OLIG3

oligodendrocyte transcription factor 3, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 6:137492199-137494394

Links

ENSG00000177468 ∙ NCBI:167826 ∙ OMIM:609323 ∙ HGNC:18003 ∙ Uniprot:Q7RTU3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OLIG3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OLIG3 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				2		2
missense			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	2	0

Variants in OLIG3

This is a list of pathogenic ClinVar variants found in the OLIG3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-137493398-G-T		not specified	Uncertain significance (Nov 07, 2022)
6-137493422-G-A		not specified	Uncertain significance (Mar 28, 2023)
6-137493483-C-G		not specified	Uncertain significance (Jun 16, 2024)
6-137493530-G-C		not specified	Uncertain significance (Dec 19, 2022)
6-137493570-C-A		not specified	Uncertain significance (Jan 23, 2024)
6-137493583-T-C			Likely benign (May 01, 2022)
6-137493624-G-T		not specified	Uncertain significance (Dec 07, 2021)
6-137493654-G-A		not specified	Uncertain significance (Oct 13, 2023)
6-137493689-C-T		not specified	Uncertain significance (Feb 14, 2023)
6-137493705-G-A		not specified	Uncertain significance (Apr 20, 2024)
6-137493716-T-C		not specified	Uncertain significance (Dec 22, 2023)
6-137493784-G-A			Likely benign (Jul 01, 2022)
6-137493812-T-C		not specified	Uncertain significance (Nov 21, 2022)
6-137493963-A-G		not specified	Uncertain significance (Dec 01, 2022)
6-137494006-G-C		not specified	Uncertain significance (May 18, 2022)
6-137494018-C-A		not specified	Uncertain significance (Jul 25, 2023)
6-137494030-C-T		not specified	Uncertain significance (Feb 27, 2023)
6-137494032-T-C		not specified	Uncertain significance (Oct 07, 2022)
6-137494094-T-C		not specified	Uncertain significance (Jun 10, 2024)
6-137494112-A-C		not specified	Uncertain significance (Dec 01, 2022)
6-137494131-A-T		not specified	Uncertain significance (Dec 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OLIG3	protein_coding	protein_coding	ENST00000367734	1	2196

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.834	0.163	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.248	159	150	1.06	0.00000702	1743
Missense in Polyphen		45	53.984	0.83358		665
Synonymous	-0.791	78	69.6	1.12	0.00000343	578
Loss of Function	2.25	0	5.91	0.00	2.56e-7	72

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: dbNSFP

• Function: 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.
• Pathway: Neural Crest Differentiation (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• pHI: 0.531
• hipred: Y
• hipred_score: 0.736
• ghis: 0.445

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.988

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olig3
• Phenotype: cellular phenotype; homeostasis/metabolism 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); 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); respiratory system phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;spinal cord motor neuron cell fate specification;spinal cord motor neuron migration
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;transcription corepressor activity;protein binding;protein dimerization activity