Aliases for ORMDL3 Gene

Aliases for ORMDL3 Gene

  • ORMDL Sphingolipid Biosynthesis Regulator 3 2 3 5
  • ORM1-Like Protein 3 3 4
  • ORM1 (S. Cerevisiae)-Like 3 2
  • ORM1-Like 3 (S. Cerevisiae) 2
  • ORMDL3 5

External Ids for ORMDL3 Gene

Previous GeneCards Identifiers for ORMDL3 Gene

  • GC17P037421
  • GC17U900023
  • GC17M037987
  • GC17M038452
  • GC17M035330
  • GC17M038077
  • GC17M033871

Summaries for ORMDL3 Gene

GeneCards Summary for ORMDL3 Gene

ORMDL3 (ORMDL Sphingolipid Biosynthesis Regulator 3) is a Protein Coding gene. Diseases associated with ORMDL3 include Asthma and Inflammatory Bowel Disease 22. Among its related pathways are Sphingolipid metabolism and Innate Immune System. An important paralog of this gene is ORMDL1.

UniProtKB/Swiss-Prot Summary for ORMDL3 Gene

  • Negative regulator of sphingolipid synthesis. May indirectly regulate endoplasmic reticulum-mediated Ca(+2) signaling.

Additional gene information for ORMDL3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ORMDL3 Gene

Genomics for ORMDL3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ORMDL3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J039916 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 629.8 +4.2 4232 14.4 BRCA1 SP1 HNRNPL CREB1 GATAD2A CTCF ATF7 PRDM10 REST ZNF629 ORMDL3 GSDMB lnc-GSDMB-1 lnc-LRRC3C-2 CDK12 MED1 SMARCE1 ENSG00000264968 IGFBP4 ENSG00000266208
GH17J039859 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 36.9 +63.2 63172 9.7 SP1 GATAD2A ZNF629 TFE3 ZNF512 SOX13 IKZF1 NFKBIZ CTCF POLR2A IKZF3 ZPBP2 GSDMB ORMDL3 MED24 TMEM99 MSL1 MED1 GSDMA CDK12
GH17J039753 Promoter/Enhancer 2 FANTOM5 ENCODE CraniofacialAtlas dbSUPER 20.4 +171.0 171007 7.1 ZNF221 SP1 HNRNPL CTCF PRDM10 ZNF629 NFKBIZ ZNF692 POLR2A ZNF7 GSDMB ORMDL3 THRA CDK12 IKZF3 MSL1 STARD3 MED24 MED1 SNORA21
GH17J039766 Promoter/Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 20.2 +152.7 152714 17.2 RNF2 CREB1 GATAD2A PRDM10 ZNF629 ZNF692 POLR2A ZNF174 JUND FOXA1 GSDMB MED1 ORMDL3 GSDMA SNORD124 MED24 CDK12 ERBB2 MIEN1 GRB7
GH17J039903 Enhancer 1.1 Ensembl ENCODE 25.5 +23.6 23605 2.4 GATAD2A TFE3 LEF1 SOX13 IKZF1 NFKBIZ RCOR2 DDX20 RXRB IKZF2 ORMDL3 TMEM99 MED24 MED1 GSDMA lnc-ORMDL3-1 piR-61945-206 GSDMB ZPBP2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ORMDL3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ORMDL3

Top Transcription factor binding sites by QIAGEN in the ORMDL3 gene promoter:
  • AP-4
  • c-Ets-1
  • C/EBPbeta
  • COUP
  • COUP-TF
  • COUP-TF1
  • HNF-4alpha1
  • HNF-4alpha2
  • HOXA5
  • LCR-F1

Genomic Locations for ORMDL3 Gene

Genomic Locations for ORMDL3 Gene
chr17:39,921,041-39,927,601
(GRCh38/hg38)
Size:
6,561 bases
Orientation:
Minus strand
chr17:38,077,294-38,083,884
(GRCh37/hg19)
Size:
6,591 bases
Orientation:
Minus strand

Genomic View for ORMDL3 Gene

Genes around ORMDL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ORMDL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ORMDL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ORMDL3 Gene

Proteins for ORMDL3 Gene

  • Protein details for ORMDL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N138-ORML3_HUMAN
    Recommended name:
    ORM1-like protein 3
    Protein Accession:
    Q8N138
    Secondary Accessions:
    • B3KS83
    • Q6UY83

    Protein attributes for ORMDL3 Gene

    Size:
    153 amino acids
    Molecular mass:
    17495 Da
    Quaternary structure:
    • Interacts with SPTLC1.
    Miscellaneous:
    • SNPs on 17q21 locus that are associated with childhood asthma also show a consistent and strong association with transcript levels of ORMDL3, indicating that genetic variants regulating ORMDL3 expression are determinants of susceptibility to childhood asthma.

