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

    Gene ID: 94103, updated on 3-Dec-2024

    Summary

    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
    NEW
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    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    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
     

    NCBI Reference Sequences (RefSeq)

    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_001320801.2NP_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:11146
      ORMDL; ORMDL family
    2. NM_001320802.2NP_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:11146
      ORMDL; ORMDL family
    3. NM_001320803.1NP_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:11146
      ORMDL; ORMDL family
    4. NM_139280.4NP_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:11146
      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_047437093.1XP_047293049.1  ORM1-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KS83, Q6UY83, Q8N138
      UniProtKB/TrEMBL
      J3QRM9
    2. XM_047437094.1XP_047293050.1  ORM1-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KS83, Q6UY83, Q8N138
      UniProtKB/TrEMBL
      J3QRM9
    3. XM_047437095.1XP_047293051.1  ORM1-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KS83, Q6UY83, Q8N138
      UniProtKB/TrEMBL
      J3QRM9
      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_054317832.1XP_054173807.1  ORM1-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KS83, Q6UY83, Q8N138
      UniProtKB/TrEMBL
      J3QRM9
    2. XM_054317833.1XP_054173808.1  ORM1-like protein 3 isoform X1

      UniProtKB/Swiss-Prot
      B3KS83, Q6UY83, Q8N138
      UniProtKB/TrEMBL
      J3QRM9

    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.