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DEGS2 delta 4-desaturase, sphingolipid 2 [ Homo sapiens (human) ]

Gene ID: 123099, updated on 5-Mar-2024

Summary

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Official Symbol
DEGS2provided by HGNC
Official Full Name
delta 4-desaturase, sphingolipid 2provided by HGNC
Primary source
HGNC:HGNC:20113
See related
Ensembl:ENSG00000168350 MIM:610862; AllianceGenome:HGNC:20113
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
DES2; FADS8; C14orf66
Summary
This gene encodes a bifunctional enzyme that is involved in the biosynthesis of phytosphingolipids in human skin and in other phytosphingolipid-containing tissues. This enzyme can act as a sphingolipid delta(4)-desaturase, and also as a sphingolipid C4-hydroxylase. [provided by RefSeq, Oct 2008]
Expression
Biased expression in small intestine (RPKM 14.4), duodenum (RPKM 11.1) and 13 other tissues See more
Orthologs
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Genomic context

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See DEGS2 in Genome Data Viewer
Location:
14q32.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (100143957..100166886, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (94377005..94399934, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (100610294..100625982, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene Enah/Vasp-like Neighboring gene uncharacterized LOC124903381 Neighboring gene microRNA 342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100605397-100606101 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100604691-100605396 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100611023-100611523 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9025 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100613080-100613600 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:100613601-100614119 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6073 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6074 Neighboring gene uncharacterized LOC124903380 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100632407-100632908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100632909-100633408 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6075 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6076 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6077 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:100680080-100680580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9029 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100684247-100684748 Neighboring gene Sharpr-MPRA regulatory region 8458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100698662-100699162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100699163-100699663 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:100704543-100705395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6081 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6082 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6083 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:100711928-100712136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:100744670-100745650 Neighboring gene YY1 transcription factor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6085 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6086 Neighboring gene solute carrier family 25 member 29 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9033 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:100771717-100772283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6087 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6088 Neighboring gene microRNA 6764

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
  • 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. DEGS2 polymorphism associated with cognition in schizophrenia is associated with gene expression in brain. Ohi K, et al. Transl Psychiatry, 2015 Apr 14. PMID 25871975, Free PMC Article
  2. Identification of the human sphingolipid C4-hydroxylase, hDES2, and its up-regulation during keratinocyte differentiation. Mizutani Y, et al. FEBS Lett, 2004 Apr 9. PMID 15063729
  3. Bifunctional DEGS2 has higher hydroxylase activity toward substrates with very-long-chain fatty acids in the production of phytosphingosine ceramides. Ota A, et al. J Biol Chem, 2023 Apr. PMID 36907437, Free PMC Article
  4. Dihydroceramide-based response to hypoxia. Devlin CM, et al. J Biol Chem, 2011 Nov 4. PMID 21914808, Free PMC Article
  5. GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease. Aouizerat BE, et al. BMC Cardiovasc Disord, 2011 Jun 10. PMID 21658281, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Bifunctional DEGS2 has higher hydroxylase activity toward substrates with very-long-chain fatty acids in the production of phytosphingosine ceramides.
    Title: Bifunctional DEGS2 has higher hydroxylase activity toward substrates with very-long-chain fatty acids in the production of phytosphingosine ceramides.
  2. Findings demonstrate that a SNP showing genome-wide association study significant association with cognition in schizophrenia is also associated with regulation of DEGS2 expression, implicating a molecular mechanism for the clinical association.
    Title: DEGS2 polymorphism associated with cognition in schizophrenia is associated with gene expression in brain.
  3. overexpression of DEGS1 or DEGS2 attenuates the DHC accumulation and increased cell proliferation during hypoxia
    Title: Dihydroceramide-based response to hypoxia.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: An approach based on a genome-wide association study reveals candidate loci for narcolepsy.
  5. DES2 was identified and its up-regulation followed during keratinocyte differentiation.
    Title: Identification of the human sphingolipid C4-hydroxylase, hDES2, and its up-regulation during keratinocyte differentiation.
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

EBI GWAS Catalog

Description
GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease.
EBI GWAS Catalog

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 sphingolipid C4-monooxygenase activity IEA
Inferred from Electronic Annotation
more info
  
enables sphingolipid delta-4 desaturase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables sphingosine hydroxylase activity TAS
Traceable Author Statement
more info
  
Process Evidence Code Pubs
involved_in ceramide biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in sphinganine metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in sphingolipid biosynthetic process TAS
Traceable Author Statement
more info
  
Component Evidence Code Pubs
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
sphingolipid delta(4)-desaturase/C4-monooxygenase DES2
Names
degenerative spermatocyte homolog 2, lipid desaturase
dihydroceramide desaturase 2
sphingolipid 4-desaturase
sphingolipid C4-hydroxylase/delta 4-desaturase
sphingolipid C4-monooxygenase
sphingolipid delta 4 desaturase/C-4 hydroxylase
sphingolipid delta(4)-desaturase 2
sphingolipid delta(4)-desaturase/C4-hydroxylase DES2
NP_996801.2
XP_006720106.1
XP_054231403.1

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.

mRNA and Protein(s)

  1. NM_206918.3 → NP_996801.2  sphingolipid delta(4)-desaturase/C4-monooxygenase DES2

    See identical proteins and their annotated locations for NP_996801.2

    Status: REVIEWED

    Source sequence(s)
    AI380009, AL133523, AY541700, BC063598, BM789564
    Consensus CDS
    CCDS9956.1
    UniProtKB/Swiss-Prot
    Q6P492, Q6QHC5
    Related
    ENSP00000307126.5, ENST00000305631.7
    Conserved Domains (2) summary
    cd03508
    Location:26 → 314
    Delta4-sphingolipid-FADS-like; The Delta4-sphingolipid Fatty Acid Desaturase (Delta4-sphingolipid-FADS)-like CD includes the integral-membrane enzymes, dihydroceramide Delta-4 desaturase, involved in the synthesis of sphingosine; and the human membrane fatty acid (lipid) desaturase ...
    pfam08557
    Location:6 → 42
    Lipid_DES; Sphingolipid Delta4-desaturase (DES)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    100143957..100166886 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006720043.4 → XP_006720106.1  sphingolipid delta(4)-desaturase/C4-monooxygenase DES2 isoform X1

    See identical proteins and their annotated locations for XP_006720106.1

    Conserved Domains (2) summary
    cd03508
    Location:1 → 278
    Delta4-sphingolipid-FADS-like; The Delta4-sphingolipid Fatty Acid Desaturase (Delta4-sphingolipid-FADS)-like CD includes the integral-membrane enzymes, dihydroceramide Delta-4 desaturase, involved in the synthesis of sphingosine; and the human membrane fatty acid (lipid) desaturase ...
    pfam00487
    Location:32 → 258
    FA_desaturase; Fatty acid desaturase

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    94377005..94399934 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054375428.1 → XP_054231403.1  sphingolipid delta(4)-desaturase/C4-monooxygenase DES2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6QHC5.2 GenPept UniProtKB/Swiss-Prot:Q6QHC5

Gene LinkOut

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