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

Gene ID: 94103, updated on 3-Apr-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 SPOTS complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in fat (RPKM 53.9), liver (RPKM 33.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
17q21.1
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (39921041..39927601, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (40784755..40791324, complement)
105.20220307 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. Regulation of the sensitivity of hepatocarcinoma cells by ORMDL3, to sorafenib by autophagy. Sun Y, et al. Med Oncol, 2022 Aug 16. PMID 35972600, Free PMC Article
  2. Asthma Susceptibility Gene ORMDL3 Promotes Autophagy in Human Bronchial Epithelium. Guo F, et al. Am J Respir Cell Mol Biol, 2022 Jun. PMID 35353673, Free PMC Article
  3. Increased expression of ORMDL3 in allergic asthma: a case control and in vitro study. Nowakowska J, et al. J Asthma, 2023 Mar. PMID 35321632
  4. Single cell sequencing analysis identifies genetics-modulated ORMDL3(+) cholangiocytes having higher metabolic effects on primary biliary cholangitis. Xiang B, et al. J Nanobiotechnology, 2021 Dec 6. PMID 34872583, Free PMC Article
  5. ORMDL3 overexpression facilitates FcεRI-mediated transcription of proinflammatory cytokines and thapsigargin-mediated PERK phosphorylation in RBL-2H3 cells. Ogi K, et al. Immun Inflamm Dis, 2021 Dec. PMID 34288557, Free PMC Article

See all (127) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. Asthma Susceptibility Gene ORMDL3 Promotes Autophagy in Human Bronchial Epithelium.
    Title: Asthma Susceptibility Gene ORMDL3 Promotes Autophagy in Human Bronchial Epithelium.
  6. 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.
  7. ORMDL3/GSDMB genotype is associated with distinct phenotypes of adult asthma.
    Title: ORMDL3/GSDMB genotype is associated with distinct phenotypes of adult asthma.
  8. 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.
  9. 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.
  10. ORMDL3 overexpression facilitates FcepsilonRI-mediated transcription of proinflammatory cytokines and thapsigargin-mediated PERK phosphorylation in RBL-2H3 cells.
    Title: ORMDL3 overexpression facilitates FcεRI-mediated transcription of proinflammatory cytokines and thapsigargin-mediated PERK phosphorylation in RBL-2H3 cells.
Submit: New GeneRIF Correction See all GeneRIFs (87)

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)

Genotypes

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
part_of SPOTS complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of SPOTS complex IDA
Inferred from Direct Assay
more info
 PubMed 
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
  
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_2023_10

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.

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