BCOR

BCL6 corepressor, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): X:40049814-40177329

Links

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

Phenotypes

GenCC

Source: genCC

• microphthalmia, syndromic 2 (Definitive), mode of inheritance: XLD
• 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

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 (323 variants)
• not provided (193 variants)
• not specified (60 variants)
• Inborn genetic diseases (58 variants)
• BCOR-related condition (7 variants)
• Microphthalmia, syndromic 1;Oculofaciocardiodental syndrome (6 variants)
• History of neurodevelopmental disorder (5 variants)
• BCOR-related disorders (3 variants)
• Developmental cataract (2 variants)
• Intellectual disability (2 variants)
• Anterior segment dysgenesis 8 (1 variants)
• Abnormal brain morphology (1 variants)
• Glioblastoma (1 variants)
• Microphthalmia, syndromic 1 (1 variants)
• Congenital cerebellar hypoplasia;Corpus callosum, agenesis of;Mild fetal ventriculomegaly;Microcephaly;Brachycephaly (1 variants)
• Oculofaciocardiodental syndrome;Microphthalmia, syndromic 1 (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.

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			4	73	40	117
missense	1		204	25	20	250
nonsense	16	2	1			19
start loss						0
frameshift	30	6				36
inframe indel		1	6	1		8
splice donor/acceptor (+/-2bp)		3	1			4
splice region			1	2	1	4
non coding			1	16	20	37
Total	47	12	217	115	80

Highest pathogenic variant AF is 0.00000906

Variants in BCOR

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

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

Position	Type	Phenotype	Significance	ClinVar
X-40051808-A-ATT			Benign (Aug 31, 2019)
X-40052137-C-A		Inborn genetic diseases	Uncertain significance (Mar 07, 2024)
X-40052143-T-G		not specified • Oculofaciocardiodental syndrome	Uncertain significance (Aug 15, 2022)
X-40052184-G-A		Oculofaciocardiodental syndrome	Benign (Aug 11, 2023)
X-40052187-C-T		Oculofaciocardiodental syndrome	Benign (Aug 31, 2022)
X-40052203-T-G			Uncertain significance (May 25, 2016)
X-40052220-T-A		Oculofaciocardiodental syndrome	Uncertain significance (Sep 01, 2021)
X-40052225-G-A		Inborn genetic diseases	Uncertain significance (Apr 25, 2022)
X-40052233-G-A		Oculofaciocardiodental syndrome	Uncertain significance (Sep 17, 2022)
X-40052243-C-T		Inborn genetic diseases	Uncertain significance (Jan 03, 2017)
X-40052315-C-G			Uncertain significance (Aug 28, 2023)
X-40052319-G-A		Oculofaciocardiodental syndrome	Benign (Mar 03, 2023)
X-40052320-T-C		Inborn genetic diseases	Uncertain significance (Oct 17, 2023)
X-40052325-A-C			Uncertain significance (Jan 01, 2024)
X-40052335-C-T		Oculofaciocardiodental syndrome • Inborn genetic diseases	Conflicting classifications of pathogenicity (Sep 22, 2022)
X-40052336-G-A		Inborn genetic diseases	Uncertain significance (Jan 23, 2024)
X-40052340-T-A		Oculofaciocardiodental syndrome	Benign (Mar 28, 2022)
X-40052342-T-G			Uncertain significance (Oct 01, 2023)
X-40052348-A-G		Oculofaciocardiodental syndrome	Uncertain significance (Oct 28, 2023)
X-40052363-T-C		BCOR-related disorder	Uncertain significance (Jan 21, 2024)
X-40052371-ACAT-A		Oculofaciocardiodental syndrome	Uncertain significance (Nov 25, 2021)
X-40052376-C-T		Oculofaciocardiodental syndrome • BCOR-related disorder	Benign/Likely benign (Jun 27, 2023)
X-40052377-G-A		Oculofaciocardiodental syndrome	Uncertain significance (Aug 04, 2023)
X-40052396-G-A		Oculofaciocardiodental syndrome	Conflicting classifications of pathogenicity (Dec 08, 2020)
X-40052402-TAC-CAA		Oculofaciocardiodental syndrome	Likely pathogenic (Mar 30, 2021)

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