OLIG3

gene
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Also known as Bhlhb7bHLHe20

Summary

OLIG3 (oligodendrocyte transcription factor 3, HGNC:18003) is a protein-coding gene on chromosome 6q23.3, encoding Oligodendrocyte transcription factor 3 (Q7RTU3). May determine the distinct specification program of class A neurons in the dorsal part of the spinal cord and suppress specification of class B neurons.

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in axon development; positive regulation of transcription by RNA polymerase II; and sensory organ development. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II; spinal cord motor neuron cell fate specification; and spinal cord motor neuron migration. Predicted to be located in chromatin. Predicted to be active in nucleus.

Source: NCBI Gene 167826 — RefSeq curated summary.

At a glance

  • GWAS associations: 21
  • Clinical variants (ClinVar): 44 total
  • MANE Select transcript: NM_175747

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18003
Approved symbolOLIG3
Nameoligodendrocyte transcription factor 3
Location6q23.3
Locus typegene with protein product
StatusApproved
AliasesBhlhb7, bHLHe20
Ensembl geneENSG00000177468
Ensembl biotypeprotein_coding
OMIM609323
Entrez167826

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000367734

RefSeq mRNA: 1 — MANE Select: NM_175747 NM_175747

CCDS: CCDS5186

Canonical transcript exons

ENST00000367734 — 1 exons

ExonStartEnd
ENSE00001445513137492199137494394

Expression profiles

Bgee: expression breadth broad, 15 present calls, max score 53.55.

FANTOM5 (CAGE): breadth broad, TPM avg 2.3116 / max 169.6180, expressed in 191 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
758232.3116191

Top tissues by expression

237 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
islet of LangerhansUBERON:000000653.55gold quality
cerebellar vermisUBERON:000472049.48gold quality
thymusUBERON:000237044.46gold quality
lower lobe of lungUBERON:000894943.40silver quality
skeletal muscle tissue of rectus abdominisUBERON:000451143.37gold quality
amniotic fluidUBERON:000017342.81gold quality
secondary oocyteCL:000065542.57gold quality
quadriceps femorisUBERON:000137742.30gold quality
vastus lateralisUBERON:000137941.41gold quality
superficial temporal arteryUBERON:000161441.33gold quality
palpebral conjunctivaUBERON:000181241.10gold quality
mucosa of paranasal sinusUBERON:000503040.98gold quality
ganglionic eminenceUBERON:000402340.61gold quality
jejunal mucosaUBERON:000039940.59gold quality
biceps brachiiUBERON:000150740.57gold quality
medulla oblongataUBERON:000189640.52gold quality
epithelium of nasopharynxUBERON:000195140.45gold quality
myocardiumUBERON:000234940.45gold quality
gingival epitheliumUBERON:000194940.43gold quality
duodenumUBERON:000211440.34gold quality
germinal epithelium of ovaryUBERON:000130440.33gold quality
esophagus squamous epitheliumUBERON:000692040.29gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450240.27gold quality
jejunumUBERON:000211540.18gold quality
cartilage tissueUBERON:000241840.06gold quality
oviduct epitheliumUBERON:000480440.03gold quality
mammary ductUBERON:000176539.98gold quality
mucosa of sigmoid colonUBERON:000499339.95gold quality
deltoidUBERON:000147639.83gold quality
saphenous veinUBERON:000731839.83gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no1.15

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

TargetRegulation
NEUROG1Unknown

JASPAR motifs

MotifNameFamily
MA0827.1OLIG3Tal-related

JASPAR matrix evidence (PMIDs): PMID:20959288

miRNA regulators (miRDB)

77 targeting OLIG3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-7110-3P100.0073.182486
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-574-5P100.0066.01989
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-569699.9872.364487
HSA-MIR-50799.9770.111915
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-55799.9670.011640
HSA-MIR-335-3P99.9373.364958
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-311999.9271.342390
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-3529-3P99.9073.553045
HSA-MIR-990299.8969.152250
HSA-MIR-579-3P99.8671.663628
HSA-MIR-806799.8669.592260
HSA-MIR-664B-3P99.8471.653590
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-7110-5P99.8067.841712
HSA-MIR-6842-5P99.8067.541587
HSA-MIR-6817-3P99.7968.352126

