BCORL1

BCL6 corepressor like 1, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): X:129981107-130058071

Previous symbols: [ "CXorf10" ]

Links

ENSG00000085185 ∙ NCBI:63035 ∙ OMIM:300688 ∙ HGNC:25657 ∙ Uniprot:Q5H9F3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Shukla-Vernon syndrome (Limited), mode of inheritance: XL
• syndromic intellectual disability (Supportive), mode of inheritance: AD
• Shukla-Vernon syndrome (Limited), mode of inheritance: XL
• Shukla-Vernon syndrome (Strong), mode of inheritance: XL
• Shukla-Vernon syndrome (Limited), mode of inheritance: XL
• Shukla-Vernon syndrome (Limited), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Shukla-Vernon syndrome	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	24123876; 30941876

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BCORL1 gene.

• Neurodevelopmental delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCORL1 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			1	29	11	41
missense		2	229	17	2	250
nonsense	1		4			5
start loss						0
frameshift		1	5			6
inframe indel			5			5
splice donor/acceptor (+/-2bp)			1			1
splice region				2		2
non coding			2			2
Total	1	3	247	46	13

Variants in BCORL1

This is a list of pathogenic ClinVar variants found in the BCORL1 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-130005257-G-A		Shukla-Vernon syndrome	Uncertain significance (Feb 09, 2021)
X-130005259-G-A			Uncertain significance (Dec 12, 2022)
X-130005268-A-G			Uncertain significance (Dec 14, 2023)
X-130005293-G-A			Likely benign (Jul 01, 2022)
X-130005295-A-C			Uncertain significance (Oct 03, 2022)
X-130005295-A-G		not specified	Uncertain significance (Feb 28, 2024)
X-130005320-GA-G			Uncertain significance (Oct 03, 2024)
X-130012586-C-T		Shukla-Vernon syndrome	Likely pathogenic (-)
X-130012588-C-G			Uncertain significance (Dec 13, 2022)
X-130012594-G-A			Uncertain significance (Jan 20, 2021)
X-130012596-TGAG-T			Uncertain significance (Dec 07, 2022)
X-130012655-G-A		Shukla-Vernon syndrome	Uncertain significance (Apr 14, 2023)
X-130012960-C-T		not specified	Uncertain significance (Nov 07, 2023)
X-130012969-G-A		not specified	Uncertain significance (Oct 13, 2023)
X-130012972-G-C		Shukla-Vernon syndrome	Uncertain significance (Mar 09, 2023)
X-130012986-C-T			Likely benign (Aug 01, 2023)
X-130012986-CG-C			Uncertain significance (Mar 02, 2016)
X-130013002-A-T			Uncertain significance (Jun 14, 2023)
X-130013052-G-A			Likely benign (Jul 21, 2018)
X-130013056-C-T			Uncertain significance (Jul 13, 2021)
X-130013073-T-C		not specified	Uncertain significance (May 16, 2024)
X-130013080-GGAA-G			Uncertain significance (Aug 06, 2022)
X-130013082-A-C			Uncertain significance (Apr 30, 2024)
X-130013084-C-T			Likely benign (Jun 01, 2024)
X-130013085-G-A		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCORL1	protein_coding	protein_coding	ENST00000540052	12	76976

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000917	125697	5	6	125708	0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.06	581	739	0.786	0.0000624	10997
Missense in Polyphen		124	222.97	0.55613		3368
Synonymous	1.02	302	325	0.928	0.0000297	3783
Loss of Function	5.67	2	41.4	0.0483	0.00000350	623

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000223	0.000208
Ashkenazi Jewish	0.00	0.00
East Asian	0.000579	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000130	0.00000879
Middle Eastern	0.000579	0.000217
South Asian	0.00	0.00
Other	0.000255	0.000163

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. This repression may be mediated at least in part by histone deacetylase activities which can associate with this corepressor. {ECO:0000269|PubMed:17379597}.
• Pathway: Mesodermal Commitment Pathway;Pathways Affected in Adenoid Cystic Carcinoma (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.338
• rvis_EVS: -2.12
• rvis_percentile_EVS: 1.52

Haploinsufficiency Scores

• pHI: 0.193
• hipred: Y
• hipred_score: 0.655
• ghis: 0.628

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.670

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bcorl1

Gene ontology

• Biological process: chromatin organization
• Cellular component: nucleoplasm;plasma membrane