BCL6B

protein-coding

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

Gene summary

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in several processes, including regulation of gene expression; regulation of inflammatory response; and type 2 immune response. Predicted to be located in nucleus. Predicted to be active in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

ZNF62

MANE transcript

NM_181844.4

Inheritance

—

ClinVar variants

U:27

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr17:7,023,050-7,030,290

External References & Databases

Ensembl (ENSG00000161940)

Transcript & Mutation Effects

hg38 • Region Span ~7.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BCL6B variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 26

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_181844.4. 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						0
missense			27 clinvar			27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	27	0	0	27

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_181844.4	RefSeq	NP_862827.2	8	MANE Select
ENST00000293805.10	Ensembl	ENSP00000293805.5	8	MANE Select
ENST00000537931.2	Ensembl	ENSP00000445010.2	4	Standard
ENST00000573503.1	Ensembl	ENSP00000460282.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000293805
Coding exons: 8
Length: 7271
Individuals with no LoFs: 124809
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 124826
p: 0.0000681

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.963	268	316	0.848	0.0000207	3072
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0.000049	0.000046	rare
European (Non-Finnish)	0.000056	0.000053	rare
South Asian	0.00013	0.00013	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.853

Gene Damage Prediction

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