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

Gene ID: 94103, updated on 7-Jun-2020

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
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
Expression
Ubiquitous expression in fat (RPKM 53.9), liver (RPKM 33.4) and 25 other tissues See more
Orthologs

Genomic context

See ORMDL3 in Genome Data Viewer
Location:
17q21.1
Exon count:
7
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (39921041..39927601, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (38077294..38083884, 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 uncharacterized LOC112268187 Neighboring gene leucine rich repeat containing 3C 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

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cellular sphingolipid homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ceramide metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ceramide metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of ceramide biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of ceramide biosynthetic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
neutrophil degranulation TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
SPOTS complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
SPOTS complex IDA
Inferred from Direct Assay
more info
PubMed 
endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
secretory granule membrane TAS
Traceable Author Statement
more info
 
specific granule membrane TAS
Traceable Author Statement
more info
 

NCBI Reference Sequences (RefSeq)

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_001320801.1NP_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, BU633754, DB054498
    Consensus CDS
    CCDS11355.1
    UniProtKB/Swiss-Prot
    Q8N138
    UniProtKB/TrEMBL
    A0A024R1W6
    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
    Q8N138
    UniProtKB/TrEMBL
    A0A024R1W6
    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

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1 through 4 encode the same protein.
    Source sequence(s)
    AC090844, AF373101, BU633754, DB042662, DB054498
    Consensus CDS
    CCDS11355.1
    UniProtKB/Swiss-Prot
    Q8N138
    UniProtKB/TrEMBL
    A0A024R1W6
    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
    Q8N138
    UniProtKB/TrEMBL
    A0A024R1W6
    Related
    ENSP00000304858.2, ENST00000304046.7
    Conserved Domains (1) summary
    pfam04061
    Location:11146
    ORMDL; ORMDL family

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

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

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.
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