Literature-anchored findings (GeneRIF, showing 2)

  • SNP within the OLIG3/TNFAIP3 locus (rs6920220) was associated with being less likely to maintain MTX monotherapy (PMID:20921970)
  • Two identified variants revealed novel candidate genes for hip and knee osteoarthritis. OLIG3 and FIP1L1 have specific roles in transcription and may effect expression of other genes. Identified variants in these genes may thus have a role in the regulatory events leading to osteoarthritis. (PMID:30157244)

Cross-species orthologs

8 orthologs

OrganismSymbolGene ID
danio_rerioolig3ENSDARG00000074253
mus_musculusOlig3ENSMUSG00000045591
rattus_norvegicusOlig3ENSRNOG00000064127
drosophila_melanogasteramosFBGN0003270
drosophila_melanogasteratoFBGN0010433
drosophila_melanogastertapFBGN0015550
caenorhabditis_elegansWBGENE00003018
caenorhabditis_elegansWBGENE00003595

Paralogs (15): NEUROG3 (ENSG00000122859), NEUROD4 (ENSG00000123307), BHLHE23 (ENSG00000125533), NEUROD1 (ENSG00000162992), NEUROD6 (ENSG00000164600), ATOH8 (ENSG00000168874), NEUROD2 (ENSG00000171532), ATOH1 (ENSG00000172238), NEUROG2 (ENSG00000178403), ATOH7 (ENSG00000179774), BHLHA15 (ENSG00000180535), BHLHE22 (ENSG00000180828), NEUROG1 (ENSG00000181965), OLIG1 (ENSG00000184221), OLIG2 (ENSG00000205927)

Protein

Protein identifiers

Oligodendrocyte transcription factor 3Q7RTU3 (reviewed: Q7RTU3)

Alternative names: Class B basic helix-loop-helix protein 7, Class E basic helix-loop-helix protein 20

All UniProt accessions (1): Q7RTU3

UniProt curated annotations — full annotation on UniProt →

Function. May determine the distinct specification program of class A neurons in the dorsal part of the spinal cord and suppress specification of class B neurons.

Subcellular location. Nucleus.

RefSeq proteins (1): NP_786923* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR011598bHLH_domDomain
IPR032659Olig3_bHLHDomain
IPR036638HLH_DNA-bd_sfHomologous_superfamily
IPR050359bHLH_transcription_factorsFamily

Pfam: PF00010

UniProt features (7 total): compositionally biased region 3, chain 1, domain 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q7RTU3-F163.670.26

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 140 (showing top): GOBP_SPINAL_CORD_DEVELOPMENT, CREL_01, BENPORATH_ES_WITH_H3K27ME3, GOBP_NEUROGENESIS, RACCACAR_AML_Q6, FOXO4_01, FOXO1_01, GOBP_CELL_DIFFERENTIATION_IN_SPINAL_CORD, GOBP_SPINAL_CORD_MOTOR_NEURON_DIFFERENTIATION, EVI1_05, GOBP_VENTRAL_SPINAL_CORD_DEVELOPMENT, GOBP_SPINAL_CORD_MOTOR_NEURON_CELL_FATE_SPECIFICATION, AML_Q6, GOBP_NEURON_FATE_SPECIFICATION, GOBP_CENTRAL_NERVOUS_SYSTEM_NEURON_DIFFERENTIATION

GO Biological Process (8): negative regulation of transcription by RNA polymerase II (GO:0000122), sensory organ development (GO:0007423), spinal cord motor neuron cell fate specification (GO:0021520), positive regulation of transcription by RNA polymerase II (GO:0045944), axon development (GO:0061564), spinal cord motor neuron migration (GO:0097476), regulation of gene expression (GO:0010468), spinal cord motor neuron differentiation (GO:0021522)

