BCOR (BCL-6 corepressor) variants and mutations
BCOR (also known as BCL-6 corepressor) is a human protein-coding gene encoding a BCL-6 corepressor protein. It participates in transcriptional repression through noncanonical Polycomb complexes and helps regulate developmental and hematopoietic gene expression. Germline loss-of-function variants cause oculofaciocardiodental syndrome, while somatic BCOR alterations occur in myeloid and other cancers. This analysis covers 3,236 BCOR variants and mutations. Of these, 47% have computational variant effect predictions. Disease context includes microphthalmia, syndromic 2, microphthalmia, Lenz type, and hereditary disease. Example BCOR variants include S3*, S3L, and S3T.
Variant analysis overview
- Gene: BCOR
- Protein: BCL-6 corepressor
- UniProt accession: Q6W2J9
- Organism: Homo sapiens
- Variants analyzed: 3236
- Variant scope: all variants
- Completed: 2026-08-20
Variant and mutation evidence
- Variant composition: 3,047 unspecified-consequence records; 1 stop lost; 82 missense variants; 91 synonymous variants; 5 frameshift variants; 1 stop retained variant; 3 in-frame deletions; 3 splice-region variants; 3 substitution
- Prediction scores: 1,525 variants have prediction scores (47% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: microphthalmia, syndromic 2, microphthalmia, Lenz type, hereditary disease, endometrial cancer, acute myeloid leukemia, gastric adenocarcinoma, B-cell chronic lymphocytic leukemia, Developmental cataract, colorectal adenocarcinoma, retinoblastoma, skin basal cell carcinoma, syndromic microphthalmia.
Protein structure and variant hotspots
- Protein features: 11 post-translational modification sites.
- PTM context: 16 variants overlap post-translational modification sites.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, 3D Hotspot Analysis, Interaction Network Analysis, AlphaFold DB, gnomAD constraint, Open Targets, MaveDB, LitVar.
Notable BCOR variants
Examples include S3*, S3L, S3T, A4V, A4S, T5N, P6T, P6Q. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- S3* (p.Ser3Ter), NCI-TCGA Cosmic COSV6070, cosmic curated COSV60705, Variant assessed as somatic; high impact.
- S3L (p.Ser3Leu), NCI-TCGA Cosmic COSV6070, cosmic curated COSV60704, Ensembl rs2147332685, Variant assessed as somatic; moderate impact.
- S3T (p.Ser3Thr), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- A4V (p.Ala4Val), rs587778092, ClinGen CA157283, ClinVar RCV000120205, Ensembl rs587778092, AlphaMissense 0.87, MetaLR 0.19
- A4S (p.Ala4Ser), cosmic curated COSV10522
- T5N (p.Thr5Asn), cosmic curated COSV60699, Ensembl rs1935891285
- P6T (p.Pro6Thr), ExAC rs763933195, gnomAD rs763933195, REVEL 0.42, CADD 24.60
- P6Q (p.Pro6Gln), cosmic curated COSV60718
- P6S (p.Pro6Ser), cosmic curated COSV10968
- L7C (p.Leu7Cys), NCI-TCGA Cosmic COSV6071, Variant assessed as somatic; high impact.
- L7P (p.Leu7Pro), ExAC rs775825598, gnomAD rs775825598
- Y8C (p.Tyr8Cys), Ensembl rs1569162374, REVEL 0.49, CADD 26.80
- G9R (p.Gly9Arg), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- V11A (p.Val11Ala), ExAC rs759722005, gnomAD rs759722005, REVEL 0.31, CADD 25.10
- V11F (p.Val11Phe), ExAC rs772165033, gnomAD rs772165033, REVEL 0.29, CADD 24.80
- V11I (p.Val11Ile), rs772165033, NCI-TCGA Cosmic COSV6070, cosmic curated COSV60702, ExAC rs772165033, REVEL 0.08, CADD 21.20, Variant assessed as somatic; moderate impact.
- H12Q (p.His12Gln), cosmic curated COSV60722
- S13G (p.Ser13Gly), rs1935888587, ClinGen CA412749680, ClinVar RCV001204867, ClinVar RCV003442765, AlphaMissense 0.18, MetaLR 0.19, Uncertain significance, Oculofaciocardiodental syndrome; not provided
- W14* (p.Trp14Ter), Ensembl rs1935888361
- N16H (p.Asn16His), NCI-TCGA TCGA novel, Variant assessed as somatic; moderate impact.
