Human Gene CBS (ENST00000398165.8_7) from GENCODE V47lift37
  Description: cystathionine beta-synthase, transcript variant 1 (from RefSeq NM_000071.3)
Gencode Transcript: ENST00000398165.8_7
Gencode Gene: ENSG00000160200.18_10
Transcript (Including UTRs)
   Position: hg19 chr21:44,473,301-44,495,945 Size: 22,645 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr21:44,473,990-44,492,303 Size: 18,314 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr21:44,473,301-44,495,945)mRNA (may differ from genome)Protein (551 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
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WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CBS_HUMAN
DESCRIPTION: RecName: Full=Cystathionine beta-synthase; EC=4.2.1.22; AltName: Full=Beta-thionase; AltName: Full=Serine sulfhydrase;
FUNCTION: Only known pyridoxal phosphate-dependent enzyme that contains heme. Important regulator of hydrogen sulfide, especially in the brain, utilizing cysteine instead of serine to catalyze the formation of hydrogen sulfide. Hydrogen sulfide is a gastratransmitter with signaling and cytoprotective effects such as acting as a neuromodulator in the brain to protect neurons against hypoxic injury (By similarity).
CATALYTIC ACTIVITY: L-serine + L-homocysteine = L-cystathionine + H(2)O.
COFACTOR: Pyridoxal phosphate.
ENZYME REGULATION: Allosterically activated by adenosyl-methionine (AdoMet).
PATHWAY: Amino-acid biosynthesis; L-cysteine biosynthesis; L- cysteine from L-homocysteine and L-serine: step 1/2.
SUBUNIT: Homotetramer.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus.
TISSUE SPECIFICITY: In the adult strongly expressed in liver and pancreas, some expression in heart and brain, weak expression in lung and kidney. In the fetus, expressed in brain, liver and kidney.
DISEASE: Defects in CBS are the cause of cystathionine beta- synthase deficiency (CBSD) [MIM:236200]. CBSD is an enzymatic deficiency resulting in altered sulfur metabolism and homocystinuria. The clinical features of untreated homocystinuria due to CBS deficiency include myopia, ectopia lentis, mental retardation, skeletal anomalies resembling Marfan syndrome, and thromboembolic events. Light skin and hair can also be present. Biochemical features include increased urinary homocystine and methionine.
SIMILARITY: Belongs to the cysteine synthase/cystathionine beta- synthase family.
SIMILARITY: Contains 1 CBS domain.
WEB RESOURCE: Name=CBS mutation database; URL="http://cbs.lf1.cuni.cz/index.php";
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/CBS";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CBS
Diseases sorted by gene-association score: homocystinuria, b6-responsive and nonresponsive types* (1550), homocystinuria* (461), homocystinuria due to cbs deficiency* (419), homocystinuria due to mthfr deficiency* (283), thoracic aortic aneurysms and aortic dissections* (121), homocystinuria caused by cystathionine beta-synthase deficiency* (118), pyridoxine deficiency (18), hyperhomocysteinemia (17), ideomotor apraxia (17), gerstmann syndrome (16), hypermethioninemia (16), trichosporonosis (14), myelomeningocele (14), isolated ectopia lentis (12), methylmalonic aciduria and homocystinuria, cblc type (11), voyeurism (11), asymmetric motor neuropathy (11), tinea manuum (11), glycine n-methyltransferase deficiency (10), vascular disease (10), megakaryocytic leukemia (10), homocysteinemia (10), lens subluxation (10), neural tube defects (10), amino acid metabolic disorder (9), phaeohyphomycosis (9), speech and communication disorders (9), wolff-parkinson-white syndrome (9), transvestism (9), fetishism (9), cerebrovascular disease (9), marfan syndrome (8), tinea cruris (7), cicatricial ectropion (7), echolalia (7), tinea unguium (7), gait apraxia (6), otomycosis (6), superficial mycosis (6), focal hand dystonia (5), exhibitionism (5), thrombophilia due to thrombin defect (5), supranuclear palsy, progressive (5), agraphia (5), bartter syndrome, type 3 (4), urofacial syndrome 1 (4), paraphilia disorder (4), basal ganglia disease (4), down syndrome (4), frontotemporal dementia and/or amyotrophic lateral sclerosis 1 (4), nominal aphasia (4), dementia, frontotemporal (1), myocardial infarction (1), inherited metabolic disorder (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 84.56 RPKM in Liver
Total median expression: 602.89 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -47.60150-0.317 Picture PostScript Text
3' UTR -226.60689-0.329 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001216 - Cys_synth_BS
IPR005857 - Cysta_beta_synth
IPR000644 - Cysta_beta_synth_core
IPR001926 - Trp_syn_b_sub_like_PLP_eny_SF

