BCOR

BCL6 corepressor, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): X:40049815-40177329

Links

ENSG00000183337 ∙ NCBI:54880 ∙ OMIM:300485 ∙ HGNC:20893 ∙ Uniprot:Q6W2J9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• microphthalmia, Lenz type (Supportive), mode of inheritance: XL
• microphthalmia, syndromic 2 (Supportive), mode of inheritance: XL
• microphthalmia, syndromic 2 (Definitive), mode of inheritance: XL
• microphthalmia, syndromic 2 (Definitive), mode of inheritance: XL
• microphthalmia, syndromic 2 (Limited), mode of inheritance: Unknown
• microphthalmia, syndromic 2 (Strong), mode of inheritance: XL
• microphthalmia, syndromic 2 (Definitive), mode of inheritance: XL
• microphthalmia, syndromic 2 (Limited), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Microphthalmia, syndromic 2 (Oculofaciocardiodental syndrome)	XL	Cardiovascular	The condition can involve congenital anomalies (eg, cardiac anomalies), and awareness may allow early management	Cardiovascular; Craniofacial; Dental; Gastrointestinal; Genitourinary; Ophthalmologic; Musculoskeletal; Renal	13963827; 1225823; 10069716; 15004558; 15770227; 15957158; 20301694; 21740180; 22301464
The condition can involve multiple congenital anomalies

ClinVar

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

• Oculofaciocardiodental_syndrome (449 variants)
• not_provided (241 variants)
• Inborn_genetic_diseases (116 variants)
• not_specified (64 variants)
• BCOR-related_disorder (60 variants)
• Intellectual_disability (9 variants)
• Microphthalmia,_syndromic_1 (8 variants)
• History_of_neurodevelopmental_disorder (4 variants)
• Developmental_cataract (3 variants)
• sellar_metastasis_from_primary_bronchial_carcinoid_tumor (1 variants)
• Anterior_segment_dysgenesis_8 (1 variants)
• Glioblastoma (1 variants)
• Oculofaciocardiodental_syndrome_(OFCD) (1 variants)
• Corpus_callosum,_agenesis_of (1 variants)
• Abnormal_brain_morphology (1 variants)
• Microcephaly (1 variants)
• Mild_fetal_ventriculomegaly (1 variants)
• Congenital_anomaly_of_kidney_and_urinary_tract (1 variants)
• Congenital_cerebellar_hypoplasia (1 variants)
• Brachycephaly (1 variants)
• Acute_myeloid_leukemia (1 variants)
• Isolated_anophthalmia-microphthalmia_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCOR gene is commonly pathogenic or not. These statistics are base on transcript: NM_001123385.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			4	119	37	160
missense	3	3	328	65	14	413
nonsense	17	8	4			29
start loss						0
frameshift	54	14	4			72
splice donor/acceptor (+/-2bp)	1	9	2			12
Total	75	34	342	184	51

Highest pathogenic variant AF is 0.000022332413

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCOR	protein_coding	protein_coding	ENST00000378444	14	127515

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000280	125463	0	2	125465	0.00000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.88	601	745	0.806	0.0000630	11434
Missense in Polyphen		210	319.11	0.65808		5119
Synonymous	-0.598	338	324	1.04	0.0000304	3600
Loss of Function	5.91	2	44.6	0.0449	0.00000352	767

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)	0.0000251	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional corepressor. May specifically inhibit gene expression when recruited to promoter regions by sequence- specific DNA-binding proteins such as BCL6 and MLLT3. This repression may be mediated at least in part by histone deacetylase activities which can associate with this corepressor. Involved in the repression of TFAP2A; impairs binding of BCL6 and KDM2B to TFAP2A promoter regions. Via repression of TFAP2A acts as a negative regulator of osteo-dentiogenic capacity in adult stem cells; the function implies inhibition of methylation on histone H3 'Lys-4' (H3K4me3) and 'Lys-36' (H3K36me2). {ECO:0000269|PubMed:10898795, ECO:0000269|PubMed:15004558, ECO:0000269|PubMed:18280243, ECO:0000269|PubMed:19578371, ECO:0000269|PubMed:23911289}.
• Pathway: Ectoderm Differentiation;Pathways Affected in Adenoid Cystic Carcinoma;Signaling events mediated by HDAC Class II (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.0627
• rvis_EVS: -3.03
• rvis_percentile_EVS: 0.51

Haploinsufficiency Scores

• pHI: 0.368
• hipred: Y
• hipred_score: 0.775
• ghis: 0.636

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.956

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bcor
• 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); immune system phenotype; embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; growth/size/body region 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); cellular phenotype

Zebrafish Information Network

• Gene name: bcor
• Affected structure: retina
• Phenotype tag: abnormal
• Phenotype quality: perforate

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;negative regulation of histone H3-K36 methylation;blastocyst hatching;heart development;negative regulation of bone mineralization;histone H2A monoubiquitination;odontogenesis;negative regulation of transcription, DNA-templated;negative regulation of histone H3-K4 methylation;roof of mouth development;specification of axis polarity;negative regulation of tooth mineralization
• Cellular component: nucleus;BCOR complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;transcription corepressor activity;ubiquitin-protein transferase activity;protein binding;transcription factor binding;heat shock protein binding;histone deacetylase binding;transcription regulatory region DNA binding