    Alternative splice isoforms for ORMDL3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ORMDL3 Gene

Post-translational modifications for ORMDL3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ORMDL3 Gene

Domains & Families for ORMDL3 Gene

Gene Families for ORMDL3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted membrane proteins

Protein Domains for ORMDL3 Gene

InterPro:
Blocks:
  • ORMDL
ProtoNet:

Suggested Antigen Peptide Sequences for ORMDL3 Gene

GenScript: Design optimal peptide antigens:
  • ORM1-like protein 3 (ORML3_HUMAN)
  • ORM1-like 3 (S. cerevisiae), isoform CRA_a (Q9P0R7_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8N138

UniProtKB/Swiss-Prot:

ORML3_HUMAN :
  • Belongs to the ORM family.
Family:
  • Belongs to the ORM family.
genes like me logo Genes that share domains with ORMDL3: view

Function for ORMDL3 Gene

Molecular function for ORMDL3 Gene

UniProtKB/Swiss-Prot Function:
Negative regulator of sphingolipid synthesis. May indirectly regulate endoplasmic reticulum-mediated Ca(+2) signaling.

Phenotypes From GWAS Catalog for ORMDL3 Gene

Gene Ontology (GO) - Molecular Function for ORMDL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 20182505
genes like me logo Genes that share ontologies with ORMDL3: view
genes like me logo Genes that share phenotypes with ORMDL3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ORMDL3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ORMDL3 Gene

Localization for ORMDL3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ORMDL3 Gene

Endoplasmic reticulum membrane. Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ORMDL3 gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 5
extracellular 2
mitochondrion 2
nucleus 2
cytoskeleton 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ORMDL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005783 endoplasmic reticulum IDA 12093374
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with ORMDL3: view

Pathways & Interactions for ORMDL3 Gene

genes like me logo Genes that share pathways with ORMDL3: view

Pathways by source for ORMDL3 Gene

Gene Ontology (GO) - Biological Process for ORMDL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006672 ceramide metabolic process IEA,IMP 20182505
GO:0043312 neutrophil degranulation TAS --
GO:0090156 cellular sphingolipid homeostasis IEA,IBA 21873635
GO:1900060 negative regulation of ceramide biosynthetic process IMP 25691431
genes like me logo Genes that share ontologies with ORMDL3: view

No data available for SIGNOR curated interactions for ORMDL3 Gene

Drugs & Compounds for ORMDL3 Gene

No Compound Related Data Available

Transcripts for ORMDL3 Gene

mRNA/cDNA for ORMDL3 Gene

5 REFSEQ mRNAs :
21 NCBI additional mRNA sequence :
8 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ORMDL3

Alternative Splicing Database (ASD) splice patterns (SP) for ORMDL3 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b · 8c · 8d · 8e · 8f ^ 9
SP1:
SP2: - - - -
SP3: - - - -
SP4: - - - -
SP5: - - -
SP6: -
SP7: - -

Relevant External Links for ORMDL3 Gene

GeneLoc Exon Structure for
ORMDL3

Expression for ORMDL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ORMDL3 Gene

mRNA differential expression in normal tissues according to GTEx for ORMDL3 Gene

This gene is overexpressed in Liver (x5.0).

Protein differential expression in normal tissues from HIPED for ORMDL3 Gene

This gene is overexpressed in Bone (10.8) and Plasma (9.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ORMDL3 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ORMDL3

SOURCE GeneReport for Unigene cluster for ORMDL3 Gene:

Hs.514151

mRNA Expression by UniProt/SwissProt for ORMDL3 Gene:

Q8N138-ORML3_HUMAN
Tissue specificity: Widely expressed. Expressed in adult and fetal heart, brain, lung, liver, skeletal muscle and kidney. Expressed in adult pancreas and placenta and in fetal spleen abd thymus.