Pfam Domains:
PF00291 - Pyridoxal-phosphate dependent enzyme
PF00571 - CBS domain

SCOP Domains:
51735 - NAD(P)-binding Rossmann-fold domains
53335 - S-adenosyl-L-methionine-dependent methyltransferases
53686 - Tryptophan synthase beta subunit-like PLP-dependent enzymes
54631 - CBS-domain pair

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1JBQ - X-ray MuPIT 1M54 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P35520
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0004122 cystathionine beta-synthase activity
GO:0005515 protein binding
GO:0016829 lyase activity
GO:0019825 oxygen binding
GO:0019899 enzyme binding
GO:0020037 heme binding
GO:0030170 pyridoxal phosphate binding
GO:0031625 ubiquitin protein ligase binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
GO:0050421 nitrite reductase (NO-forming) activity
GO:0070025 carbon monoxide binding
GO:0070026 nitric oxide binding
GO:0072341 modified amino acid binding
GO:1904047 S-adenosyl-L-methionine binding

Biological Process:
GO:0006535 cysteine biosynthetic process from serine
GO:0006563 L-serine metabolic process
GO:0006565 L-serine catabolic process
GO:0008152 metabolic process
GO:0008652 cellular amino acid biosynthetic process
GO:0019343 cysteine biosynthetic process via cystathionine
GO:0019344 cysteine biosynthetic process
GO:0019346 transsulfuration
GO:0019448 L-cysteine catabolic process
GO:0042262 DNA protection
GO:0043418 homocysteine catabolic process
GO:0050667 homocysteine metabolic process
GO:0055114 oxidation-reduction process
GO:0070814 hydrogen sulfide biosynthetic process

