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SC5D sterol-C5-desaturase [ Homo sapiens (human) ]

Gene ID: 6309, updated on 3-Nov-2024

Summary

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Official Symbol
SC5Dprovided by HGNC
Official Full Name
sterol-C5-desaturaseprovided by HGNC
Primary source
HGNC:HGNC:10547
See related
Ensembl:ENSG00000109929 MIM:602286; AllianceGenome:HGNC:10547
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ERG3; S5DES; SC5DL
Summary
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]
Expression
Ubiquitous expression in liver (RPKM 29.7), prostate (RPKM 24.2) and 23 other tissues See more
Orthologs
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Genomic context

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See SC5D in Genome Data Viewer
Location:
11q23.3-q24.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (121292771..121313410)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (121317829..121338469)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (121163480..121184119)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:121117070-121117656 Neighboring gene NANOG hESC enhancer GRCh37_chr11:121119641-121120200 Neighboring gene ribosomal protein S4X pseudogene 12 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5642 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:121165985-121166526 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:121166527-121167069 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4001 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5646 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:121243330-121244107 Neighboring gene bone morphogenetic protein receptor type 1A pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:121260007-121260508 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:121260509-121261008 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:121276805-121277684 Neighboring gene NANOG hESC enhancer GRCh37_chr11:121277972-121278473 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:121297351-121297863 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5647 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5648 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5650 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5651 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4003 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5653 Neighboring gene SORL1 antisense RNA 1 Neighboring gene sortilin related receptor 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Lathosterolosis. Adam MP, et al. , 1993. PMID 38060690
  2. Evidence that liver microsomes of human neonates desaturate essential fatty acids. Poisson JP, et al. Biochim Biophys Acta, 1993 Apr 7. PMID 8466936
  3. Molecular cloning and mapping of a human cDNA (SC5DL) encoding a protein homologous to fungal sterol-C5-desaturase. Matsushima M, et al. Cytogenet Cell Genet, 1996. PMID 8976377
  4. Relationship between Body Mass Index, C-Peptide, and Delta-5-Desaturase Enzyme Activity Estimates in Adult Males. Pickens CA, et al. PLoS One, 2016. PMID 27023786, Free PMC Article
  5. 7-Dehydrocholesterol dictates ferroptosis sensitivity. Li Y, et al. Nature, 2024 Feb. PMID 38297130, Free PMC Article

See all (37) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The relationship between C-peptide concentrations and D5D enzyme activity estimates remained significant after adjusting for body mass index, waist circumference, and TNF-alpha.
    Title: Relationship between Body Mass Index, C-Peptide, and Delta-5-Desaturase Enzyme Activity Estimates in Adult Males.
  2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  3. The EGR3 may not play a major role in schizophrenia susceptibility in the Chinese Han population.
    Title: No association between EGR gene family polymorphisms and schizophrenia in the Chinese population.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Lathosterolosis
MedGen: C1846421 OMIM: 607330 GeneReviews: Lathosterolosis
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables C-5 sterol desaturase activity EXP
Inferred from Experiment
more info
 PubMed 
enables C-5 sterol desaturase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables delta7-sterol 5(6)-desaturase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables iron ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cholesterol biosynthetic process via desmosterol TAS
Traceable Author Statement
more info
  
involved_in cholesterol biosynthetic process via lathosterol IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cholesterol biosynthetic process via lathosterol IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cholesterol biosynthetic process via lathosterol TAS
Traceable Author Statement
more info
  
involved_in negative regulation of ferroptosis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
lathosterol oxidase
Names
3beta-hydroxysteroid-delta5-desaturase
C-5 sterol desaturase
delta(7)-sterol 5(6)-desaturase
delta(7)-sterol 5-desaturase
delta(7)-sterol C5(6)-desaturase
fungal ERG3, delta-5-desaturase-like
lathosterol 5-desaturase
lathosterol dehydrogenase
sterol-C5-desaturase (ERG3 delta-5-desaturase homolog, S. cerevisiae)-like
NP_001020127.1
NP_008849.2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009446.1 RefSeqGene

    Range
    5093..25732
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001024956.3 → NP_001020127.1  lathosterol oxidase

    See identical proteins and their annotated locations for NP_001020127.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate 5' exon compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AP002959, BC012333
    Consensus CDS
    CCDS8435.1
    UniProtKB/Swiss-Prot
    O00119, O75845, Q6GTM5, Q9UK15
    Related
    ENSP00000376539.2, ENST00000392789.2
    Conserved Domains (1) summary
    COG3000
    Location:34 → 257
    ERG3; Sterol desaturase/sphingolipid hydroxylase, fatty acid hydroxylase superfamily [Lipid transport and metabolism]

  2. NM_006918.5 → NP_008849.2  lathosterol oxidase

    See identical proteins and their annotated locations for NP_008849.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AK223141, AP002959
    Consensus CDS
    CCDS8435.1
    UniProtKB/Swiss-Prot
    O00119, O75845, Q6GTM5, Q9UK15
    Related
    ENSP00000264027.4, ENST00000264027.9
    Conserved Domains (1) summary
    COG3000
    Location:34 → 257
    ERG3; Sterol desaturase/sphingolipid hydroxylase, fatty acid hydroxylase superfamily [Lipid transport and metabolism]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    121292771..121313410
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    121317829..121338469
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75845.2 GenPept UniProtKB/Swiss-Prot:O75845

Gene LinkOut

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