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Aliases for SDS Gene

Aliases for SDS Gene

  • Serine Dehydratase 2 3 5
  • L-Threonine Dehydratase 3 4
  • L-Serine Ammonia-Lyase 2 3
  • L-Serine Deaminase 3 4
  • SDH 3 4
  • TDH 3 4
  • L-Serine Dehydratase/L-Threonine Deaminase 3
  • L-Serine Dehydratase 3
  • EC 4.3.1.17 4
  • EC 4.3.1.19 4

External Ids for SDS Gene

Previous GeneCards Identifiers for SDS Gene

  • GC12M112739
  • GC12M113349
  • GC12M113613
  • GC12M112242
  • GC12M112292
  • GC12M113830
  • GC12M110841

Summaries for SDS Gene

Entrez Gene Summary for SDS Gene

  • This gene encodes one of three enzymes that are involved in metabolizing serine and glycine. L-serine dehydratase converts L-serine to pyruvate and ammonia and requires pyridoxal phosphate as a cofactor. The encoded protein can also metabolize threonine to NH4+ and 2-ketobutyrate. The encoded protein is found predominantly in the liver. [provided by RefSeq, Jul 2008]

GeneCards Summary for SDS Gene

SDS (Serine Dehydratase) is a Protein Coding gene. Diseases associated with SDS include Deafness, Autosomal Dominant 69. Among its related pathways are threonine degradation and Amino Acid metabolism. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and L-serine ammonia-lyase activity. An important paralog of this gene is SDSL.

Additional gene information for SDS Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SDS Gene

Genomics for SDS Gene

GeneHancer (GH) Regulatory Elements for SDS Gene

Promoters and enhancers for SDS Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12I113403 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 550.3 +22.2 22200 1 HDAC1 TAF1 YY1 ZNF335 ZNF316 VEZF1 NFE2 SMARCE1 PHF21A RXRA SDS SDSL PLBD2 LHX5 LOC105369989
GH12I113425 Enhancer 1 Ensembl ENCODE 550.8 +0.5 491 1.3 HDGF RB1 NFXL1 BATF IRF4 RAD21 ARID2 EGR1 ZNF143 IKZF2 SDS SDSL
GH12I113356 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE 1.4 +67.7 67695 4 HDGF PKNOX1 ARNT MLX ARID4B SIN3A ZNF2 YY1 ZNF766 ZNF143 PLBD2 SLC8B1 RBM19 SDSL DDX54 RITA1 ENSG00000201208 RPL6 SDS LOC105369989
GH12I113417 Enhancer 1.3 FANTOM5 Ensembl ENCODE 1.9 +7.9 7888 1 ELF3 FOXA2 ARID4B DNMT3B RAD21 RARA YY1 ATF7 THAP11 RXRA SDSL PLBD2 SLC8B1 SDS OAS2 OAS3 LOC105369989
GH12I113270 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 1.3 +154.3 154263 2.3 ELF3 ARID4B SIN3A DMAP1 ZNF48 ZSCAN9 RAD21 EGR1 EGR2 CEBPB GC12M113256 SDSL RASAL1 RITA1 SLC8B1 RBM19 OAS2 OAS3 OAS1 PLBD2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SDS on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SDS gene promoter:

Genomic Locations for SDS Gene

Genomic Locations for SDS Gene
chr12:113,392,445-113,426,301
(GRCh38/hg38)
Size:
33,857 bases
Orientation:
Minus strand
chr12:113,830,250-113,864,106
(GRCh37/hg19)

Genomic View for SDS Gene

Genes around SDS on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SDS Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SDS Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SDS Gene

Proteins for SDS Gene

  • Protein details for SDS Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P20132-SDHL_HUMAN
    Recommended name:
    L-serine dehydratase/L-threonine deaminase
    Protein Accession:
    P20132
    Secondary Accessions:
    • A8K9P5

