbSNP
rs17849313	p.Ala69Pro	missense variant	-	NC_000021.9:g.43071989C>G	UniProt,dbSNP
rs786204608	p.Pro78Arg	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43068592G>C	UniProt,dbSNP
rs786204757	p.Leu101Pro	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43068523A>G	UniProt,dbSNP
rs786204609	p.Lys102Asn	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43068519C>G	UniProt,dbSNP
rs778220779	p.Cys109Arg	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43066369A>G	UniProt,dbSNP
rs121964964	p.Ala114Val	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43066353G>A	UniProt,dbSNP
rs760214620	p.Gly116Arg	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43066348C>T	UniProt,dbSNP
rs775992753	p.Arg121Cys	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43066333G>A	UniProt,dbSNP
rs770095972	p.Arg121His	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43066332C>T	UniProt,dbSNP
rs770095972	p.Arg121Leu	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43066332C>A	UniProt,dbSNP
rs781444670	p.Arg125Gln	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43066320C>T	UniProt,dbSNP
rs1555875351	p.Glu131Asp	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43066301C>G	UniProt,dbSNP
rs121964965	p.Gly139Arg	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43066279C>T	UniProt,dbSNP
rs370167302	p.Ile143Met	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43066265G>C	UniProt,dbSNP
rs121964966	p.Glu144Lys	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43066264C>T	UniProt,dbSNP
rs121964963	p.Pro145Leu	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43066260G>A	UniProt,dbSNP
rs373782713	p.Gly151Arg	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43066243C>T	UniProt,dbSNP
rs1429138569	p.Ala155Thr	missense variant	Cystathionine beta-synthase deficiency (CBSD)	NC_000021.9:g.43065684C>T	UniProt,dbSNP

Showing 1 to 20 of 846 entries

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Disease or phenotype associated information

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Disease ID	Disease Name	Disease Type	Source
C0002395	Alzheimer's Disease	disease	BEFREE;LHGDN
C0002418	Amblyopia	phenotype	HPO
C0002895	Anemia, Sickle Cell	disease	BEFREE
C0002949	Aneurysm, Dissecting	disease	BEFREE
C0003706	Arachnodactyly	disease	HPO
C0003838	Arterial Occlusive Diseases	group	BEFREE
C0003850	Arteriosclerosis	disease	BEFREE
C0003857	Congenital arteriovenous malformation	disease	HPO
C0004153	Atherosclerosis	disease	BEFREE
C0004352	Autistic Disorder	group	BEFREE
C0005586	Bipolar Disorder	disease	BEFREE;PSYGENET
C0006142	Malignant neoplasm of breast	disease	BEFREE
C0006849	Oral candidiasis	disease	BEFREE
C0007102	Malignant tumor of colon	disease	BEFREE
C0007222	Cardiovascular Diseases	group	BEFREE;CTD_human;LHGDN
C0007766	Intracranial Aneurysm	disease	BEFREE
C0007785	Cerebral Infarction	disease	BEFREE
C0007786	Brain Ischemia	disease	HPO
C0009241	Cognition Disorders	group	BEFREE
C0009402	Colorectal Carcinoma	disease	BEFREE

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Gene Ontology (GO)/biological pathways

GO:Molecular Function

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GO ID	GO Term	Evidence
GO:0004122	cystathionine beta-synthase activity	IDA
GO:0004124	cysteine synthase activity	IBA
GO:0005515	protein binding	IPI
GO:0019825	oxygen binding	IDA
GO:0019899	enzyme binding	IPI
GO:0020037	heme binding	IMP
GO:0020037	heme binding	IBA
GO:0020037	heme binding	IDA
GO:0030170	pyridoxal phosphate binding	IDA
GO:0030170	pyridoxal phosphate binding	IBA
GO:0031625	ubiquitin protein ligase binding	IPI
GO:0042802	identical protein binding	IPI
GO:0042803	protein homodimerization activity	IDA
GO:0046872	metal ion binding	IEA
GO:0050421	nitrite reductase (NO-forming) activity	IDA
GO:0070025	carbon monoxide binding	IDA
GO:0070026	nitric oxide binding	IDA
GO:0072341	modified amino acid binding	IDA
GO:1904047	S-adenosyl-L-methionine binding	IDA

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GO:Biological Process

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GO ID	GO Term	Evidence
GO:0006535	cysteine biosynthetic process from serine	IBA
GO:0006563	L-serine metabolic process	IDA
GO:0006565	L-serine catabolic process	IDA
GO:0019343	cysteine biosynthetic process via cystathionine	IEA
GO:0019344	cysteine biosynthetic process	IDA
GO:0019346	transsulfuration	IBA
GO:0019346	transsulfuration	TAS
GO:0019448	L-cysteine catabolic process	IDA
GO:0042262	DNA protection	IMP
GO:0043418	homocysteine catabolic process	IDA
GO:0050667	homocysteine metabolic process	IDA
GO:0050667	homocysteine metabolic process	IBA
GO:0055114	oxidation-reduction process	IEA
GO:0070814	hydrogen sulfide biosynthetic process	ISS
GO:0070814	hydrogen sulfide biosynthetic process	IDA
GO:0070814	hydrogen sulfide biosynthetic process	IBA

