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Aliases for SC5D Gene

Aliases for SC5D Gene

  • Sterol-C5-Desaturase 2 3 4 5
  • Sterol-C5-Desaturase (ERG3 Delta-5-Desaturase Homolog, S. Cerevisiae)-Like 2 3
  • Delta(7)-Sterol C5(6)-Desaturase 3 4
  • Delta(7)-Sterol 5-Desaturase 3 4
  • Lathosterol 5-Desaturase 3 4
  • C-5 Sterol Desaturase 3 4
  • Lathosterol Oxidase 2 3
  • SC5DL 3 4
  • Sterol-C5-Desaturase (ERG3 Delta-5-Desaturase Homolog, Fungal)-Like 2
  • Sterol-C5-Desaturase (Fungal ERG3, Delta-5-Desaturase)-Like 2
  • 3beta-Hydroxysteroid-Delta5-Desaturase 3
  • Fungal ERG3, Delta-5-Desaturase-Like 3
  • Lathosterol Dehydrogenase 3
  • EC 1.14.19.20 4
  • S5DES 3
  • ERG3 3

External Ids for SC5D Gene

Previous HGNC Symbols for SC5D Gene

  • SC5DL

Previous GeneCards Identifiers for SC5D Gene

  • GC11P121163

Summaries for SC5D Gene

Entrez Gene Summary for SC5D Gene

  • This gene encodes an enzyme of cholesterol biosynthesis. The encoded protein catalyzes the conversion of lathosterol into 7-dehydrocholesterol. Mutations in this gene have been associated with lathosterolosis. Alternatively spliced transcript variants encoding the same protein have been described. [provided by RefSeq, Jul 2008]

GeneCards Summary for SC5D Gene

SC5D (Sterol-C5-Desaturase) is a Protein Coding gene. Diseases associated with SC5D include Lathosterolosis and Mevalonic Aciduria. Among its related pathways are cholesterol biosynthesis I and Terpenoid backbone biosynthesis. GO annotations related to this gene include oxidoreductase activity and C-5 sterol desaturase activity.

UniProtKB/Swiss-Prot for SC5D Gene

  • Catalyzes a dehydrogenation to introduce C5-6 double bond into lathosterol.

Gene Wiki entry for SC5D Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SC5D Gene

Genomics for SC5D Gene

Regulatory Elements for SC5D Gene

Enhancers for SC5D Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11G121458 2 FANTOM5 Ensembl ENCODE dbSUPER 10.4 +171.7 171687 10.9 HDGF PKNOX1 FOXA2 MLX ZFP64 WRNIP1 ARID4B SIN3A DMAP1 YY1 SC5D TECTA SORL1 GC11M121459 GC11M121471
GH11G121235 1.8 FANTOM5 Ensembl ENCODE dbSUPER 9.2 -53.5 -53463 7.8 PKNOX1 ARNT ZFP64 FEZF1 YY1 TCF12 GLIS2 KLF7 FOS JUNB SC5D LOC105369533 LOC105369534
GH11G121446 1.6 FANTOM5 ENCODE dbSUPER 10.1 +160.0 160042 11.3 HDGF PKNOX1 MLX ARNT WRNIP1 ARID4B SIN3A FEZF1 ZNF2 ZNF48 SORL1 TBCEL SC5D LOC105369536
GH11G121248 0.9 ENCODE dbSUPER 17.9 -43.4 -43401 0.8 CTCF ZNF654 FOXA2 TRIM22 REST CHD7 RAD21 EGR1 SMC3 SC5D LOC105369534 RPS4XP12
GH11G121493 1.5 FANTOM5 Ensembl ENCODE dbSUPER 10.4 +202.2 202200 1.7 TBL1XR1 MTA2 ZBED1 MAX TBX21 ARID3A EGR1 EED IKZF1 ETV6 SORL1 LOC105369536 SC5D TECTA GC11M121490 GC11M121501
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SC5D on UCSC Golden Path with GeneCards custom track

Promoters for SC5D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000045982 547 2001 PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 FOS KLF13

Genomic Location for SC5D Gene

Chromosome:
11
Start:
121,292,453 bp from pter
End:
121,313,410 bp from pter
Size:
20,958 bases
Orientation:
Plus strand

Genomic View for SC5D Gene

Genes around SC5D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SC5D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SC5D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SC5D Gene

Proteins for SC5D Gene

  • Protein details for SC5D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75845-SC5D_HUMAN
    Recommended name:
    Lathosterol oxidase
    Protein Accession:
    O75845
    Secondary Accessions:
    • O00119
    • Q6GTM5
    • Q9UK15

    Protein attributes for SC5D Gene

    Size:
    299 amino acids
    Molecular mass:
    35301 Da
    Cofactor:
    Name=Fe cation; Xref=ChEBI:CHEBI:24875;
    Quaternary structure:
    No Data Available

neXtProt entry for SC5D Gene

Post-translational modifications for SC5D Gene

  • Ubiquitination at Lys255, Lys263, and Lys297
  • Modification sites at PhosphoSitePlus