    Protein attributes for SDS Gene

    Size:
    328 amino acids
    Molecular mass:
    34625 Da
    Cofactor:
    Name=pyridoxal 5-phosphate; Xref=ChEBI:CHEBI:597326;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for SDS Gene

neXtProt entry for SDS Gene

Post-translational modifications for SDS Gene

No Post-translational modifications

Other Protein References for SDS Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SDS Gene

Domains & Families for SDS Gene

Gene Families for SDS Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for SDS Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P20132

UniProtKB/Swiss-Prot:

SDHL_HUMAN :
  • Belongs to the serine/threonine dehydratase family.
Family:
  • Belongs to the serine/threonine dehydratase family.
genes like me logo Genes that share domains with SDS: view

Function for SDS Gene

Molecular function for SDS Gene

GENATLAS Biochemistry:
serine dehydratase,liver,murine ortholog
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=23 mM for serine {ECO:0000269 PubMed:18342636}; KM=31 mM for threonine {ECO:0000269 PubMed:18342636};
UniProtKB/Swiss-Prot CatalyticActivity:
L-serine = pyruvate + NH(3).
UniProtKB/Swiss-Prot CatalyticActivity:
L-threonine = 2-oxobutanoate + NH(3).

Enzyme Numbers (IUBMB) for SDS Gene

Phenotypes From GWAS Catalog for SDS Gene

Gene Ontology (GO) - Molecular Function for SDS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003941 L-serine ammonia-lyase activity IDA 15689518
GO:0004794 L-threonine ammonia-lyase activity IEA --
GO:0016829 lyase activity IEA --
GO:0030170 pyridoxal phosphate binding IDA,IEA 15689518
GO:0042803 protein homodimerization activity IDA 15689518
genes like me logo Genes that share ontologies with SDS: view
genes like me logo Genes that share phenotypes with SDS: view

Animal Model Products

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SDS Gene

Localization for SDS Gene

Subcellular locations from UniProtKB/Swiss-Prot for SDS Gene

Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SDS gene
Compartment Confidence
mitochondrion 5
cytosol 5
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Mitochondria (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SDS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IDA --
GO:0005829 cytosol IDA --
genes like me logo Genes that share ontologies with SDS: view

Pathways & Interactions for SDS Gene

genes like me logo Genes that share pathways with SDS: view

UniProtKB/Swiss-Prot P20132-SDHL_HUMAN

  • Pathway: Carbohydrate biosynthesis; gluconeogenesis.

Gene Ontology (GO) - Biological Process for SDS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006094 gluconeogenesis IEA --
GO:0006520 cellular amino acid metabolic process IEA --
GO:0006565 L-serine catabolic process IDA 15689518
GO:0042866 pyruvate biosynthetic process IDA 15689518
genes like me logo Genes that share ontologies with SDS: view

No data available for SIGNOR curated interactions for SDS Gene

Drugs & Compounds for SDS Gene

(32) Drugs for SDS Gene - From: DrugBank, ClinicalTrials, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Pyridoxal Phosphate Approved, Investigational Nutra Target, cofactor 17
Citalopram Approved Pharma 526
Ammonia Approved Pharma 0
Water Approved Pharma 0
L-Threonine Approved Nutra 0

(3) Additional Compounds for SDS Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
2-Aminoacrylic acid
  • (alpha)-(beta)-di-dehydroalanine
  • 2-Aminoacrylate
  • 2-Aminoacrylic acid
  • a-b-Di-dehydroalanine
  • alpha-beta-Di-dehydroalanine
28453-71-6
genes like me logo Genes that share compounds with SDS: view

Transcripts for SDS Gene

Unigene Clusters for SDS Gene

Serine dehydratase:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SDS Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8
SP1: - -
SP2: - -
SP3: -
SP4: - - - - -
SP5:

Relevant External Links for SDS Gene

GeneLoc Exon Structure for
SDS
ECgene alternative splicing isoforms for
SDS

Expression for SDS Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SDS Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SDS Gene

This gene is overexpressed in Liver (x40.9).

