BCL9L

BCL9 like, the group of Wnt enhanceosome complex

Basic information

Region (hg38): 11:118893874-118925926

Links

ENSG00000186174 ∙ NCBI:283149 ∙ OMIM:609004 ∙ HGNC:23688 ∙ Uniprot:Q86UU0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BCL9L gene.

• Inborn genetic diseases (82 variants)
• not provided (13 variants)
• not specified (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCL9L 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				2	9	11
missense			74	1	5	80
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8	1	1	10
Total	0	0	82	4	15

Variants in BCL9L

This is a list of pathogenic ClinVar variants found in the BCL9L region.

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

Position	Type	Phenotype	Significance	ClinVar
11-118893899-A-G		not specified	Uncertain significance (Dec 12, 2023)
11-118893922-T-G		not specified	Uncertain significance (Dec 01, 2022)
11-118894004-G-A		not specified	Uncertain significance (Dec 15, 2022)
11-118894125-A-T		not specified	Uncertain significance (Jan 30, 2024)
11-118894372-C-T			Benign (Jun 29, 2018)
11-118894376-G-A		not specified	Uncertain significance (Mar 02, 2023)
11-118894412-G-A		not specified	Uncertain significance (Nov 17, 2022)
11-118894418-A-G		not specified	Uncertain significance (Mar 01, 2023)
11-118894448-G-A		not specified	Uncertain significance (May 23, 2023)
11-118894456-C-T			Likely benign (May 13, 2018)
11-118894462-G-A		not specified	Uncertain significance (Jan 03, 2024)
11-118894487-T-A		not specified	Uncertain significance (Oct 25, 2023)
11-118894523-G-A		not specified	Uncertain significance (May 06, 2022)
11-118894548-G-A		not specified	Uncertain significance (Jun 09, 2022)
11-118894565-G-T		not specified	Uncertain significance (May 30, 2023)
11-118894611-G-T		not specified	Uncertain significance (Dec 08, 2023)
11-118894622-C-T		not specified	Uncertain significance (Dec 19, 2023)
11-118898438-C-T		not specified	Likely benign (Oct 26, 2022)
11-118898492-G-A		not specified	Uncertain significance (Dec 15, 2022)
11-118898510-T-G		not specified	Uncertain significance (Jan 03, 2022)
11-118898550-C-T			Benign (Dec 31, 2019)
11-118898558-G-A		not specified	Uncertain significance (Nov 10, 2022)
11-118898569-G-A		not specified	Uncertain significance (Nov 29, 2021)
11-118898594-C-T			Benign (Mar 29, 2018)
11-118898618-A-T		not specified	Uncertain significance (Jan 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCL9L	protein_coding	protein_coding	ENST00000334801	8	31734

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000610	125733	0	9	125742	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	857	952	0.900	0.0000591	9674
Missense in Polyphen		214	262.32	0.8158		2468
Synonymous	-2.10	456	402	1.13	0.0000278	3196
Loss of Function	5.40	5	43.4	0.115	0.00000221	432

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000718	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional regulator that acts as an activator. Promotes beta-catenin transcriptional activity. Plays a role in tumorigenesis. Enhances the neoplastic transforming activity of CTNNB1 (By similarity). {ECO:0000250}.
• Pathway: Signaling by WNT;Signal Transduction;Formation of the beta-catenin:TCF transactivating complex;TCF dependent signaling in response to WNT (Consensus)

Recessive Scores

• pRec: 0.200

Intolerance Scores

• loftool: 0.143
• rvis_EVS: -1.47
• rvis_percentile_EVS: 3.73

Haploinsufficiency Scores

• pHI: 0.496
• hipred: N
• hipred_score: 0.376
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.416

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bcl9l
• Phenotype: muscle phenotype

Gene ontology

• Biological process: positive regulation of epithelial to mesenchymal transition;regulation of cell morphogenesis;negative 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: nucleus;nucleoplasm;nucleolus;beta-catenin-TCF complex
• Molecular function: transcription coactivator activity;beta-catenin binding