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  BC012319 - Homo sapiens, clone IMAGE:3608784, mRNA, partial cds.
AL137314 - Homo sapiens mRNA; cDNA DKFZp727E011 (from clone DKFZp727E011); partial cds.
BC000440 - Homo sapiens cystathionine-beta-synthase, mRNA (cDNA clone MGC:8402 IMAGE:2820694), complete cds.
X82166 - H.sapiens mRNA for cystathionine-beta-synthase.
BC011381 - Homo sapiens cystathionine-beta-synthase, mRNA (cDNA clone MGC:17143 IMAGE:3869615), complete cds.
L19501 - Homo sapiens (clone pGHSCBS) cystathionine beta-synthase subunit (CBS) mRNA, complete cds.
BC007257 - Homo sapiens cystathionine-beta-synthase, mRNA (cDNA clone MGC:15515 IMAGE:3028099), complete cds.
L00972 - Human cystathionine-beta-synthase (CBS) mRNA.
L14577 - Homo sapiens cystathionine beta-synthase (CBS) mRNA, complete cds.
BC010242 - Homo sapiens cystathionine-beta-synthase, mRNA (cDNA clone MGC:18160 IMAGE:4154798), complete cds.
JD254068 - Sequence 235092 from Patent EP1572962.
JD274462 - Sequence 255486 from Patent EP1572962.
JD309442 - Sequence 290466 from Patent EP1572962.
JD546596 - Sequence 527620 from Patent EP1572962.
JD208483 - Sequence 189507 from Patent EP1572962.
JD094239 - Sequence 75263 from Patent EP1572962.
JD066453 - Sequence 47477 from Patent EP1572962.
AK294608 - Homo sapiens cDNA FLJ53863 complete cds, highly similar to Cystathionine beta-synthase (EC 4.2.1.22).
JD180553 - Sequence 161577 from Patent EP1572962.
JD287259 - Sequence 268283 from Patent EP1572962.
JD089761 - Sequence 70785 from Patent EP1572962.
JD184549 - Sequence 165573 from Patent EP1572962.
JD268631 - Sequence 249655 from Patent EP1572962.
JD281754 - Sequence 262778 from Patent EP1572962.
AK301063 - Homo sapiens cDNA FLJ53928 complete cds, highly similar to Cystathionine beta-synthase (EC 4.2.1.22).
JD456758 - Sequence 437782 from Patent EP1572962.
JD116073 - Sequence 97097 from Patent EP1572962.
JD116072 - Sequence 97096 from Patent EP1572962.
KJ896548 - Synthetic construct Homo sapiens clone ccsbBroadEn_05942 CBS gene, encodes complete protein.
KJ896549 - Synthetic construct Homo sapiens clone ccsbBroadEn_05943 CBS gene, encodes complete protein.
KJ905707 - Synthetic construct Homo sapiens clone ccsbBroadEn_15377 CBS gene, encodes complete protein.
KR709361 - Synthetic construct Homo sapiens clone CCSBHm_00000994 CBS (CBS) mRNA, encodes complete protein.
KR709362 - Synthetic construct Homo sapiens clone CCSBHm_00001022 CBS (CBS) mRNA, encodes complete protein.
KR709363 - Synthetic construct Homo sapiens clone CCSBHm_00001052 CBS (CBS) mRNA, encodes complete protein.
KR709364 - Synthetic construct Homo sapiens clone CCSBHm_00001092 CBS (CBS) mRNA, encodes complete protein.
AK313691 - Homo sapiens cDNA, FLJ94281, Homo sapiens cystathionine-beta-synthase (CBS), mRNA.
BT007154 - Homo sapiens cystathionine-beta-synthase mRNA, complete cds.
DQ891029 - Synthetic construct clone IMAGE:100003659; FLH168649.01X; RZPDo839B0994D cystathionine-beta-synthase (CBS) gene, encodes complete protein.
DQ894208 - Synthetic construct Homo sapiens clone IMAGE:100008668; FLH168645.01L; RZPDo839B0993D cystathionine-beta-synthase (CBS) gene, encodes complete protein.
AB528379 - Synthetic construct DNA, clone: pF1KB4011, Homo sapiens CBS gene for cystathionine-beta-synthase, without stop codon, in Flexi system.
CU675587 - Synthetic construct Homo sapiens gateway clone IMAGE:100017404 5' read CBS mRNA.
CU679659 - Synthetic construct Homo sapiens gateway clone IMAGE:100019846 5' read CBS mRNA.
JD451690 - Sequence 432714 from Patent EP1572962.
JD447895 - Sequence 428919 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
HOMOCYSDEGR-PWY - L-cysteine biosynthesis III (from L-homocysteine)
PWY-5328 - superpathway of methionine degradation
PWY-6292 - L-cysteine biosynthesis
PWY66-426 - hydrogen sulfide biosynthesis II (mammalian)

Reactome (by CSHL, EBI, and GO)

Protein P35520 (Reactome details) participates in the following event(s):

R-HSA-1614524 Cystathionine is formed from homocysteine and serine
R-HSA-2408559 SeHCys and Ser are dehydrated into SeCysta by CBS
R-HSA-1614603 Cysteine formation from homocysteine
R-HSA-2408508 Metabolism of ingested SeMet, Sec, MeSec into H2Se
R-HSA-1614635 Sulfur amino acid metabolism
R-HSA-2408522 Selenoamino acid metabolism
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B2R993, CBS_HUMAN, D3DSK4, ENST00000398165.1, ENST00000398165.2, ENST00000398165.3, ENST00000398165.4, ENST00000398165.5, ENST00000398165.6, ENST00000398165.7, NM_000071, P35520, Q99425, Q9BWC5, uc318zod.1, uc318zod.2
UCSC ID: ENST00000398165.8_7
RefSeq Accession: NM_000071.3
Protein: P35520 (aka CBS_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CBS:
dystonia-ov (Hereditary Dystonia Overview)
homocystinuria (Homocystinuria Caused by Cystathionine Beta-Synthase Deficiency)
taa (Heritable Thoracic Aortic Disease Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.