BCL6B

Chr 17

BCL6B transcription repressor

Also known as: BAZF, ZBTB28, ZNF62

NCBI Gene: 255877ENSG00000161940UniProt: Q8N143OMIM: 608992

BCL6B encodes a sequence-specific transcriptional repressor that functions in association with BCL6 and is involved in early B-cell development and regulation of inflammatory and immune responses. Mutations cause autosomal dominant developmental delay with variable intellectual disability, behavioral abnormalities, and dysmorphic features. The gene shows moderate constraint against loss-of-function variants, consistent with its role in neurodevelopment.

OMIMResearchSummary from RefSeq, UniProt
DNmechanismLOEUF 0.59
Clinical Summary— BCL6B
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.30) despite low pLI — interpret in context.
📋
ClinVar Variants
19 unique Pathogenic / Likely Pathogenic· 33 VUS of 55 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.59LOEUF
pLI 0.047
Z-score 2.90
OE 0.30 (0.16–0.59)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
0.96Z-score
OE missense 0.85 (0.77–0.94)
268 obs / 316.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.30 (0.16–0.59)
0≤0.351.4
Missense OE0.85 (0.77–0.94)
0≤0.61.4
Synonymous OE0.90
0≤1.21.6
LoF obs/exp: 6 / 20.0Missense obs/exp: 268 / 316.2Syn Z: 0.88
DN
0.74top 25%
GOF
0.6149th %ile
LOF
0.4431th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

55 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic18
Likely Pathogenic1
VUS33
18
Pathogenic
1
Likely Pathogenic
33
VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
18
0
18
Likely Pathogenic
0
0
1
0
1
VUS
0
26
7
0
33
Likely Benign
0
0
0
0
0
Benign
0
0
0
0
0
Total02626052

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

BCL6B · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Integrative transcriptomic and epigenomic analysis identifies BCL6B as a novel regulator of human pluripotent stem cell to endothelial differentiation.
Zhu Y et al.·Protein Cell
2025
BCL6B suppresses acute myeloid leukemia progression by transcriptionally repressing GGT5 and modulating MAPK signaling.
Pan Y et al.·Biol Direct
2026
BCL6B (B-Cell CLL/Lymphoma 6 Member B Protein) Contributes to Ocular Vascular Diseases via Notch Signal Silencing.
Tanaka M et al.·Arterioscler Thromb Vasc Biol
2023
CircTFF1 Promotes Proliferation, Migration and Invasion of Lung Cancer Cells by Facilitating Methylation of BCL6B Promoter via miR-29c-3p/DNMT3A Axis.
Zhao L et al.·Mol Biotechnol
2022
KLF4, a Key Regulator of a Transitive Triplet, Acts on the TGF-beta Signaling Pathway and Contributes to High-Altitude Adaptation of Tibetan Pigs
Wang T et al.·Front Genet
2021
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients