BCL3

BCL3 transcription coactivator, the group of Ankyrin repeat domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 19:44747705-44760044

Previous symbols: [ "D19S37", "BCL4" ]

Links

ENSG00000069399

∙ NCBI:602 ∙ OMIM:109560 ∙ HGNC:998 ∙ Uniprot:P20749 ∙ 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 BCL3 gene.

not_specified (50 variants)
not_provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCL3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005178.5. 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					2 clinvar	2
missense			51 clinvar		1 clinvar	52
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	51	0	3

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCL3	protein_coding	protein_coding	ENST00000164227	9	12340

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.989	0.0113	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.27	142	241	0.588	0.0000149	2808
Missense in Polyphen		20	66.222	0.30202		783
Synonymous	2.82	70	107	0.654	0.00000720	1040
Loss of Function	3.41	0	13.5	0.00	7.04e-7	165

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Contributes to the regulation of transcriptional activation of NF-kappa-B target genes. In the cytoplasm, inhibits the nuclear translocation of the NF-kappa-B p50 subunit. In the nucleus, acts as transcriptional activator that promotes transcription of NF-kappa-B target genes. Contributes to the regulation of cell proliferation (By similarity). {ECO:0000250, ECO:0000269|PubMed:8453667}.;
Disease: DISEASE: Note=A chromosomal aberration involving BCL3 may be a cause of B-cell chronic lymphocytic leukemia (B-CLL). Translocation t(14;19)(q32;q13.1) with immunoglobulin gene regions. {ECO:0000269|PubMed:2180580, ECO:0000269|PubMed:7896265}.;
Pathway: TNF signaling pathway - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);Apoptosis-related network due to altered Notch3 in ovarian cancer;Photodynamic therapy-induced AP-1 survival signaling.;TNFalpha;Atypical NF-kappaB pathway (Consensus)

Recessive Scores

pRec: 0.288

Haploinsufficiency Scores

pHI: 0.526
hipred: Y
hipred_score: 0.771
ghis: 0.460

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Bcl3
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; immune system phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process: obsolete protein import into nucleus, translocation;follicular dendritic cell differentiation;marginal zone B cell differentiation;humoral immune response mediated by circulating immunoglobulin;germinal center formation;transcription, DNA-templated;cellular response to DNA damage stimulus;I-kappaB kinase/NF-kappaB signaling;response to virus;response to UV-C;antimicrobial humoral response;extracellular matrix organization;DNA damage response, signal transduction by p53 class mediator;positive regulation of interferon-gamma production;T-helper 1 type immune response;negative regulation of tumor necrosis factor biosynthetic process;defense response to bacterium;intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator;defense response to protozoan;regulation of apoptotic process;negative regulation of apoptotic process;T-helper 2 cell differentiation;positive regulation of interleukin-10 biosynthetic process;negative regulation of interleukin-8 biosynthetic process;positive regulation of translation;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;negative regulation of JAK-STAT cascade;spleen development;regulation of DNA binding;maintenance of protein location in nucleus;regulation of NIK/NF-kappaB signaling
Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;plasma membrane;midbody;protein-containing complex;Bcl3-Bcl10 complex;Bcl3/NF-kappaB2 complex;intracellular membrane-bounded organelle;perinuclear region of cytoplasm
Molecular function: DNA binding;DNA-binding transcription factor activity;protein binding;transcription factor binding;protein binding, bridging