BCL9
Basic information
Region (hg38): 1:147541501-147626216
Links
Phenotypes
GenCC
Source:
- congenital heart disease (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- 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 | 6 | |||||
missense | 200 | 209 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 201 | 12 | 3 |
GnomAD
Source:
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:
- 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