BCL3

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

Basic information

Region (hg38): 19:44747704-44760044

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.

• Inborn genetic diseases (24 variants)
• not provided (4 variants)
• not specified (1 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.

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					1	1
missense			25		1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	25	1	2

Variants in BCL3

This is a list of pathogenic ClinVar variants found in the BCL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-44748798-G-A		not specified	Uncertain significance (Jun 16, 2023)
19-44748854-G-A		not specified	Uncertain significance (Jun 16, 2023)
19-44748897-C-T		not specified	Uncertain significance (Jan 04, 2022)
19-44748920-C-A		not specified	Uncertain significance (Jul 13, 2022)
19-44748923-G-A		not specified	Uncertain significance (Sep 27, 2022)
19-44748924-C-A		not specified	Uncertain significance (Jul 14, 2021)
19-44748924-C-T		not specified	Uncertain significance (May 03, 2023)
19-44748926-G-T		not specified	Uncertain significance (Feb 10, 2022)
19-44748942-C-A		not specified	Uncertain significance (Aug 13, 2021)
19-44748972-G-A		not specified	Uncertain significance (Aug 17, 2021)
19-44748983-G-A		not specified	Uncertain significance (Aug 12, 2021)
19-44748993-C-T		not specified	Uncertain significance (Oct 29, 2021)
19-44749026-C-T		not specified	Uncertain significance (May 24, 2023)
19-44749034-C-G		not specified	Uncertain significance (Apr 12, 2022)
19-44749034-C-T		not specified	Uncertain significance (Jun 22, 2023)
19-44751285-C-A		not specified	Uncertain significance (Nov 15, 2021)
19-44751305-C-A		not specified	Uncertain significance (Nov 09, 2021)
19-44751346-G-A		not specified	Uncertain significance (Feb 28, 2024)
19-44751359-G-A		not specified	Uncertain significance (Jul 05, 2023)
19-44756330-A-G		not specified	Uncertain significance (Dec 14, 2023)
19-44756336-G-A		not specified	Uncertain significance (Feb 28, 2024)
19-44757093-T-C			Benign (Apr 03, 2018)
19-44757137-G-C		not specified	Uncertain significance (Nov 21, 2022)
19-44757162-G-A		not specified	Uncertain significance (Feb 22, 2023)
19-44757374-G-A		not specified	Uncertain significance (Apr 26, 2023)

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