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GO:Cellular Component

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GO ID	GO Term	Evidence
GO:0005634	nucleus	IDA
GO:0005737	cytoplasm	IBA
GO:0005737	cytoplasm	IDA
GO:0005829	cytosol	HDA
GO:0005829	cytosol	TAS

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Reactome Pathway

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Reactome ID	Reactome Term	Evidence
R-HSA-1430728	Metabolism	TAS
R-HSA-1430728	Metabolism	IEA
R-HSA-1614603	Cysteine formation from homocysteine	TAS
R-HSA-1614635	Sulfur amino acid metabolism	TAS
R-HSA-2408508	Metabolism of ingested SeMet, Sec, MeSec into H2Se	IEA
R-HSA-2408522	Selenoamino acid metabolism	IEA
R-HSA-71291	Metabolism of amino acids and derivatives	TAS
R-HSA-71291	Metabolism of amino acids and derivatives	IEA

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Drugs and compounds information

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ID	Drug Name	Action	PubMed
C002741	N-nitrosomorpholine	N-nitrosomorpholine results in increased expression of CBS protein	19716841
C004925	methylmercuric chloride	methylmercuric chloride results in increased expression of CBS mRNA	23103053
C004925	methylmercuric chloride	methylmercuric chloride results in increased expression of CBS mRNA	23179753; 26272509;
C004925	methylmercuric chloride	[NOG protein co-treated with methylmercuric chloride co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of CBS mRNA	27188386
C005460	uranyl acetate	uranyl acetate results in decreased expression of CBS protein	26523793; 26991019;
C006253	pirinixic acid	pirinixic acid results in decreased expression of CBS mRNA	23811191
C006253	pirinixic acid	pirinixic acid results in decreased expression of CBS mRNA	17164430
C006551	2-amino-2-methyl-1-propanol	2-amino-2-methyl-1-propanol results in decreased expression of CBS mRNA	25088246
C006780	bisphenol A	bisphenol A affects the expression of CBS mRNA	30903817
C006780	bisphenol A	bisphenol A results in decreased expression of CBS mRNA	20678512
C006780	bisphenol A	bisphenol A results in increased expression of CBS mRNA	30245210
C006780	bisphenol A	bisphenol A results in decreased expression of CBS mRNA	25181051
C006780	bisphenol A	bisphenol A results in increased expression of CBS mRNA	30816183
C008070	4-hydroxyphenylacetic acid	4-hydroxyphenylacetic acid inhibits the reaction [Peroxynitrous Acid results in decreased activity of CBS protein]	19733148
C012589	trichostatin A	[NOG protein co-treated with trichostatin A co-treated with dorsomorphin co-treated with 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide] results in increased expression of CBS mRNA	27188386
C012589	trichostatin A	trichostatin A results in increased expression of CBS mRNA	24935251; 26272509;
C013418	bromfenacoum	bromfenacoum results in decreased expression of CBS protein	28903499
C014707	nitrosobenzylmethylamine	nitrosobenzylmethylamine results in decreased expression of CBS mRNA	17616710
C015499	schizandrin B	schizandrin B inhibits the reaction [Carbon Tetrachloride results in decreased expression of CBS mRNA]	31150632
C015586	propiverine	propiverine binds to CBS protein	29273565

Showing 1 to 20 of 239 entries

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Functional annotations

Keywords

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Keyword ID	Keyword Term
KW-0002	3D-structure
KW-0021	Allosteric enzyme
KW-0025	Alternative splicing
KW-0028	Amino-acid biosynthesis
KW-0129	CBS domain
KW-0198	Cysteine biosynthesis
KW-0225	Disease mutation
KW-0349	Heme
KW-0408	Iron
KW-0456	Lyase
KW-0479	Metal-binding
KW-0539	Nucleus
KW-0597	Phosphoprotein
KW-0621	Polymorphism
KW-0663	Pyridoxal phosphate
KW-0832	Ubl conjugation
KW-0963	Cytoplasm
KW-1017	Isopeptide bond
KW-1185	Reference proteome

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Interpro

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InterPro ID	InterPro Term
IPR000644	CBS_dom
IPR001216	P-phosphate_BS
IPR001926	PLP-dep
IPR005857	Cysta_beta_synth
IPR036052	Trypto_synt_PLP_dependent

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PROSITE

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PROSITE ID	PROSITE Term
PS00901	CYS_SYNTHASE
PS51371	CBS

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Pfam

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Pfam ID	Pfam Term
PF00291	PALP
PF00571	CBS

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Gene: CBS

Basic information

Gene expression in different tissues (ENCODE)

Protein structural annotations

3D structure in PDB database

Protein disorder information

Orthologous information

There is no orthologous record for this gene !

Identified variants/mutations related to cleft phenotype

Other genetic variants/mutations

Disease or phenotype associated information

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO:Biological Process

GO:Cellular Component

Reactome Pathway

Drugs and compounds information

Functional annotations

Keywords

Interpro

PROSITE

Pfam

Protein-protein interaction

Protein-miRNA interaction