BCL9

BCL9 transcription coactivator, the group of Wnt enhanceosome complex

Basic information

Region (hg38): 1:147541501-147626216

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.

not_specified (206 variants)
not_provided (11 variants)
BCL9-related_disorder (5 variants)
Congenital_long_QT_syndrome (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. These statistics are base on transcript: NM_000004326.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar	1 clinvar	6
missense			200 clinvar	7 clinvar	2 clinvar	209
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	201	12	3

Loading clinvar variants...

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