OLIG2

protein-coding

oligodendrocyte transcription factor 2, the group of Basic helix-loop-helix proteins

Gene summary

This gene encodes a basic helix-loop-helix transcription factor which is expressed in oligodendroglial tumors of the brain. The protein is an essential regulator of ventral neuroectodermal progenitor cell fate. The gene is involved in a chromosomal translocation t(14;21)(q11.2;q22) associated with T-cell acute lymphoblastic leukemia. Its chromosomal location is within a region of chromosome 21 which has been suggested to play a role in learning deficits associated with Down syndrome. [provided by RefSeq, Jul 2008]

Previous symbols:

PRKCBP2
BHLHB1

MANE transcript

NM_005806.4

Inheritance

—

ClinVar variants

U:31B:1

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.42

Max pathogenic AF

—

Genomic locus

chr21:33,025,935-33,029,196

External References & Databases

Ensembl (ENSG00000205927)

Transcript & Mutation Effects

hg38 • Region Span ~3.3 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to OLIG2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 30

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Inborn genetic diseasesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005806.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			31 clinvar			31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	31	1	0	32

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005806.4	RefSeq	NP_005797.1	1	MANE Select
ENST00000382357.4	Ensembl	ENSP00000371794.3	1	MANE Select
ENST00000333337.3	Ensembl	ENSP00000331040.3	1	Standard
ENST00000430860.1	Ensembl	ENSP00000391183.1	1	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
olig2	Danio rerio	Structure: dopaminergic neuron Quality: decreased amount abnormal

Gene / Model

Organism

Observed Phenotype

olig2

Danio rerio

Structure: dopaminergic neuron

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neural Crest Differentiation

Biological Process

negative regulation of transcription by RNA polymerase II
spinal cord motor neuron differentiation
spinal cord oligodendrocyte cell fate specification
thalamus development
myelination

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
protein homodimerization activity
HMG box domain binding

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000333337
Coding exons: 1
Length: 3352
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.66	87	143	0.609	0.00000657	2032
Missense (PolyPhen)		13	50.564	0.2571		537
Synonymous	-1.10	77	65.7	1.17	0.00000327	718
Loss of Function	1.16	2	4.73	0.423	2.02e-7	58

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for oligodendrocyte and motor neuron specification in the spinal cord, as well as for the development of somatic motor neurons in the hindbrain. Functions together with ZNF488 to promote oligodendrocyte differentiation. Cooperates with OLIG1 to establish the pMN domain of the embryonic neural tube. Antagonist of V2 interneuron and of NKX2-2-induced V3 interneuron development. {ECO:0000250|UniProtKB:Q9EQW6}.;
Disease: DISEASE: Note=A chromosomal aberration involving OLIG2 may be a cause of a form of T-cell acute lymphoblastic leukemia (T-ALL). Translocation t(14;21)(q11.2;q22) with TCRA. {ECO:0000269|PubMed:10737801}.;

Recessive Scores

pRec: 0.360

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.854

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium