BCOR

Chr XXLD

BCL6 corepressor

Also known as: ANOP2, MAA2, MCOPS2

NCBI Gene: 54880ENSG00000183337UniProt: Q6W2J9

The protein encoded by this gene was identified as an interacting corepressor of BCL6, a POZ/zinc finger transcription repressor that is required for germinal center formation and may influence apoptosis. This protein selectively interacts with the POZ domain of BCL6, but not with eight other POZ proteins. Specific class I and II histone deacetylases (HDACs) have been shown to interact with this protein, which suggests a possible link between the two classes of HDACs. Several transcript variants encoding different isoforms have been found for this gene. A pseudogene of this gene is found on chromosome Y.[provided by RefSeq, Jun 2010]

Primary Disease Associations & Inheritance

Microphthalmia, syndromic 2MIM #300166
XLD
7
Active trials
136
Pathogenic / LP
677
ClinVar variants
6
Pubs (1 yr)
1.9
Missense Z
0.14
LOEUF· LoF intolerant
Clinical Summary— BCOR
🧬
Gene-Disease Validity (ClinGen)
microphthalmia, syndromic 2 · XLDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
136 Pathogenic / Likely Pathogenic· 296 VUS of 677 total submissions
💊
Clinical Trials
7 active or recruiting trials — potential therapeutic options may be available
📖
GeneReview available — BCOR
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.14LOEUF
pLI 1.000
Z-score 5.91
OE 0.04 (0.02–0.14)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.88Z-score
OE missense 0.81 (0.75–0.86)
601 obs / 745.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.04 (0.02–0.14)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.81 (0.75–0.86)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.04
0≤1.21.6
LoF obs/exp: 2 / 44.6Missense obs/exp: 601 / 745.4Syn Z: -0.60
DN
0.18100th %ile
GOF
0.2298th %ile
LOF
0.88top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · 43% of P/LP variants are LoF · LOEUF 0.14

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

677 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic109
Likely Pathogenic27
VUS296
Likely Benign157
Benign69
Conflicting19
109
Pathogenic
27
Likely Pathogenic
296
VUS
157
Likely Benign
69
Benign
19
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
40
0
69
0
109
Likely Pathogenic
18
1
8
0
27
VUS
3
271
17
5
296
Likely Benign
0
32
31
94
157
Benign
0
11
22
36
69
Conflicting
—19
Total61315147135677

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

View in ClinVar →

Protein Context — Lollipop Plot

BCOR · protein map & ClinVar variants

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

Gene2Phenotype Curations

BCOR-related syndromic microphthalmia

definitive
Monoallelic X HeterozygousLoss Of FunctionAbsent Gene Product
Dev. DisordersEye
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
AMLMDS

Molecular Genetics Guide the Maintenance Therapy After Allogeneic Hematopoietic Stem Cell Transplantation

RECRUITING
NCT06972641Phase PHASE2, PHASE3Ruijin HospitalStarted 2025-06-10
DecitabineSorafenib (BAY-43-9006)，giritinibAvastinib
B Cell Lymphoma

BCOR and ZC3H12 Genes Knock-out CD19-targeting CAR-T Cell Therapy in r/r B Cell Lymphoma

RECRUITING
NCT07009002Phase PHASE1, PHASE2Chinese PLA General HospitalStarted 2025-06-20
CAR19TIF cellsFludarabineCyclophosphamide
Acute Lymphocytic Leukemia

BCOR and ZC3H12 Genes Knock-out CD19-targeting CAR-T Cell Therapy in r/r B-ALL

RECRUITING
NCT07008885Phase PHASE1, PHASE2Chinese PLA General HospitalStarted 2025-06-20
CAR19TIF cellsFludarabineCyclophosphamide
AstroblastomaBCOR ITD SarcomaCNS Sarcoma

International Rare Brain Tumor Registry

RECRUITING
NCT05697874Children's National Research InstituteStarted 2023-01-01
Bone Marrow Failure DisordersVEXAS SyndromeHemoglobinurea, Paroxysmal

Molecular and Clinical Analysis of Bone Marrow Failure: A Secondary Research Study

ENROLLING BY INVITATION
NCT07102849National Heart, Lung, and Blood Institute (NHLBI)Started 2025-09-09
Congenital CataractTooth AbnormalitiesOcular Pathologies

Associations Between Dental Anomalies and Ocular, Cutaneous and Skin Appendages Features

NOT YET RECRUITING
NCT06950619Phase NAUniversity of PaviaStarted 2026-02
Whole Genome SequencingCephalometric tracing
Chronic Myeloid Leukemia, Chronic PhaseWithdrawal;Drug

Efficacy and Safety of TKIs' Withdrawal After a Two-step Dose Reduction in Patients with Chronic Myeloid Leukemia

ACTIVE NOT RECRUITING
NCT04147533Phase PHASE2Masaryk UniversityStarted 2020-06-16
Imatinib withdrawalDasatinibNilotinib
Clinical Literature
Landmark / reviewRecent case evidence
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
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