BCL9

BCL9 transcription coactivator, the group of Wnt enhanceosome complex

Basic information

Region (hg38): 1:147541501-147626216

Links

ENSG00000116128NCBI:607OMIM:602597HGNC:1008Uniprot:O00512AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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.

EffectPLPVUSLBBSum
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

GeneTypeBio TypeTranscript Coding Exons Length
BCL9protein_codingprotein_codingENST00000234739 784836
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.4960.5041257140341257480.000135
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.03528378400.9970.00004609341
Missense in Polyphen352363.80.967563953
Synonymous-2.103533061.150.00001733049
Loss of Function4.65941.20.2180.00000249413

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004250.000362
Ashkenazi Jewish0.000.00
East Asian0.00005450.0000544
Finnish0.00004690.0000462
European (Non-Finnish)0.0002230.000193
Middle Eastern0.00005450.0000544
South Asian0.00006610.0000653
Other0.0001630.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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