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GeneBe

BCL9

BCL9 transcription coactivator, the group of Wnt enhanceosome complex

Basic information

Region (hg38): 1:147541500-147626216

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.

  • 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
clinvar
1
clinvar
4
missense
61
clinvar
2
clinvar
1
clinvar
64
nonsense
1
clinvar
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)2639121
1-147612946-C-G Inborn genetic diseases Uncertain significance (Aug 28, 2023)2590246
1-147612962-A-G Inborn genetic diseases Uncertain significance (Sep 07, 2022)2311144
1-147613166-C-T BCL9-related condition Likely benign (Feb 28, 2023)3046009
1-147614489-C-T Inborn genetic diseases Uncertain significance (Sep 26, 2022)2313219
1-147614507-C-A Inborn genetic diseases Uncertain significance (Aug 10, 2021)2242573
1-147615884-G-C Inborn genetic diseases Uncertain significance (Apr 10, 2023)2535680
1-147618808-G-T Benign/Likely benign (Dec 01, 2023)718807
1-147618841-A-G Inborn genetic diseases Conflicting classifications of pathogenicity (Jan 01, 2024)2466362
1-147618873-G-A Inborn genetic diseases Uncertain significance (Mar 22, 2023)2519714
1-147618937-C-T Inborn genetic diseases Uncertain significance (Mar 24, 2023)2509680
1-147618967-C-T Inborn genetic diseases Uncertain significance (Feb 15, 2023)2484810
1-147618969-C-T Inborn genetic diseases Uncertain significance (Jun 11, 2021)2357568
1-147619060-G-A BCL9-related condition Likely benign (Feb 22, 2023)708511
1-147619150-C-T Benign (Feb 01, 2024)3024758
1-147619302-G-A Likely benign (Dec 31, 2019)752986
1-147619359-C-A Inborn genetic diseases Uncertain significance (Oct 27, 2022)2321517
1-147619548-A-G Inborn genetic diseases Uncertain significance (Jan 11, 2023)2475500
1-147619587-G-C Inborn genetic diseases Uncertain significance (Nov 19, 2022)2401629
1-147619610-G-A Benign (Dec 31, 2019)777923
1-147619684-T-C Inborn genetic diseases Uncertain significance (Sep 17, 2021)2251112
1-147619684-T-G Inborn genetic diseases Uncertain significance (May 27, 2022)2292356
1-147619701-C-G Inborn genetic diseases Uncertain significance (Aug 30, 2022)2397321
1-147619705-C-T Inborn genetic diseases Uncertain significance (Mar 16, 2022)2278525
1-147619719-C-G Inborn genetic diseases Uncertain significance (May 01, 2022)2223332

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