Other Protein References for SC5D Gene

No data available for DME Specific Peptides for SC5D Gene

Domains & Families for SC5D Gene

Gene Families for SC5D Gene

Protein Domains for SC5D Gene

InterPro:
Blocks:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

O75845

UniProtKB/Swiss-Prot:

SC5D_HUMAN :
  • The histidine box domains may contain the active site and/or be involved in metal ion binding.
  • Belongs to the sterol desaturase family.
Domain:
  • The histidine box domains may contain the active site and/or be involved in metal ion binding.
Family:
  • Belongs to the sterol desaturase family.
genes like me logo Genes that share domains with SC5D: view

Function for SC5D Gene

Molecular function for SC5D Gene

UniProtKB/Swiss-Prot CatalyticActivity:
A Delta(7)-sterol + 2 ferrocytochrome b5 + O(2) + 2 H(+) = a Delta(5,7)-sterol + 2 ferricytochrome b5 + 2 H(2)O.
UniProtKB/Swiss-Prot Function:
Catalyzes a dehydrogenation to introduce C5-6 double bond into lathosterol.

Enzyme Numbers (IUBMB) for SC5D Gene

Gene Ontology (GO) - Molecular Function for SC5D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000248 C-5 sterol desaturase activity IBA --
GO:0005506 iron ion binding IEA --
GO:0016491 oxidoreductase activity IEA --
GO:0050046 lathosterol oxidase activity IBA --
genes like me logo Genes that share ontologies with SC5D: view
genes like me logo Genes that share phenotypes with SC5D: view

Human Phenotype Ontology for SC5D Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SC5D Gene

MGI Knock Outs for SC5D:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for SC5D Gene

Localization for SC5D Gene

Subcellular locations from UniProtKB/Swiss-Prot for SC5D Gene

Endoplasmic reticulum membrane; Multi-pass membrane protein.

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 SC5D gene
Compartment Confidence
endoplasmic reticulum 4
plasma membrane 3
peroxisome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for SC5D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0043231 intracellular membrane-bounded organelle IEA --
genes like me logo Genes that share ontologies with SC5D: view

Pathways & Interactions for SC5D Gene

genes like me logo Genes that share pathways with SC5D: view

Gene Ontology (GO) - Biological Process for SC5D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process TAS 8976377
GO:0006633 fatty acid biosynthetic process IEA --
GO:0006694 steroid biosynthetic process IEA --
GO:0008202 steroid metabolic process IEA --
GO:0016126 sterol biosynthetic process IEA --
genes like me logo Genes that share ontologies with SC5D: view

No data available for SIGNOR curated interactions for SC5D Gene

Drugs & Compounds for SC5D Gene

(7) Drugs for SC5D Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
FAD Approved Pharma 0
Oxygen Approved, Vet_approved Pharma 0
Water Approved Pharma 0
Flavin Mononucleotide Experimental Pharma 6
NAD Pharma Full agonist, Agonist 0

(14) Additional Compounds for SC5D Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
7-dehydrocholesterol
  • (-)-7-dehydrocholesterol
  • (3b)-Cholesta-5,7-dien-3-ol
  • (3beta)-Cholesta-5,7-dien-3-ol
  • 10,13-Dimethyl-17-(6-methylheptan-2-yl)-2,3,4,9,11,12,14,15,16,17-decahydro-1H-cyclopenta[a]phenanthren-3-ol
  • 17-(1,5-Dimethylhexyl)-10,13-dimethyl-2,3,4,9,10,11,12,13,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-ol
434-16-2
lathosterol
  • (3beta)-Cholest-7-en-3-ol
  • (3beta,5alpha)-Cholest-7-en-3-ol
  • (3beta,alpha)-Cholest-7-en-3-ol
  • (7)-Cholestenol
  • 3b-Hydroxy-5-cholestene
80-99-9
5,7,24(28)-Ergostatrienol
5-Dehydroavenasterol
5-Dehydroepisterol
  • Campesta-7,24(28)-dien-3beta-ol
  • Ergosta-5,7,24(28)-trien-3beta-ol
23582-83-4
genes like me logo Genes that share compounds with SC5D: view

Transcripts for SC5D Gene

Unigene Clusters for SC5D Gene

Sterol-C5-desaturase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SC5D Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5a · 5b
SP1: -
SP2: - -
SP3:

Relevant External Links for SC5D Gene

GeneLoc Exon Structure for
SC5D
ECgene alternative splicing isoforms for
SC5D

Expression for SC5D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SC5D Gene

mRNA differential expression in normal tissues according to GTEx for SC5D Gene

This gene is overexpressed in Liver (x5.5).

