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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 Regulation of cholesterol biosynthesis by SREBP (SREBF) and cholesterol biosynthesis I. Gene Ontology (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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for SC5D Gene

Promoters and enhancers for SC5D 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
GH11I121291 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 557.1 +0.5 456 2.7 FOXA2 PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B FOS SC5D GC11M121292
GH11I121297 Promoter/Enhancer 1.1 EPDnew ENCODE 558.1 +6.1 6079 2.3 USF1 OSR2 ZNF121 ATF4 GLIS1 TRIM24 ZBTB33 FOS WT1 SETDB1 SC5D GC11M121292 LOC105369536 SORL1
GH11I121446 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.1 +160.0 160041 11.3 HDGF FOXA2 SMAD1 MLX ARNT ARID4B ZNF48 YY1 SLC30A9 ZNF143 SORL1 LOC105369536 TBCEL SC5D
GH11I121458 Enhancer 1.8 FANTOM5 Ensembl ENCODE dbSUPER 10.4 +171.7 171687 10.9 HDGF PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A DMAP1 IRF4 YY1 SC5D TECTA SORL1 GC11M121459 GC11M121471
GH11I121235 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 9.2 -53.5 -53462 7.8 PKNOX1 SMAD1 ARNT FEZF1 YY1 TCF12 GLIS2 ATF7 KLF7 RUNX3 LOC105369533 SC5D LOC105369534
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SC5D on UCSC Golden Path with GeneCards custom track

Genomic Locations for SC5D Gene

Genomic Locations for SC5D Gene
chr11:121,292,453-121,313,410
(GRCh38/hg38)
Size:
20,958 bases
Orientation:
Plus strand
chr11:121,163,162-121,184,119
(GRCh37/hg19)

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 posLast=255255, posLast=263263, and isoforms=297

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

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted membrane proteins

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

Phenotypes From GWAS Catalog 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

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

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Endoplasmic reticulum (2)
  • Nucleoplasm (2)
  • Plasma membrane (2)
See all subcellular structures

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,IBA --
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:0006694 steroid biosynthetic process IEA --
GO:0008202 steroid metabolic process IEA --
GO:0008610 lipid biosynthetic 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

(8) 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
NADH Approved Nutra 0
Flavin Mononucleotide Pharma 8

(13) 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

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

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 33
  • 99.22 (n)
SC5D 34
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SC5D 33 34
  • 88.07 (n)
cow
(Bos Taurus)
Mammalia SC5DL 34
  • 83 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Sc5d 33 16 34
  • 80.82 (n)
rat
(Rattus norvegicus)
Mammalia Sc5d 33
  • 79.93 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SC5D 34
  • 75 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SC5D 34
  • 74 (a)
OneToOne
chicken
(Gallus gallus)
Aves SC5D 34
  • 67 (a)
OneToOne
SC5DL 33
  • 64.47 (n)
lizard
(Anolis carolinensis)
Reptilia SC5D 34
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100490845 33
  • 68.05 (n)
zebrafish
(Danio rerio)
Actinopterygii sc5d 34 33
  • 66.22 (n)
OneToOne
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F08855g 33
  • 54.1 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ERG3 33 34 36
  • 52.54 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR151C 33
  • 50.83 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G02590 33
  • 53.22 (n)
rice
(Oryza sativa)
Liliopsida Os01g0134500 33
  • 46.25 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes erg31 33
  • 55.6 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU06207 33
  • 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 Variation AA Info Type
rs1005813750 uncertain-significance, Lathosterolosis 121,292,700(+) T/G 5_prime_UTR_variant, genic_upstream_transcript_variant, upstream_transcript_variant
rs1015473697 uncertain-significance, Lathosterolosis 121,308,110(+) T/C 3_prime_UTR_variant
rs104894295 pathogenic, Lathosterolosis, Lathosterolosis (LATHST) [MIM:607330] 121,303,461(+) G/A coding_sequence_variant, missense_variant
rs104894296 pathogenic, Lathosterolosis, Lathosterolosis (LATHST) [MIM:607330] 121,307,244(+) G/A coding_sequence_variant, missense_variant
rs104894297 pathogenic, Lathosterolosis, Lathosterolosis (LATHST) [MIM:607330] 121,303,512(+) A/C/G coding_sequence_variant, missense_variant

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)

Additional Variant Information 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

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

Disorder Aliases PubMed IDs
lathosterolosis
  • sterol c5-desaturase deficiency
mevalonic aciduria
  • meva
chondrodysplasia punctata syndrome
  • chondrodysplasia punctata
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.

Additional Disease Information for 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 (Cytogenetics and cell genetics 1996) 2 3 4 22 58
  2. Lathosterolosis: an inborn error of human and murine cholesterol synthesis due to lathosterol 5-desaturase deficiency. (PMID: 12812989) Krakowiak PA … Porter FD (Human molecular genetics 2003) 3 4 22 58
  3. Lathosterolosis, a novel multiple-malformation/mental retardation syndrome due to deficiency of 3beta-hydroxysteroid-delta5-desaturase. (PMID: 12189593) Brunetti-Pierri N … Parenti G (American journal of human genetics 2002) 3 4 22 58
  4. Molecular cloning and structural analysis of human sterol C5 desaturase. (PMID: 11731337) Sugawara T … Ishibashi T (Biochimica et biophysica acta 2001) 3 22 25 58
  5. cDNA cloning of the mammalian sterol C5-desaturase and the expression in yeast mutant. (PMID: 10786622) Nishi S … Ishibashi T (Biochimica et biophysica acta 2000) 3 4 22 58

Products for SC5D Gene

Sources for SC5D Gene

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