BCL9

BCL9 transcription coactivator, the group of Wnt enhanceosome complex

Basic information

Region (hg38): 1:147541500-147626216

Links

ENSG00000116128 ∙ NCBI:607 ∙ OMIM:602597 ∙ HGNC:1008 ∙ Uniprot:O00512 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital heart disease (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BCL9 gene.

• Inborn genetic diseases (61 variants)
• not provided (8 variants)
• BCL9-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCL9 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				3	1	4
missense			61	2	1	64
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	62	5	2

Variants in BCL9

This is a list of pathogenic ClinVar variants found in the BCL9 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-147611851-C-T			Likely benign (Jun 01, 2022)
1-147612915-G-A		not specified	Uncertain significance (Oct 03, 2023)
1-147612946-C-G		not specified	Uncertain significance (Aug 28, 2023)
1-147612962-A-G		not specified	Uncertain significance (Sep 07, 2022)
1-147613166-C-T		BCL9-related disorder	Likely benign (Feb 28, 2023)
1-147614489-C-T		not specified	Uncertain significance (Sep 26, 2022)
1-147614495-A-T		not specified	Uncertain significance (Sep 22, 2023)
1-147614507-C-A		not specified	Uncertain significance (Aug 10, 2021)
1-147614523-C-A		not specified	Uncertain significance (Jan 23, 2024)
1-147615843-G-A		not specified	Uncertain significance (Jan 29, 2024)
1-147615884-G-C		not specified	Uncertain significance (Apr 10, 2023)
1-147618808-G-T			Benign/Likely benign (Dec 01, 2023)
1-147618841-A-G		not specified	Conflicting classifications of pathogenicity (Jan 01, 2024)
1-147618863-A-C		not specified	Uncertain significance (Feb 02, 2024)
1-147618873-G-A		not specified	Uncertain significance (Mar 22, 2023)
1-147618922-C-T		not specified	Uncertain significance (Dec 16, 2023)
1-147618937-C-T		not specified	Uncertain significance (Mar 24, 2023)
1-147618967-C-T		not specified	Uncertain significance (Feb 15, 2023)
1-147618969-C-T		not specified	Uncertain significance (Jun 11, 2021)
1-147619060-G-A		BCL9-related disorder	Likely benign (Feb 22, 2023)
1-147619150-C-T			Benign (Feb 01, 2024)
1-147619302-G-A		not specified	Conflicting classifications of pathogenicity (Jan 08, 2024)
1-147619318-C-T		not specified	Uncertain significance (Oct 10, 2023)
1-147619359-C-A		not specified	Uncertain significance (Oct 27, 2022)
1-147619548-A-G		not specified	Uncertain significance (Jan 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCL9	protein_coding	protein_coding	ENST00000234739	7	84836

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.496	0.504	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0352	837	840	0.997	0.0000460	9341
Missense in Polyphen		352	363.8	0.96756		3953
Synonymous	-2.10	353	306	1.15	0.0000173	3049
Loss of Function	4.65	9	41.2	0.218	0.00000249	413

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000425	0.000362
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.000223	0.000193
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000661	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in signal transduction through the Wnt pathway. Promotes beta-catenin's transcriptional activity (By similarity). {ECO:0000250, ECO:0000269|PubMed:11955446}.
• Pathway: WNT-Ncore;Wnt Signaling Pathway;Wnt-beta-catenin Signaling Pathway in Leukemia;Signaling by WNT;Signal Transduction;Wnt;Wnt Canonical;Regulation of nuclear beta catenin signaling and target gene transcription;Formation of the beta-catenin:TCF transactivating complex;TCF dependent signaling in response to WNT;Wnt Mammals (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.250
• rvis_EVS: -1.63
• rvis_percentile_EVS: 2.88

Haploinsufficiency Scores

• pHI: 0.808
• hipred: Y
• hipred_score: 0.694
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bcl9
• Phenotype: muscle phenotype

Gene ontology

• Biological process: myotube differentiation involved in skeletal muscle regeneration;regulation of transforming growth factor beta receptor signaling pathway;somatic stem cell population maintenance;skeletal muscle cell differentiation;positive regulation of transcription by RNA polymerase II;canonical Wnt signaling pathway;beta-catenin-TCF complex assembly
• Cellular component: nucleoplasm;cis-Golgi network;beta-catenin-TCF complex
• Molecular function: transcription coactivator activity;protein binding;beta-catenin binding