Protein differential expression in normal tissues from HIPED for SDS Gene

This gene is overexpressed in Liver (65.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SDS Gene



Protein tissue co-expression partners for SDS Gene

NURSA nuclear receptor signaling pathways regulating expression of SDS Gene:

SDS

SOURCE GeneReport for Unigene cluster for SDS Gene:

Hs.439023

Evidence on tissue expression from TISSUES for SDS Gene

  • Liver(4.9)
  • Lung(4.1)
  • Kidney(2)
genes like me logo Genes that share expression patterns with SDS: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SDS Gene

Orthologs for SDS Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SDS Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SDS 33 34
  • 99.49 (n)
cow
(Bos Taurus)
Mammalia SDS 33 34
  • 83.75 (n)
mouse
(Mus musculus)
Mammalia Sds 33 16 34
  • 82.57 (n)
rat
(Rattus norvegicus)
Mammalia Sds 33
  • 81.8 (n)
oppossum
(Monodelphis domestica)
Mammalia SDS 34
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SDS 34
  • 67 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SDS 34
  • 59 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia sds 33
  • 67.29 (n)
Str.12213 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.1669 33
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes CHA1 34
  • 31 (a)
OneToMany
SDL1 36
bread mold
(Neurospora crassa)
Ascomycetes NCU03761 33
  • 49.2 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 49 (a)
OneToMany
Species where no ortholog for SDS was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for SDS Gene

ENSEMBL:
Gene Tree for SDS (if available)
TreeFam:
Gene Tree for SDS (if available)

Paralogs for SDS Gene

Paralogs for SDS Gene

(1) SIMAP similar genes for SDS Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with SDS: view

Variants for SDS Gene

Sequence variations from dbSNP and Humsavar for SDS Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs1000213283 -- 113,403,972(-) C/T upstream_transcript_variant
rs1000263857 -- 113,404,158(-) C/T upstream_transcript_variant
rs1000541369 -- 113,399,440(-) G/A intron_variant
rs1000914192 -- 113,404,252(-) T/C/G upstream_transcript_variant
rs1001137862 -- 113,393,201(-) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SDS Gene

Variant ID Type Subtype PubMed ID
esv3630792 CNV gain 21293372
esv3892265 CNV gain 25118596
nsv519540 CNV gain+loss 19592680

Variation tolerance for SDS Gene

Residual Variation Intolerance Score: 32.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.18; 39.50% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SDS Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SDS

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SDS Gene

Disorders for SDS Gene

MalaCards: The human disease database

(1) MalaCards diseases for SDS Gene - From: DISEASES

Disorder Aliases PubMed IDs
deafness, autosomal dominant 69
  • dfna69
- elite association - COSMIC cancer census association via MalaCards
Search SDS in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SDS

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SDS: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SDS Gene

Publications for SDS Gene

  1. A catalytic mechanism that explains a low catalytic activity of serine dehydratase like-1 from human cancer cells: crystal structure and site-directed mutagenesis studies. (PMID: 18342636) Yamada T … Takusagawa F (Biochimica et biophysica acta 2008) 3 4 22 58
  2. Crystallization and preliminary crystallographic analysis of human serine dehydratase. (PMID: 14646100) Sun L … Rao Z (Acta crystallographica. Section D, Biological crystallography 2003) 3 4 22 58
  3. Human liver serine dehydratase. cDNA cloning and sequence homology with hydroxyamino acid dehydratases from other sources. (PMID: 2674117) Ogawa H … Fujioka M (The Journal of biological chemistry 1989) 2 3 4 58
  4. Association between sorbitol dehydrogenase gene polymorphisms and type 2 diabetic retinopathy. (PMID: 18289528) Szaflik JP … Blasiak J (Experimental eye research 2008) 3 44 58
  5. Crystal structure of the pyridoxal-5'-phosphate-dependent serine dehydratase from human liver. (PMID: 15689518) Sun L … Rao Z (Protein science : a publication of the Protein Society 2005) 3 22 58

Products for SDS Gene

Sources for SDS Gene

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