GO Molecular Function (6): DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), protein dimerization activity (GO:0046983), E-box binding (GO:0070888), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of transcription by RNA polymerase II3
transcription by RNA polymerase II2
negative regulation of DNA-templated transcription1
animal organ development1
spinal cord motor neuron differentiation1
neuron fate specification1
positive regulation of DNA-templated transcription1
neuron projection development1
motor neuron migration1
gene expression1
regulation of macromolecule biosynthetic process1
cell differentiation in spinal cord1
ventral spinal cord development1
central nervous system neuron differentiation1
chromatin1
RNA polymerase II transcription regulatory region sequence-specific DNA binding1
DNA-binding transcription factor activity1
protein binding1
RNA polymerase II cis-regulatory region sequence-specific DNA binding1
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
binding1
chromosome1
cellular anatomical structure1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

866 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
OLIG3TNFAIP3P21580801
OLIG3AVPR2P30518668
OLIG3PTPN22Q9Y2R2644
OLIG3PIP4K2CQ8TBX8626
OLIG3TRAF1Q13077606
OLIG3DBX1A6NMT0571
OLIG3PADI4Q9UM07568
OLIG3GBX2P52951560
OLIG3NKX2-2O95096553
OLIG3TCF3P15883539
OLIG3KIF5AQ12840536
OLIG3IRF5Q13568532
OLIG3TNFRSF14Q92956491
OLIG3DBX2Q6ZNG2484
OLIG3PAX6P26367479

IntAct

110 interactions, top by confidence:

ABTypeScore
OLIG3TRAF1psi-mi:“MI:0915”(physical association)0.720
MDFIOLIG3psi-mi:“MI:0915”(physical association)0.720
OLIG3MDFIpsi-mi:“MI:0915”(physical association)0.720
TRAF1OLIG3psi-mi:“MI:0915”(physical association)0.720
ARID5AOLIG3psi-mi:“MI:0915”(physical association)0.600
TLE5OLIG3psi-mi:“MI:0915”(physical association)0.560
BYSLOLIG3psi-mi:“MI:0915”(physical association)0.560
OLIG3BYSLpsi-mi:“MI:0915”(physical association)0.560
KRTAP10-8OLIG3psi-mi:“MI:0915”(physical association)0.560
CADPSOLIG3psi-mi:“MI:0915”(physical association)0.560
MFAP1OLIG3psi-mi:“MI:0915”(physical association)0.560
KRTAP1-1OLIG3psi-mi:“MI:0915”(physical association)0.560
CYSRT1OLIG3psi-mi:“MI:0915”(physical association)0.560
OLIG3CARD10psi-mi:“MI:0915”(physical association)0.560
KRTAP6-3OLIG3psi-mi:“MI:0915”(physical association)0.560
PROP1OLIG3psi-mi:“MI:0915”(physical association)0.560
OLIG3WWOXpsi-mi:“MI:0915”(physical association)0.560
OLIG3PLAGL2psi-mi:“MI:0915”(physical association)0.560
KRTAP19-5OLIG3psi-mi:“MI:0915”(physical association)0.560

BioGRID (35): OLIG3 (Two-hybrid), OLIG3 (Two-hybrid), OLIG3 (Two-hybrid), OLIG3 (Two-hybrid), TRAF1 (Two-hybrid), OLIG3 (Two-hybrid), OLIG3 (Two-hybrid), OLIG3 (Two-hybrid), OLIG3 (Two-hybrid), OLIG3 (Two-hybrid), OLIG3 (Two-hybrid), OLIG3 (Two-hybrid), OLIG3 (Two-hybrid), OLIG3 (Two-hybrid), OLIG3 (Two-hybrid)

ESM2 similar proteins: A3KMR8, A7Z017, B3DM47, B4R090, D3ZNT6, O35317, O35984, O42290, O57342, O75030, O75444, P10083, P23091, P25932, P40424, P40425, P40426, P41778, P54841, P54842, P54843, P54844, P56224, P57102, P61295, P61296, P79745, P79746, Q05192, Q0V9K1, Q27350, Q2PFS4, Q32NP8, Q4U1U2, Q504L8, Q61039, Q6DE84, Q6PFG8, Q789F3, Q7RTU3

