BCL6B

BCL6B transcription repressor, the group of BTB domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 17:7023049-7030290

Previous symbols: [ "ZNF62" ]

Links

ENSG00000161940 ∙ NCBI:255877 ∙ OMIM:608992 ∙ HGNC:1002 ∙ Uniprot:Q8N143 ∙ 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 BCL6B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCL6B 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						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in BCL6B

This is a list of pathogenic ClinVar variants found in the BCL6B region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7023708-T-C		not specified	Uncertain significance (Jan 03, 2024)
17-7023709-A-G		not specified	Uncertain significance (Jul 19, 2022)
17-7023771-C-T		not specified	Uncertain significance (Dec 16, 2023)
17-7024214-C-G		not specified	Uncertain significance (Dec 28, 2022)
17-7024228-C-T		not specified	Uncertain significance (Feb 28, 2024)
17-7024270-G-T		not specified	Uncertain significance (Aug 08, 2023)
17-7024427-G-A		not specified	Uncertain significance (Mar 01, 2023)
17-7024475-G-A		not specified	Uncertain significance (Sep 12, 2023)
17-7024624-G-C		not specified	Uncertain significance (Nov 12, 2021)
17-7024692-C-G		not specified	Uncertain significance (Jan 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCL6B	protein_coding	protein_coding	ENST00000293805	8	7271

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0469	0.952	124809	0	17	124826	0.0000681

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.963	268	316	0.848	0.0000207	3072
Missense in Polyphen		85	106.88	0.79532		1077
Synonymous	0.876	116	129	0.902	0.00000868	1024
Loss of Function	2.90	6	20.0	0.301	9.89e-7	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.000105	0.0000993
East Asian	0.000112	0.000111
Finnish	0.0000490	0.0000464
European (Non-Finnish)	0.0000564	0.0000530
Middle Eastern	0.000112	0.000111
South Asian	0.000131	0.000131
Other	0.000334	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a sequence-specific transcriptional repressor in association with BCL6. May function in a narrow stage or be related to some events in the early B-cell development. {ECO:0000269|PubMed:11855826}.

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.404
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.02

Haploinsufficiency Scores

• pHI: 0.442
• hipred: Y
• hipred_score: 0.736
• ghis: 0.654

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.853

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bcl6b
• Phenotype: hematopoietic system phenotype; immune system phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;metal ion binding