BCL9L

protein-coding

BCL9 like, the group of Wnt enhanceosome complex

Gene summary

Enables beta-catenin binding activity. Involved in several processes, including negative regulation of transforming growth factor beta receptor signaling pathway; positive regulation of epithelial to mesenchymal transition; and positive regulation of transcription by RNA polymerase II. Located in fibrillar center and nucleoplasm. Part of beta-catenin-TCF complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001378213.1

Inheritance

ClinVar variants

U:289B:19

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr11:118,893,875-118,925,926

External References & Databases

Ensembl (ENSG00000186174)

Transcript & Mutation Effects

hg38 • Region Span ~32.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

visceral heterotaxyMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0018677

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BCL9L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 284

not providedTotal: 18

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001378213.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	3 clinvar	6 clinvar	12
missense			279 clinvar	5 clinvar	5 clinvar	289
nonsense						0
start loss						0
frameshift			3 clinvar			3
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	289	8	11	308

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001378213.1	RefSeq	NP_001365142.1	8	MANE Select
ENST00000683865.1	Ensembl	ENSP00000507778.1	8	MANE Select
NM_001378214.1	RefSeq	NP_001365143.1	7	Standard
NM_001437465.1	RefSeq	NP_001424394.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signaling by WNT
Signal Transduction
Formation of the beta-catenin:TCF transactivating complex
TCF dependent signaling in response to WNT

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

Molecular Function

transcription coactivator activity
beta-catenin binding

Cellular Component

nucleus
nucleoplasm
nucleolus
beta-catenin-TCF complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000334801
Coding exons: 8
Length: 31734
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125742
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.10	857	952	0.900	0.0000591	9674
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000072	0.000070	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.200

Intolerance Scores

LoFtool: 0.143
RVIS EVS: -1.47
RVIS percentile EVS: 3.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.416

Gene Damage Prediction

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