- N16K (p.Asn16Lys), gnomAD rs1935888054
- S17G (p.Ser17Gly), cosmic curated COSV10522
- S17R (p.Ser17Arg), rs771428828, ClinGen CA10387120, ClinVar RCV001370349, ClinVar RCV003169903, REVEL 0.23, CADD 17.80, Uncertain significance, Inborn genetic diseases; Oculofaciocardiodental syndrome
- S17C (p.Ser17Cys), cosmic curated COSV10968, NCI-TCGA Cosmic COSV6070, cosmic curated COSV60709, TOPMed rs1935887272, Variant assessed as somatic; moderate impact.
- E18G (p.Glu18Gly), ExAC rs749734466, gnomAD rs749734466, REVEL 0.29, CADD 27.20
- E18K (p.Glu18Lys), Ensembl rs2147331292, REVEL 0.22, CADD 25.20, Uncertain significance, not provided
- V20A (p.Val20Ala), rs2520275494, ClinGen CA16621960, ClinVar RCV002625212, REVEL 0.28, CADD 25.60, Uncertain significance, Oculofaciocardiodental syndrome
- V20I (p.Val20Ile), NCI-TCGA TCGA novel, Ensembl rs2147331187, Variant assessed as somatic; moderate impact.
- R21H (p.Arg21His), rs778129253, NCI-TCGA Cosmic COSV6071, cosmic curated COSV60719, ExAC rs778129253, REVEL 0.30, CADD 26.10, Variant assessed as somatic; moderate impact.
- M22I (p.Met22Ile), TOPMed rs947946150, gnomAD rs947946150, REVEL 0.18, CADD 22.80
- M22L (p.Met22Leu), ESP rs377693413, ExAC rs377693413, TOPMed rs377693413, gnomAD rs377693413, REVEL 0.23, CADD 22.90, Uncertain significance, Oculofaciocardiodental syndrome
- M22T (p.Met22Thr), ExAC rs748428774, TOPMed rs748428774, gnomAD rs748428774, REVEL 0.35, CADD 23.00
- A25V (p.Ala25Val), cosmic curated COSV60710
- A25T (p.Ala25Thr), ExAC rs779804763, TOPMed rs779804763, gnomAD rs779804763, REVEL 0.06, CADD 16.90
- S26N (p.Ser26Asn), Ensembl rs1935884983
- S26R (p.Ser26Arg), NCI-TCGA TCGA novel, ExAC rs778509180, gnomAD rs778509180, REVEL 0.09, CADD 20.50, Variant assessed as somatic; moderate impact.
- E27K (p.Glu27Lys), NCI-TCGA Cosmic COSV6071, cosmic curated COSV60712, REVEL 0.21, CADD 23.90, Variant assessed as somatic; moderate impact.
- D28H (p.Asp28His), NCI-TCGA Cosmic COSV1006, cosmic curated COSV10065, Variant assessed as somatic; moderate impact.
- N34K (p.Asn34Lys), cosmic curated COSV60705
- N34S (p.Asn34Ser), cosmic curated COSV60709
- D35N (p.Asp35Asn), gnomAD rs1241716094, REVEL 0.20, CADD 27.90
- D35Y (p.Asp35Tyr), NCI-TCGA Cosmic COSV6070, cosmic curated COSV60705, Variant assessed as somatic; moderate impact.
- G36V (p.Gly36Val), rs982778263, []
- D37E (p.Asp37Glu), NCI-TCGA TCGA novel, REVEL 0.08, CADD 8.56, Variant assessed as somatic; moderate impact.