Protein differential expression in normal tissues from HIPED for SC5D Gene

This gene is overexpressed in Fetal testis (28.0), Gallbladder (13.1), and Adrenal (9.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SC5D Gene



NURSA nuclear receptor signaling pathways regulating expression of SC5D Gene:

SC5D

SOURCE GeneReport for Unigene cluster for SC5D Gene:

Hs.287749

Evidence on tissue expression from TISSUES for SC5D Gene

  • Nervous system(4.9)
  • Kidney(4.5)
  • Liver(4.5)
  • Lung(4.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SC5D Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cerebellum
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • meninges
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • skull
Abdomen:
  • kidney
  • liver
  • spleen
Pelvis:
  • penis
Limb:
  • ankle
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
General:
  • blood
  • blood vessel
  • bone marrow
  • coagulation system
  • lymph node
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with SC5D: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for SC5D Gene

Orthologs for SC5D Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SC5D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SC5DL 34
  • 99.22 (n)
SC5D 35
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SC5D 34 35
  • 88.07 (n)
cow
(Bos Taurus)
Mammalia SC5DL 35
  • 83 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sc5d 34 16 35
  • 80.82 (n)
rat
(Rattus norvegicus)
Mammalia Sc5d 34
  • 79.93 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SC5D 35
  • 75 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SC5D 35
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves SC5D 35
  • 67 (a)
OneToOne
SC5DL 34
  • 64.47 (n)
lizard
(Anolis carolinensis)
Reptilia SC5D 35
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100490845 34
  • 68.05 (n)
zebrafish
(Danio rerio)
Actinopterygii sc5d 34 35
  • 66.22 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F08855g 34
  • 54.1 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ERG3 34 35 37
  • 52.54 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR151C 34
  • 50.83 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G02590 34
  • 53.22 (n)
rice
(Oryza sativa)
Liliopsida Os01g0134500 34
  • 46.25 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes erg31 34
  • 55.6 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU06207 34
  • 53.85 (n)
Species where no ortholog for SC5D was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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 blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SC5D Gene

ENSEMBL:
Gene Tree for SC5D (if available)
TreeFam:
Gene Tree for SC5D (if available)

Paralogs for SC5D Gene

No data available for Paralogs for SC5D Gene

Variants for SC5D Gene

Sequence variations from dbSNP and Humsavar for SC5D Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs104894295 Pathogenic, Lathosterolosis (LATHST) [MIM:607330] 121,303,461(+) CTTCC(A/G)ACAAG reference, missense
rs104894296 Pathogenic, Lathosterolosis (LATHST) [MIM:607330] 121,307,244(+) TGACG(A/G)TGATT reference, missense
rs104894297 Pathogenic, Lathosterolosis (LATHST) [MIM:607330] 121,303,512(+) CCTTT(A/C)TTTCT reference, missense
rs141633273 Likely benign 121,310,498(+) GTTGC(C/T)CCAGG utr-variant-3-prime
rs199751132 Likely benign 121,312,836(+) CTGAC(-/AT)GTGGT utr-variant-3-prime

Variation tolerance for SC5D Gene

Residual Variation Intolerance Score: 37.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.54; 11.71% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SC5D Gene

Human Gene Mutation Database (HGMD)
SC5D
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SC5D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for SC5D Gene

Disorders for SC5D Gene

MalaCards: The human disease database

(5) MalaCards diseases for SC5D Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
lathosterolosis
  • sc5d deficiency
mevalonic aciduria
  • mevalonate kinase deficiency
chondrodysplasia punctata syndrome
  • chondrodysplasia punctata
antley-bixler syndrome without genital anomalies or disordered steroidogenesis
  • trapezoidocephaly-synotsosis syndrome
congenital ichthyosiform erythroderma
  • alligator skin
- elite association - COSMIC cancer census association via MalaCards
Search SC5D in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SC5D_HUMAN
  • Lathosterolosis (LATHST) [MIM:607330]: Autosomal recessive disorder characterized by a complex phenotype, including multiple congenital anomalies, mental retardation, and liver disease. {ECO:0000269 PubMed:12189593, ECO:0000269 PubMed:12812989}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SC5D

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SC5D
genes like me logo Genes that share disorders with SC5D: view

No data available for Genatlas for SC5D Gene

Publications for SC5D Gene

  1. Molecular cloning and mapping of a human cDNA(SC5DL) encoding a protein homologous to fungal sterol-C5-desaturase. (PMID: 8976377) Matsushima M. … Nakamura Y. (Cytogenet. Cell Genet. 1996) 2 3 4 22 64
  2. Lathosterolosis: an inborn error of human and murine cholesterol synthesis due to lathosterol 5-desaturase deficiency. (PMID: 12812989) Krakowiak P.A. … Porter F.D. (Hum. Mol. Genet. 2003) 3 4 22 64
  3. Lathosterolosis, a novel multiple-malformation/mental retardation syndrome due to deficiency of 3beta-hydroxysteroid-delta5- desaturase. (PMID: 12189593) Brunetti-Pierri N. … Parenti G. (Am. J. Hum. Genet. 2002) 3 4 22 64
  4. Molecular cloning and structural analysis of human sterol C5 desaturase. (PMID: 11731337) Sugawara T. … Ishibashi T. (Biochim. Biophys. Acta 2001) 3 22 25 64
  5. cDNA cloning of the mammalian sterol C5-desaturase and the expression in yeast mutant. (PMID: 10786622) Nishi S. … Ishibashi T. (Biochim. Biophys. Acta 2000) 3 4 22 64

Products for SC5D Gene

Sources for SC5D Gene

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