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    FADS2 fatty acid desaturase 2 [ Homo sapiens (human) ]

    Gene ID: 9415, updated on 10-Dec-2024

    Summary

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    Official Symbol
    FADS2provided by HGNC
    Official Full Name
    fatty acid desaturase 2provided by HGNC
    Primary source
    HGNC:HGNC:3575
    See related
    Ensembl:ENSG00000134824 MIM:606149; AllianceGenome:HGNC:3575
    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
    D6D; DES6; TU13; FADSD6; LLCDL2; SLL0262
    Summary
    The protein encoded by this gene is a member of the fatty acid desaturase (FADS) gene family. Desaturase enzymes regulate unsaturation of fatty acids through the introduction of double bonds between defined carbons of the fatty acyl chain. FADS family members are considered fusion products composed of an N-terminal cytochrome b5-like domain and a C-terminal multiple membrane-spanning desaturase portion, both of which are characterized by conserved histidine motifs. This gene is clustered with family members at 11q12-q13.1; this cluster is thought to have arisen evolutionarily from gene duplication based on its similar exon/intron organization. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]
    Expression
    Broad expression in adrenal (RPKM 104.8), brain (RPKM 64.0) and 16 other tissues See more
    Orthologs
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    Genomic context

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    See FADS2 in Genome Data Viewer
    Location:
    11q12.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (61816203..61867354)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (61805120..61856305)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (61583675..61634826)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr11:61559319-61560296 and GRCh37_chr11:61560297-61561272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61562818-61563318 Neighboring gene flap structure-specific endonuclease 1 Neighboring gene fatty acid desaturase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3399 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61582779-61583676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3400 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3401 Neighboring gene uncharacterized LOC124902680 Neighboring gene microRNA 1908 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61594111-61594788 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61594789-61595466 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3403 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3404 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61600847-61601714 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61601715-61602582 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61602583-61603450 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61606205-61606762 Neighboring gene CRISPR perturbation-validated FADS1 cis-regulatory element TAD5.SE2.HS2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:61615048-61615548 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:61615549-61616049 Neighboring gene uncharacterized LOC124902679 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61624465-61624966 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:61628720-61629220 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:61629221-61629721 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:61642149-61642697 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61646639-61647348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61655245-61655746 Neighboring gene fatty acid desaturase 3 Neighboring gene microRNA 6746 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61657348-61658037 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:61658038-61658726 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3407 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:61666908-61667879 Neighboring gene RAB3A interacting protein like 1 Neighboring gene Sharpr-MPRA regulatory region 8487 Neighboring gene RNA, U6 small nuclear 1243, pseudogene

    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. Effects of the rs3834458 Single Nucleotide Polymorphism in FADS2 on Levels of n-3 Long-chain Polyunsaturated Fatty Acids: A Meta-analysis. Chen X, et al. Prostaglandins Leukot Essent Fatty Acids, 2019 Nov. PMID 31487670
    2. Moderation of breastfeeding effects on the IQ by genetic variation in fatty acid metabolism. Caspi A, et al. Proc Natl Acad Sci U S A, 2007 Nov 20. PMID 17984066, Free PMC Article
    3. Lower polyunsaturated fatty acid levels and FADS2 expression in adult compared to neonatal keratinocytes are associated with FADS2 promotor hypermethylation. Pararasa C, et al. Biochem Biophys Res Commun, 2022 Apr 23. PMID 35219001, Free PMC Article
    4. Characterization of a novel FADS2 transcript variant: implications for D6D activity regulation in cells. Marks KA, et al. Biochem Cell Biol, 2021 Dec. PMID 34738827
    5. FADS2 function loss at the cancer hotspot 11q13 locus diverts lipid signaling precursor synthesis to unusual eicosanoid fatty acids. Park WJ, et al. PLoS One, 2011. PMID 22140540, Free PMC Article