- A38V (p.Ala38Val), cosmic curated COSV10968, Ensembl rs1935815187
- A38T (p.Ala38Thr), rs745470688, ClinGen CA10387093, NCI-TCGA Cosmic COSV6071, cosmic curated COSV60715, REVEL 0.12, CADD 12.00, Uncertain significance, Oculofaciocardiodental syndrome
- S39P (p.Ser39Pro), TOPMed rs897050600, REVEL 0.08, CADD 21.50
- S39Y (p.Ser39Tyr), cosmic curated COSV60717
- A41T (p.Ala41Thr), TOPMed rs1213731329, gnomAD rs1213731329, REVEL 0.12, CADD 17.10
- L43V (p.Leu43Val), TOPMed rs1037383063, REVEL 0.15, CADD 24.30
- E44K (p.Glu44Lys), Ensembl rs1569161281, REVEL 0.33, CADD 26.20
- R46S (p.Arg46Ser), TOPMed rs1935813191, REVEL 0.24, CADD 24.40
- P50S (p.Pro50Ser), cosmic curated COSV60710
- P50T (p.Pro50Thr), cosmic curated COSV60711
- P50L (p.Pro50Leu), cosmic curated COSV60701
- P50H (p.Pro50His), cosmic curated COSV60719
- L51F (p.Leu51Phe), TOPMed rs1935812728
- L51S (p.Leu51Ser), gnomAD rs1316473292, REVEL 0.31, CADD 26.80
- N52S (p.Asn52Ser), ESP rs150982908, ExAC rs150982908, TOPMed rs150982908, gnomAD rs150982908, REVEL 0.10, CADD 18.70
- N54S (p.Asn54Ser), TOPMed rs1435258487, gnomAD rs1435258487, REVEL 0.05, CADD 7.35
- V55M (p.Val55Met), rs142564611, ClinGen CA10387090, ClinVar RCV001699932, ESP rs142564611, REVEL 0.24, CADD 24.70, Uncertain significance, not provided
- V56E (p.Val56Glu), Ensembl rs2147284689
- V56L (p.Val56Leu), Ensembl rs2147284749
- V56M (p.Val56Met), Ensembl rs2147284749, REVEL 0.24, CADD 32.00
- D57E (p.Asp57Glu), Ensembl rs2147284475
- D57H (p.Asp57His), Ensembl rs2147284544
- D57N (p.Asp57Asn), Ensembl rs2147284544
- D57Y (p.Asp57Tyr), Ensembl rs2147284544
- A58E (p.Ala58Glu), ExAC rs766556436, TOPMed rs766556436, gnomAD rs766556436
- A58G (p.Ala58Gly), cosmic curated COSV60702, ExAC rs766556436, TOPMed rs766556436, gnomAD rs766556436
- A58P (p.Ala58Pro), Ensembl rs2147284404
- A58S (p.Ala58Ser), Ensembl rs2147284404
- A58V (p.Ala58Val), rs766556436, NCI-TCGA Cosmic COSV6070, ExAC rs766556436, TOPMed rs766556436, REVEL 0.23, CADD 21.90, Variant assessed as somatic; moderate impact.
- S59P (p.Ser59Pro), cosmic curated COSV10888
- S59I (p.Ser59Ile), TOPMed rs1197348343, gnomAD rs1197348343, Uncertain significance
- S59N (p.Ser59Asn), rs1197348343, ClinGen CA412749286, ClinVar RCV001930302, TOPMed rs1197348343, REVEL 0.08, CADD 15.90, Uncertain significance, Oculofaciocardiodental syndrome
- S59T (p.Ser59Thr), TOPMed rs1197348343, gnomAD rs1197348343, REVEL 0.10, CADD 5.33, Uncertain significance
- T60M (p.Thr60Met), rs202121665, ClinGen CA10387078, ClinVar RCV001519682, ClinVar RCV003883688, REVEL 0.14, CADD 21.50, Benign/Likely benign, Oculofaciocardiodental syndrome; not specified; not provided
- T60P (p.Thr60Pro), Ensembl rs2147283982
- T60S (p.Thr60Ser), Ensembl rs2147283982
- A61G (p.Ala61Gly), gnomAD rs1369996967
- A61P (p.Ala61Pro), Ensembl rs2147283731
- A61S (p.Ala61Ser), Ensembl rs2147283731
- A61T (p.Ala61Thr), Ensembl rs2147283731
- A61V (p.Ala61Val), gnomAD rs1369996967, REVEL 0.05, CADD 19.20
- H62L (p.His62Leu), TOPMed rs1935738328
- H62N (p.His62Asn), TOPMed rs1170638648, Uncertain significance
- H62Q (p.His62Gln), gnomAD rs1417757785, REVEL 0.07, CADD 15.20
- H62R (p.His62Arg), cosmic curated COSV60711, TOPMed rs1935738328, REVEL 0.15, CADD 19.30
- H62Y (p.His62Tyr), rs1170638648, ClinGen CA412749268, ClinVar RCV003486024, TOPMed rs1170638648, REVEL 0.18, CADD 22.70, Uncertain significance, Oculofaciocardiodental syndrome
- R63G (p.Arg63Gly), NCI-TCGA Cosmic COSV6070, cosmic curated COSV60708, Ensembl rs2147283269, Variant assessed as somatic; moderate impact.