Diamond homologs: A8E5T6, B6VQA1, O09029, O09105, O13125, O13126, O16867, O35437, O42202, O42606, O43680, O45489, O57598, O88940, O96004, O96642, P10627, P13903, P46581, P48985, P48986, P48987, P57100, P57101, P57102, P59101, P61295, P61296, P70447, P70562, P70595, P70660, P70661, P79765, P79766, P79782, P79920, P97832, Q08DI0, Q0V9X5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 30 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Keratinization1231.8×2e-14

Disease & clinical

Clinical variants and AI predictions

ClinVar

44 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance42
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

92 predictions. Top by Δscore:

VariantEffectΔscore
6:137493354:A:ACdonor_gain0.9300
6:137493355:C:CCdonor_gain0.9300
6:137492862:C:CCacceptor_gain0.8100
6:137492861:ACTGT:Aacceptor_gain0.7600
6:137493365:T:TAdonor_gain0.7300
6:137493319:C:CAdonor_gain0.7200
6:137492862:CTGT:Cacceptor_gain0.7100
6:137492863:T:Aacceptor_gain0.6700
6:137493348:CTGCT:Cdonor_loss0.6300
6:137493350:GCTCA:Gdonor_loss0.6300
6:137493351:CTCAC:Cdonor_loss0.6300
6:137493352:TCACT:Tdonor_loss0.6300
6:137493353:CA:Cdonor_loss0.6300
6:137493354:ACTT:Adonor_loss0.6300
6:137493355:C:CAdonor_loss0.6300
6:137492900:T:TGacceptor_gain0.6200
6:137493325:T:TAdonor_gain0.5900
6:137492860:AACTG:Aacceptor_gain0.5800
6:137493347:GCTGC:Gdonor_loss0.5100
6:137492859:AAACT:Aacceptor_gain0.4800
6:137493355:CT:Cdonor_gain0.4800
6:137492861:A:ACacceptor_gain0.4600
6:137493349:TGCTC:Tdonor_loss0.4500
6:137493355:CTTGA:Cdonor_gain0.4400
6:137493143:TAC:Tdonor_gain0.4200
6:137493322:T:TAdonor_gain0.4200
6:137492858:AAAAC:Aacceptor_gain0.3900
6:137493142:C:CTdonor_gain0.3700
6:137493143:T:TTdonor_gain0.3700
6:137493355:CTT:Cdonor_gain0.3700

AlphaMissense

1766 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:137493439:G:CC244W1.000
6:137493440:C:TC244Y1.000
6:137493441:A:GC244R1.000
6:137493450:A:GC241R1.000
6:137493456:A:GC239R1.000
6:137493731:A:GL147P1.000
6:137493740:A:CM144R1.000
6:137493749:A:GL141P1.000
6:137493752:G:AS140F1.000
6:137493753:A:GS140P1.000
6:137493761:A:GL137P1.000
6:137493761:A:TL137H1.000
6:137493762:G:AL137F1.000
6:137493763:C:AM136I1.000
6:137493763:C:GM136I1.000
6:137493763:C:TM136I1.000
6:137493767:A:GL135P1.000
6:137493770:A:CI134S1.000
6:137493770:A:GI134T1.000
6:137493770:A:TI134N1.000
6:137493771:T:AI134F1.000
6:137493773:T:CY133C1.000
6:137493774:A:CY133D1.000
6:137493775:G:CN132K1.000
6:137493775:G:TN132K1.000
6:137493776:T:AN132I1.000
6:137493779:C:AR131I1.000
6:137493782:G:AA130V1.000
6:137493782:G:TA130D1.000
6:137493783:C:GA130P1.000

dbSNP variants (sampled 300 via entrez): RS1001376852 (6:137492319 AC>A), RS1001769031 (6:137492033 C>T), RS1002205706 (6:137494470 C>G,T), RS1002367157 (6:137493293 G>A,C,T), RS1002408535 (6:137493116 C>G,T), RS1002629315 (6:137495315 A>G), RS1002765118 (6:137495465 G>C,T), RS1002787055 (6:137493492 G>T), RS1004568851 (6:137495207 AT>A), RS1004919917 (6:137494913 G>A), RS1005109891 (6:137493998 C>G,T), RS1005568345 (6:137496300 T>C), RS1006079764 (6:137495295 G>A), RS1006243038 (6:137496115 T>C), RS1006625273 (6:137492725 C>A)