    See all (245) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. High Frequency of Ancestral Haplotype A of Fatty Acid Desaturase Genes in the Yakut Population.
      Title: High Frequency of Ancestral Haplotype A of Fatty Acid Desaturase Genes in the Yakut Population.
    2. FADS1/2 control lipid metabolism and ferroptosis susceptibility in triple-negative breast cancer.
      Title: FADS1/2 control lipid metabolism and ferroptosis susceptibility in triple-negative breast cancer.
    3. FADS2 confers SCD1 inhibition resistance to cancer cells by modulating the ER stress response.
      Title: FADS2 confers SCD1 inhibition resistance to cancer cells by modulating the ER stress response.
    4. Impact of FADS genotype on polyunsaturated fatty acid content in human milk extracellular vesicles: A genetic association study.
      Title: Impact of FADS genotype on polyunsaturated fatty acid content in human milk extracellular vesicles: A genetic association study.
    5. Brain tissue- and cell type-specific eQTL Mendelian randomization reveals efficacy of FADS1 and FADS2 on cognitive function.
      Title: Brain tissue- and cell type-specific eQTL Mendelian randomization reveals efficacy of FADS1 and FADS2 on cognitive function.
    6. Hsa_circ_0000073 promotes lipid synthesis of osteosarcoma through hsa-miR-1184/ FADS2 pathway.
      Title: Hsa_circ_0000073 promotes lipid synthesis of osteosarcoma through hsa-miR-1184/ FADS2 pathway.
    7. Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus.
      Title: Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus.
    8. Placental expression of Fatty Acid Desaturases 1, 2 and 3 in selected pregnancy pathologies.
      Title: Placental expression of Fatty Acid Desaturases 1, 2 and 3 in selected pregnancy pathologies.
    9. The role of fatty acid desaturase 2 in multiple tumor types revealed by bulk and single-cell transcriptomes.
      Title: The role of fatty acid desaturase 2 in multiple tumor types revealed by bulk and single-cell transcriptomes.
    10. The integrative panel of fatty acid desaturase-2 (FADS2) rs174583 gene polymorphism and dietary indices (DQI-I and HEI) affects cardiovascular risk factors among obese individuals.
      Title: The integrative panel of fatty acid desaturase-2 (FADS2) rs174583 gene polymorphism and dietary indices (DQI-I and HEI) affects cardiovascular risk factors among obese individuals.
    Submit: New GeneRIF Correction See all GeneRIFs (155)

    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
    A genome-wide association study of the metabolic syndrome in Indian Asian men.
    EBI GWAS Catalog
    An atlas of genetic influences on human blood metabolites.
    EBI GWAS Catalog
    Biological, clinical and population relevance of 95 loci for blood lipids.
    EBI GWAS Catalog
    Bivariate genome-wide association study suggests fatty acid desaturase genes and cadherin DCHS2 for variation of both compressive strength index and appendicular lean mass in males.
    EBI GWAS Catalog
    Common variants at 30 loci contribute to polygenic dyslipidemia.
    EBI GWAS Catalog
    Discovery and refinement of loci associated with lipid levels.
    EBI GWAS Catalog
    Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.
    EBI GWAS Catalog
    Genetic determinants of P wave duration and PR segment.
    EBI GWAS Catalog
    Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium.
    EBI GWAS Catalog
    Genetic variants associated with glycine metabolism and their role in insulin sensitivity and type 2 diabetes.
    EBI GWAS Catalog
    Genetics of rheumatoid arthritis contributes to biology and drug discovery.
    EBI GWAS Catalog
    Genome-wide association analysis of metabolic traits in a birth cohort from a founder population.
    EBI GWAS Catalog
    Genome-wide association of lipid-lowering response to statins in combined study populations.
    EBI GWAS Catalog
    Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
    EBI GWAS Catalog
    Genome-wide association study identifies multiple loci influencing human serum metabolite levels.
    EBI GWAS Catalog
    Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.
    EBI GWAS Catalog
    Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortiu
    EBI GWAS Catalog
    Genome-wide association study identifies three susceptibility loci for laryngeal squamous cell carcinoma in the Chinese population.
    EBI GWAS Catalog
    Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk.
    EBI GWAS Catalog
    Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts.
    EBI GWAS Catalog
    Multiple nonglycemic genomic loci are newly associated with blood level of glycated hemoglobin in East Asians.
    EBI GWAS Catalog
    Novel loci affecting iron homeostasis and their effects in individuals at risk for hemochromatosis.
    EBI GWAS Catalog
    Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
    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)

    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 linoleoyl-CoA desaturase activity TAS
    Traceable Author Statement
    more info
    		  
    enables oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables stearoyl-CoA 9-desaturase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in alpha-linolenic acid metabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in arachidonate metabolite production involved in inflammatory response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in linoleic acid metabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in lipid metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of cellular response to oxidative stress IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in unsaturated fatty acid biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane HDA PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    acyl-CoA 6-desaturase
    Names
    delta-6 fatty acid desaturase
    delta-6-desaturase
    linoleoyl-CoA desaturase (delta-6-desaturase)-like 2
    NP_001268430.1
    NP_001268431.1
    NP_004256.1
    XP_047283845.1
    XP_054226518.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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_001281501.1 → NP_001268430.1  acyl-CoA 6-desaturase isoform 2 precursor

      See identical proteins and their annotated locations for NP_001268430.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AA665550, AF084559, AF108658, AK290291, HY090295
      Consensus CDS
      CCDS60807.1
      UniProtKB/Swiss-Prot
      O95864
      Related
      ENSP00000257261.6, ENST00000257261.10
      Conserved Domains (2) summary
      cd03506
      Location:140 → 390
      Delta6-FADS-like; The Delta6 Fatty Acid Desaturase (Delta6-FADS)-like CD includes the integral-membrane enzymes: delta-4, delta-5, delta-6, delta-8, delta-8-sphingolipid, and delta-11 desaturases found in vertebrates, higher plants, fungi, and bacteria. These desaturases ...
      pfam00487
      Location:135 → 396
      FA_desaturase; Fatty acid desaturase

    2. NM_001281502.1 → NP_001268431.1  acyl-CoA 6-desaturase isoform 3

      See identical proteins and their annotated locations for NP_001268431.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AA665550, AF084559, AK299762
      Consensus CDS
      CCDS60808.1
      UniProtKB/Swiss-Prot
      O95864
      Related
      ENSP00000429500.1, ENST00000522056.5
      Conserved Domains (2) summary
      cd03506
      Location:131 → 381
      Delta6-FADS-like; The Delta6 Fatty Acid Desaturase (Delta6-FADS)-like CD includes the integral-membrane enzymes: delta-4, delta-5, delta-6, delta-8, delta-8-sphingolipid, and delta-11 desaturases found in vertebrates, higher plants, fungi, and bacteria. These desaturases ...
      pfam00487
      Location:126 → 387
      FA_desaturase; Fatty acid desaturase

    3. NM_004265.4 → NP_004256.1  acyl-CoA 6-desaturase isoform 1

      See identical proteins and their annotated locations for NP_004256.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AA665550, AF084559
      Consensus CDS
      CCDS8012.1
      UniProtKB/Swiss-Prot
      A8K2M6, B7Z634, O95864, Q6MZQ7, Q96H07, Q96SV8, Q9H3G3, Q9Y3X4
      Related
      ENSP00000278840.4, ENST00000278840.9
      Conserved Domains (2) summary
      cd03506
      Location:162 → 412
      Delta6-FADS-like; The Delta6 Fatty Acid Desaturase (Delta6-FADS)-like CD includes the integral-membrane enzymes: delta-4, delta-5, delta-6, delta-8, delta-8-sphingolipid, and delta-11 desaturases found in vertebrates, higher plants, fungi, and bacteria. These desaturases ...
      cl27737
      Location:1 → 432
      CYB5; Cytochrome b involved in lipid metabolism [Energy production and conversion, 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
      61816203..61867354
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047427889.1 → XP_047283845.1  acyl-CoA 6-desaturase isoform X1

      UniProtKB/Swiss-Prot
      A8K2M6, B7Z634, O95864, Q6MZQ7, Q96H07, Q96SV8, Q9H3G3, Q9Y3X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      61805120..61856305
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054370543.1 → XP_054226518.1  acyl-CoA 6-desaturase isoform X1

      UniProtKB/Swiss-Prot
      A8K2M6, B7Z634, O95864, Q6MZQ7, Q96H07, Q96SV8, Q9H3G3, Q9Y3X4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95864.1 GenPept UniProtKB/Swiss-Prot:O95864

    Gene LinkOut

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