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SC5D (sterol-C5-desaturase)

Identity

Alias (NCBI)ERG3
S5DES
SC5DL
HGNC (Hugo) SC5D
HGNC Alias namelathosterol oxidase
HGNC Previous nameSC5DL
HGNC Previous namesterol-C5-desaturase (fungal ERG3, delta-5-desaturase)-like
 sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, fungal)-like
 sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, S. cerevisiae)-like
LocusID (NCBI) 6309
Atlas_Id 72994
Location 11q23.3  [Link to chromosome band 11q23]
Location_base_pair Starts at 121292679 and ends at 121313410 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
SC5D (11q23.3) / ARHGEF12 (11q23.3)SC5D (11q23.3) / BCL11A (2p16.1)SORL1 (11q24.1) / SC5D (11q23.3)
TMSB4X (Xp22.2) / SC5D (11q23.3)VPS45 (1q21.2) / SC5D (11q23.3)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]
  SC5D/ARHGEF12 (11q23)
t(11;11)(q23;q24) SORL1/SC5D

External links

Nomenclature
HGNC (Hugo)SC5D   10547
Cards
Entrez_Gene (NCBI)SC5D    sterol-C5-desaturase
AliasesERG3; S5DES; SC5DL
GeneCards (Weizmann)SC5D
Ensembl hg19 (Hinxton)ENSG00000109929 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000109929 [Gene_View]  ENSG00000109929 [Sequence]  chr11:121292679-121313410 [Contig_View]  SC5D [Vega]
ICGC DataPortalENSG00000109929
TCGA cBioPortalSC5D
AceView (NCBI)SC5D
Genatlas (Paris)SC5D
SOURCE (Princeton)SC5D
Genetics Home Reference (NIH)SC5D
Genomic and cartography
GoldenPath hg38 (UCSC)SC5D  -     chr11:121292679-121313410 +  11q23.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SC5D  -     11q23.3   [Description]    (hg19-Feb_2009)
GoldenPathSC5D - 11q23.3 [CytoView hg19]  SC5D - 11q23.3 [CytoView hg38]
ImmunoBaseENSG00000109929
genome Data Viewer NCBISC5D [Mapview hg19]  
OMIM602286   607330   
Gene and transcription
Genbank (Entrez)AF069469 AF187981 AK027246 AK096847 AK222686
RefSeq transcript (Entrez)NM_001024956 NM_006918
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SC5D
Alternative Splicing GalleryENSG00000109929
Gene ExpressionSC5D [ NCBI-GEO ]   SC5D [ EBI - ARRAY_EXPRESS ]   SC5D [ SEEK ]   SC5D [ MEM ]
Gene Expression Viewer (FireBrowse)SC5D [ Firebrowse - Broad ]
GenevisibleExpression of SC5D in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6309
GTEX Portal (Tissue expression)SC5D
Human Protein AtlasENSG00000109929-SC5D [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO75845   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO75845  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO75845
Splice isoforms : SwissVarO75845
Catalytic activity : Enzyme1.14.19.20 [ Enzyme-Expasy ]   1.14.19.201.14.19.20 [ IntEnz-EBI ]   1.14.19.20 [ BRENDA ]   1.14.19.20 [ KEGG ]   [ MEROPS ]
PhosPhoSitePlusO75845
Domains : Interpro (EBI)Fatty_acid_hydroxylase   
Domain families : Pfam (Sanger)FA_hydroxylase (PF04116)   
Domain families : Pfam (NCBI)pfam04116   
Conserved Domain (NCBI)SC5D
Blocks (Seattle)SC5D
SuperfamilyO75845
Human Protein Atlas [tissue]ENSG00000109929-SC5D [tissue]
Peptide AtlasO75845
HPRD09078
IPIIPI00027181   IPI00978882   IPI00978261   
Protein Interaction databases
DIP (DOE-UCLA)O75845
IntAct (EBI)O75845
BioGRIDSC5D
STRING (EMBL)SC5D
ZODIACSC5D
Ontologies - Pathways
QuickGOO75845
Ontology : AmiGOC-5 sterol desaturase activity  C-5 sterol desaturase activity  iron ion binding  endoplasmic reticulum membrane  endoplasmic reticulum membrane  lipid metabolic process  integral component of membrane  sterol biosynthetic process  cholesterol biosynthetic process via desmosterol  cholesterol biosynthetic process via lathosterol  cholesterol biosynthetic process via lathosterol  regulation of cholesterol biosynthetic process  oxidation-reduction process  
Ontology : EGO-EBIC-5 sterol desaturase activity  C-5 sterol desaturase activity  iron ion binding  endoplasmic reticulum membrane  endoplasmic reticulum membrane  lipid metabolic process  integral component of membrane  sterol biosynthetic process  cholesterol biosynthetic process via desmosterol  cholesterol biosynthetic process via lathosterol  cholesterol biosynthetic process via lathosterol  regulation of cholesterol biosynthetic process  oxidation-reduction process  
NDEx NetworkSC5D
Atlas of Cancer Signalling NetworkSC5D
Wikipedia pathwaysSC5D
Orthology - Evolution
OrthoDB6309
GeneTree (enSembl)ENSG00000109929
Phylogenetic Trees/Animal Genes : TreeFamSC5D
HOGENOMO75845
Homologs : HomoloGeneSC5D
Homology/Alignments : Family Browser (UCSC)SC5D
Gene fusions - Rearrangements
Fusion : QuiverSC5D
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSC5D [hg38]
dbVarSC5D
ClinVarSC5D
MonarchSC5D
1000_GenomesSC5D 
Exome Variant ServerSC5D
GNOMAD BrowserENSG00000109929
Varsome BrowserSC5D
Genomic Variants (DGV)SC5D [DGVbeta]
DECIPHERSC5D [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSC5D 
Mutations
ICGC Data PortalSC5D 
TCGA Data PortalSC5D 
Broad Tumor PortalSC5D
OASIS PortalSC5D [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSC5D  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSC5D
Mutations and Diseases : HGMDSC5D
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SC5D
DgiDB (Drug Gene Interaction Database)SC5D
DoCM (Curated mutations)SC5D (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SC5D (select a term)
intoGenSC5D
Cancer3DSC5D(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM602286    607330   
Orphanet10592   
DisGeNETSC5D
MedgenSC5D
Genetic Testing Registry SC5D
NextProtO75845 [Medical]
GENETestsSC5D
Target ValidationSC5D
Huge Navigator SC5D [HugePedia]
ClinGenSC5D
Clinical trials, drugs, therapy
MyCancerGenomeSC5D
Protein Interactions : CTD
Pharm GKB GenePA34957
Clinical trialSC5D
Miscellaneous
canSAR (ICR)SC5D (select the gene name)
HarmonizomeSC5D
DataMed IndexSC5D
Probes
Litterature
PubMed26 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSC5D
EVEXSC5D
GoPubMedSC5D
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Sat Dec 5 17:26:04 CET 2020
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