OLIG2
oligodendrocyte transcription factor 2, the group of Basic helix-loop-helix proteins
Basic information
Region (hg38): 21:33025935-33029196
Previous symbols: [ "PRKCBP2", "BHLHB1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the OLIG2 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 11 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 0 | 0 |
Variants in OLIG2
This is a list of pathogenic ClinVar variants found in the OLIG2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 21-33026915-A-C | not specified | Uncertain significance (Aug 12, 2022) | ||
| 21-33027001-T-C | not specified | Uncertain significance (Nov 14, 2023) | ||
| 21-33027194-T-G | not specified | Uncertain significance (Oct 30, 2023) | ||
| 21-33027211-G-A | Inborn genetic diseases | Uncertain significance (Nov 03, 2017) | ||
| 21-33027261-G-T | not specified | Uncertain significance (Jan 03, 2024) | ||
| 21-33027461-C-G | not specified | Uncertain significance (Dec 01, 2022) | ||
| 21-33027532-C-T | not specified | Uncertain significance (Jul 30, 2023) | ||
| 21-33027543-A-G | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
| 21-33027634-C-T | not specified | Uncertain significance (Aug 16, 2021) | ||
| 21-33027694-G-A | not specified | Uncertain significance (May 25, 2022) | ||
| 21-33027730-G-T | not specified | Uncertain significance (Nov 18, 2022) | ||
| 21-33027788-C-G | not specified | Uncertain significance (Jun 03, 2024) | ||
| 21-33027803-G-C | not specified | Uncertain significance (May 23, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| OLIG2 | protein_coding | protein_coding | ENST00000333337 | 1 | 3352 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0946 | 0.780 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.66 | 87 | 143 | 0.609 | 0.00000657 | 2032 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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}.;
- Pathway
- Neural Crest Differentiation
(Consensus)
Recessive Scores
- pRec
- 0.360
Haploinsufficiency Scores
- pHI
- 0.576
- hipred
- Y
- hipred_score
- 0.577
- ghis
- 0.619
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.854
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Olig2
- Phenotype
- cellular phenotype; muscle phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm;
Zebrafish Information Network
- Gene name
- olig2
- Affected structure
- dopaminergic neuron
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;spinal cord motor neuron differentiation;spinal cord oligodendrocyte cell fate specification;thalamus development;myelination;negative regulation of neuron differentiation;neuron fate commitment;positive regulation of oligodendrocyte differentiation
- Cellular component
- nucleus;cytoplasm
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein homodimerization activity;HMG box domain binding