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    ORMDL3 ORMDL sphingolipid biosynthesis regulator 3 [ Homo sapiens (human) ]

    Gene ID: 94103, updated on 27-Nov-2024

    Summary

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    Official Symbol
    ORMDL3provided by HGNC
    Official Full Name
    ORMDL sphingolipid biosynthesis regulator 3provided by HGNC
    Primary source
    HGNC:HGNC:16038
    See related
    Ensembl:ENSG00000172057 MIM:610075; AllianceGenome:HGNC:16038
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Involved in ceramide metabolic process. Acts upstream of or within several processes, including negative regulation of B cell apoptotic process; negative regulation of ceramide biosynthetic process; and positive regulation of protein localization to nucleus. Located in endoplasmic reticulum. Part of serine palmitoyltransferase complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in fat (RPKM 53.9), liver (RPKM 33.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ORMDL3 in Genome Data Viewer
    Location:
    17q21.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (39921041..39927601, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (40784755..40791324, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (38077294..38083854, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene zona pellucida binding protein 2 Neighboring gene gasdermin B Neighboring gene GSDMB 5' regulatory region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:38079584-38080370 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:38080371-38081156 Neighboring gene uncharacterized LOC124903999 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38083108-38083718 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:38083719-38084330 Neighboring gene leucine rich repeat containing 3C Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12119 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8469 Neighboring gene gasdermin A

    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. Orosomucoid-like 3 (ORMDL3) upregulates airway smooth muscle proliferation, contraction, and Ca(2+) oscillations in asthma. Chen J, et al. J Allergy Clin Immunol, 2018 Jul. PMID 28889952, Free PMC Article
    2. ORMDL3 modulates store-operated calcium entry and lymphocyte activation. Carreras-Sureda A, et al. Hum Mol Genet, 2013 Feb 1. PMID 23100328
    3. Variants in the 17q21 asthma susceptibility locus are associated with allergic rhinitis in the Japanese population. Tomita K, et al. Allergy, 2013 Jan. PMID 23157251
    4. Association between peripheral blood mononuclear cell ORMDL3 expression and the asthma predictive index in preschool children. Li Y, et al. J Int Med Res, 2019 Aug. PMID 31342811, Free PMC Article
    5. A polymorphism in ORMDL3 is associated not only with asthma without rhinitis but also with chronic obstructive pulmonary disease. Balantic M, et al. J Investig Allergol Clin Immunol, 2013. PMID 23964555

    See all (130) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ORMDL3 regulates NLRP3 inflammasome activation by maintaining ER-mitochondria contacts in human macrophages and dictates ulcerative colitis patient outcome.
      Title: ORMDL3 regulates NLRP3 inflammasome activation by maintaining ER-mitochondria contacts in human macrophages and dictates ulcerative colitis patient outcome.
    2. Histone acetylation regulates ORMDL3 expression-mediated NLRP3 inflammasome overexpression during RSV-allergic exacerbation mice.
      Title: Histone acetylation regulates ORMDL3 expression-mediated NLRP3 inflammasome overexpression during RSV-allergic exacerbation mice.
    3. Evaluation of the association between clinical parameters and ADAM33 and ORMDL3 asthma gene single-nucleotide polymorphisms with the severity of COVID-19.
      Title: Evaluation of the association between clinical parameters and ADAM33 and ORMDL3 asthma gene single-nucleotide polymorphisms with the severity of COVID-19.
    4. Increased expression of ORMDL3 in allergic asthma: a case control and in vitro study.
      Title: Increased expression of ORMDL3 in allergic asthma: a case control and in vitro study.
    5. Regulation of the sensitivity of hepatocarcinoma cells by ORMDL3, to sorafenib by autophagy.
      Title: Regulation of the sensitivity of hepatocarcinoma cells by ORMDL3, to sorafenib by autophagy.
    6. Asthma Susceptibility Gene ORMDL3 Promotes Autophagy in Human Bronchial Epithelium.
      Title: Asthma Susceptibility Gene ORMDL3 Promotes Autophagy in Human Bronchial Epithelium.
    7. Single cell sequencing analysis identifies genetics-modulated ORMDL3(+) cholangiocytes having higher metabolic effects on primary biliary cholangitis.
      Title: Single cell sequencing analysis identifies genetics-modulated ORMDL3(+) cholangiocytes having higher metabolic effects on primary biliary cholangitis.
    8. ORMDL3/GSDMB genotype is associated with distinct phenotypes of adult asthma.
      Title: ORMDL3/GSDMB genotype is associated with distinct phenotypes of adult asthma.
    9. High-resolution targeted bisulfite sequencing reveals blood cell type-specific DNA methylation patterns in IL13 and ORMDL3.
      Title: High-resolution targeted bisulfite sequencing reveals blood cell type-specific DNA methylation patterns in IL13 and ORMDL3.
    10. ORMDL3 expression in ASM regulates hypertrophy, hyperplasia via TPM1 and TPM4, and contractility.
      Title: ORMDL3 expression in ASM regulates hypertrophy, hyperplasia via TPM1 and TPM4, and contractility.
    Submit: New GeneRIF Correction See all GeneRIFs (88)

    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 meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.
    EBI GWAS Catalog
    Association between ORMDL3, IL1RL1 and a deletion on chromosome 17q21 with asthma risk in Australia.
    EBI GWAS Catalog
    Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma.
    EBI GWAS Catalog
    Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases.
    EBI GWAS Catalog
    Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.
    EBI GWAS Catalog
    Genome-wide association identifies multiple ulcerative colitis susceptibility loci.
    EBI GWAS Catalog
    Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes.
    EBI GWAS Catalog
    Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis.
    EBI GWAS Catalog
    Genome-wide association study identifies TNFSF15 and POU2AF1 as susceptibility loci for primary biliary cirrhosis in the Japanese population.
    EBI GWAS Catalog
    Genome-wide association study to identify genetic determinants of severe asthma.
    EBI GWAS Catalog
    Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis.
    EBI GWAS Catalog
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
    EBI GWAS Catalog
    Multiple loci are associated with white blood cell phenotypes.
    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)

    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in ceramide metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in ceramide metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in intracellular sphingolipid homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in motor behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in myelination IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within negative regulation of B cell apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of ceramide biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of autophagy IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of autophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of protein localization to nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of smooth muscle contraction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in sphingolipid biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in sphingomyelin biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in secretory granule membrane TAS
    Traceable Author Statement
    more info
    		  
    part_of serine palmitoyltransferase complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of serine palmitoyltransferase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in specific granule membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    ORM1-like protein 3

    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_001320801.2 → NP_001307730.1  ORM1-like protein 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1 through 4 encode the same protein.
      Source sequence(s)
      AC090844, AF373101, AK093063, DB054498
      Consensus CDS
      CCDS11355.1
      UniProtKB/Swiss-Prot
      B3KS83, Q6UY83, Q8N138
      UniProtKB/TrEMBL
      J3QRM9
      Related
      ENSP00000377724.1, ENST00000394169.5
      Conserved Domains (1) summary
      pfam04061
      Location:11 → 146
      ORMDL; ORMDL family

    2. NM_001320802.2 → NP_001307731.1  ORM1-like protein 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 through 4 encode the same protein.
      Source sequence(s)
      AC090844, BC071833, HY004453
      Consensus CDS
      CCDS11355.1
      UniProtKB/Swiss-Prot
      B3KS83, Q6UY83, Q8N138
      UniProtKB/TrEMBL
      J3QRM9
      Related
      ENSP00000464693.1, ENST00000579695.5
      Conserved Domains (1) summary
      pfam04061
      Location:11 → 146
      ORMDL; ORMDL family

    3. NM_001320803.1 → NP_001307732.1  ORM1-like protein 3

      Status: VALIDATED

      Source sequence(s)
      AC090844, AF373101, BU633754, DB042662, DB054498
      Consensus CDS
      CCDS11355.1
      UniProtKB/Swiss-Prot
      B3KS83, Q6UY83, Q8N138
      UniProtKB/TrEMBL
      J3QRM9
      Related
      ENSP00000464298.1, ENST00000584000.1
      Conserved Domains (1) summary
      pfam04061
      Location:11 → 146
      ORMDL; ORMDL family

    4. NM_139280.4 → NP_644809.1  ORM1-like protein 3

      See identical proteins and their annotated locations for NP_644809.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 through 4 encode the same protein.
      Source sequence(s)
      AC090844, AF373101, HY004453
      Consensus CDS
      CCDS11355.1
      UniProtKB/Swiss-Prot
      B3KS83, Q6UY83, Q8N138
      UniProtKB/TrEMBL
      J3QRM9
      Related
      ENSP00000304858.2, ENST00000304046.7
      Conserved Domains (1) summary
      pfam04061
      Location:11 → 146
      ORMDL; ORMDL family

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      39921041..39927601 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047437093.1 → XP_047293049.1  ORM1-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KS83, Q6UY83, Q8N138

    2. XM_047437094.1 → XP_047293050.1  ORM1-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KS83, Q6UY83, Q8N138

    3. XM_047437095.1 → XP_047293051.1  ORM1-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KS83, Q6UY83, Q8N138
      Related
      ENSP00000464455.1, ENST00000584220.5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      40784755..40791324 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054317832.1 → XP_054173807.1  ORM1-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KS83, Q6UY83, Q8N138

    2. XM_054317833.1 → XP_054173808.1  ORM1-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KS83, Q6UY83, Q8N138

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_016471.2: Suppressed sequence

      Description
      NM_016471.2: This RefSeq was removed because it is primarily UTR sequence.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N138.1 GenPept UniProtKB/Swiss-Prot:Q8N138

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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