Evidence on tissue expression from TISSUES for ORMDL3 Gene

  • Nervous system(4.7)
  • Intestine(4.5)
  • Lung(3)
  • Liver(2.8)
  • Muscle(2.6)
  • Spleen(2.6)
  • Lymph node(2.6)
  • Skin(2.5)
  • Blood(2.5)
  • Heart(2.3)
  • Pancreas(2.3)
  • Thyroid gland(2.2)
  • Kidney(2.2)
  • Stomach(2.2)
  • Bone marrow(2.1)
genes like me logo Genes that share expression patterns with ORMDL3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for ORMDL3 Gene

Orthologs for ORMDL3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for ORMDL3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia ORMDL3 30 31
  • 99.78 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia ORMDL3 31
  • 98 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia ORMDL3 30 31
  • 93.25 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia ORMDL3 30 31
  • 92.37 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ormdl3 30
  • 91.07 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia ORMDL3 31
  • 90 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Ormdl3 30 17 31
  • 88.89 (n)
OneToOne
Chicken
(Gallus gallus)
Aves ORMDL3 30 31
  • 84.75 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia ORMDL3 31
  • 91 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii ormdl3 30 31
  • 81.92 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010566 30
  • 58.5 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta ORMDL 30 31
  • 56.58 (n)
OneToMany
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_ACL189C 30
  • 55.15 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes ORM2 30 31
  • 50.25 (n)
ManyToMany
ORM1 31 33
  • 25 (a)
ManyToMany
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0B05621g 30
  • 47.3 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 63 (a)
OneToMany
Bread mold
(Neurospora crassa)
Ascomycetes NCU11109 30
  • 50.98 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC119.09c 30
  • 48.15 (n)
Species where no ortholog for ORMDL3 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for ORMDL3 Gene

ENSEMBL:
Gene Tree for ORMDL3 (if available)
TreeFam:
Gene Tree for ORMDL3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ORMDL3: view image

Paralogs for ORMDL3 Gene

Paralogs for ORMDL3 Gene

(2) SIMAP similar genes for ORMDL3 Gene using alignment to 4 proteins:

  • ORML3_HUMAN
  • J3KTF9_HUMAN
  • J3QRM9_HUMAN
  • Q9P0R7_HUMAN

Pseudogenes.org Pseudogenes for ORMDL3 Gene

genes like me logo Genes that share paralogs with ORMDL3: view

Variants for ORMDL3 Gene

Additional dbSNP identifiers (rs#s) for ORMDL3 Gene

Structural Variations from Database of Genomic Variants (DGV) for ORMDL3 Gene

Variant ID Type Subtype PubMed ID
esv3573064 CNV gain 25503493
nsv1146669 OTHER inversion 26484159

Variation tolerance for ORMDL3 Gene

Residual Variation Intolerance Score: 37.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.17; 3.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ORMDL3 Gene

Human Gene Mutation Database (HGMD)
ORMDL3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ORMDL3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ORMDL3 Gene

Disorders for ORMDL3 Gene

MalaCards: The human disease database

(9) MalaCards diseases for ORMDL3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
asthma
  • asthma, susceptibility to
inflammatory bowel disease 22
  • ibd22
ileocolitis
  • iieocolitis
retinitis pigmentosa 26
  • rp26
bronchial disease
  • bronchospasm
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

ORML3_HUMAN
  • Asthma (ASTHMA) [MIM:600807]: The most common chronic disease affecting children and young adults. It is a complex genetic disorder with a heterogeneous phenotype, largely attributed to the interactions among many genes and between these genes and the environment. It is characterized by recurrent attacks of paroxysmal dyspnea, with wheezing due to spasmodic contraction of the bronchi. {ECO:0000269 PubMed:18395550, ECO:0000269 PubMed:18760456, ECO:0000269 PubMed:19133921}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Additional Disease Information for ORMDL3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with ORMDL3: view

No data available for Genatlas for ORMDL3 Gene

Publications for ORMDL3 Gene

  1. Genetic variation in ORM1-like 3 (ORMDL3) and gasdermin-like (GSDML) and childhood asthma. (PMID: 19133921) Wu H … London SJ (Allergy 2009) 3 4 23 41
  2. A polymorphism controlling ORMDL3 expression is associated with asthma that is poorly controlled by current medications. (PMID: 18395550) Tavendale R … Palmer CN (The Journal of allergy and clinical immunology 2008) 3 4 41
  3. ORMDL3 variants associated with asthma susceptibility in North Americans of European ancestry. (PMID: 18760456) Sleiman PM … Hakonarson H (The Journal of allergy and clinical immunology 2008) 3 4 41
  4. Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. (PMID: 17611496) Moffatt MF … Cookson WO (Nature 2007) 3 4 41
  5. Mammalian ORMDL proteins mediate the feedback response in ceramide biosynthesis. (PMID: 23066021) Siow DL … Wattenberg BW (The Journal of biological chemistry 2012) 2 3

Products for ORMDL3 Gene

Sources for ORMDL3 Gene