Disease associations

OMIM: gene MIM:609323 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

21 associations (top):

StudyTraitp-value
GCST000122_1Rheumatoid arthritis1.000000e-09
GCST000122_2Rheumatoid arthritis1.000000e-07
GCST000232_6Rheumatoid arthritis2.000000e-09
GCST000677_4Rheumatoid arthritis2.000000e-06
GCST001198_63Multiple sclerosis1.000000e-08
GCST001859_59Thiazide-induced adverse metabolic effects in hypertensive patients9.000000e-06
GCST002955_1Forced expiratory volume in 1 second (occupational environmental exposures interaction)4.000000e-07
GCST003075_10Cognitive decline rate in late mild cognitive impairment2.000000e-10
GCST003075_127Cognitive decline rate in late mild cognitive impairment2.000000e-10
GCST003129_28Primary biliary cholangitis1.000000e-10
GCST003995_32Tonsillectomy3.000000e-08
GCST005014_31Tonsillectomy3.000000e-08
GCST005523_24Celiac disease5.000000e-30
GCST005523_42Celiac disease2.000000e-07
GCST006048_2Rheumatoid arthritis (ACPA-positive)2.000000e-18
GCST007062_3Hodgkin’s lymphoma3.000000e-08
GCST007400_14Systemic lupus erythematosus2.000000e-13
GCST007798_79Asthma2.000000e-10
GCST007800_65Asthma (childhood onset)3.000000e-13
GCST008644_12Celiac disease and Rheumatoid arthritis3.000000e-27
GCST009597_316Multiple sclerosis5.000000e-25

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0004530triglyceride measurement
EFO:0004314forced expiratory volume
EFO:0006993response to mineral dust exposure
EFO:0007710cognitive decline measurement
EFO:0007924tonsillectomy risk measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

38 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression, affects cotreatment, increases expression, affects expression7
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamidedecreases expression, affects cotreatment, increases expression3
Benzo(a)pyreneaffects methylation, decreases expression, decreases methylation, increases expression3
Ethanolaffects cotreatment, increases expression, decreases expression2
bisphenol Adecreases expression1
N(4)-hydroxycytidineincreases expression1
terbufosincreases methylation1
trichostatin Aincreases expression1
arseniteincreases methylation1
tetrabromobisphenol Adecreases expression1
perfluorooctanoic acidincreases expression1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, decreases expression, affects response to substance, increases expression1
entinostataffects cotreatment, increases expression1
Chir 99021affects cotreatment, increases expression1
ramelteondecreases expression1
nilotinibincreases expression1
dorsomorphinaffects cotreatment, increases expression1
Dabigatranincreases expression1
Resveratrolaffects cotreatment, decreases expression1
Panobinostataffects cotreatment, increases expression1
Abacavirincreases expression1
Cadmiumdecreases expression, increases abundance1
Caffeineincreases expression1
Diethylhexyl Phthalatedecreases expression1
Fonofosincreases methylation1
Fluorouracildecreases expression1
Folic Acidincreases expression, affects cotreatment1
Lipopolysaccharidesincreases expression, affects cotreatment, decreases expression, affects response to substance1
Parathionincreases methylation1
Phenytoinincreases expression1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_A4Z6SEES3-1V human OLIG3, clone1Embryonic stem cellMale
CVCL_A4Z7SEES3-1V human OLIG3, clone2Embryonic stem cellMale
CVCL_A4Z8SEES3-1V human OLIG3, clone3Embryonic stem cellMale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.