- R63K (p.Arg63Lys), rs751977474, ClinGen CA10387077, cosmic curated COSV60700, ClinVar RCV001514826, REVEL 0.25, CADD 23.00, Benign, not provided; Oculofaciocardiodental syndrome
- R63M (p.Arg63Met), ExAC rs751977474, TOPMed rs751977474, gnomAD rs751977474, Benign
- R63S (p.Arg63Ser), Ensembl rs764471817, REVEL 0.38, CADD 17.90
- R63W (p.Arg63Trp), Ensembl rs2147283269
- I64F (p.Ile64Phe), TOPMed rs1055395165
- I64L (p.Ile64Leu), TOPMed rs1055395165
- I64M (p.Ile64Met), 1000Genomes rs773550639, ExAC rs773550639, TOPMed rs773550639, gnomAD rs773550639
- I64N (p.Ile64Asn), Ensembl rs2147282988
- I64V (p.Ile64Val), TOPMed rs1055395165, REVEL 0.14, CADD 23.80
- D65E (p.Asp65Glu), ExAC rs777077574, gnomAD rs777077574
- D65H (p.Asp65His), Ensembl rs2147282798
- D65N (p.Asp65Asn), NCI-TCGA Cosmic COSV6071, cosmic curated COSV60713, Ensembl rs2147282798, Variant assessed as somatic; moderate impact.
- D65V (p.Asp65Val), Ensembl rs2147282725
- D65Y (p.Asp65Tyr), cosmic curated COSV10464, Ensembl rs2147282798
- G66A (p.Gly66Ala), Ensembl rs2147282556
- G66D (p.Gly66Asp), cosmic curated COSV10590, Ensembl rs2147282556
- G66V (p.Gly66Val), Ensembl rs2147282556
- L67P (p.Leu67Pro), TOPMed rs1324288087, gnomAD rs1324288087
- L67Q (p.Leu67Gln), TOPMed rs1324288087, gnomAD rs1324288087
- L67R (p.Leu67Arg), TOPMed rs1324288087, gnomAD rs1324288087, REVEL 0.71, CADD 26.40
- L67V (p.Leu67Val), Ensembl rs2147282521
- A68G (p.Ala68Gly), Ensembl rs2147282280
- A68P (p.Ala68Pro), Ensembl rs2147282350
- A68T (p.Ala68Thr), cosmic curated COSV10065, Ensembl rs2147282350
- A68V (p.Ala68Val), Ensembl rs2147282280
- A69G (p.Ala69Gly), TOPMed rs1935736276, Uncertain significance
- A69P (p.Ala69Pro), Ensembl rs2147282110
- A69S (p.Ala69Ser), Ensembl rs2147282110
- A69T (p.Ala69Thr), Ensembl rs2147282110, REVEL 0.25, CADD 23.50
- A69V (p.Ala69Val), rs1935736276, ClinGen CA412749221, ClinVar RCV003148222, TOPMed rs1935736276, AlphaMissense 0.23, MetaLR 0.32, Uncertain significance, Oculofaciocardiodental syndrome
- L70M (p.Leu70Met), Ensembl rs2147281898, REVEL 0.39, CADD 23.20
- L70P (p.Leu70Pro), TOPMed rs1317086308, gnomAD rs1317086308, REVEL 0.78, CADD 26.90
- L70V (p.Leu70Val), Ensembl rs2147281898
- S71C (p.Ser71Cys), ExAC rs768862086, gnomAD rs768862086
- S71N (p.Ser71Asn), Ensembl rs2147281664
- S71R (p.Ser71Arg), ExAC rs768862086, gnomAD rs768862086, REVEL 0.38, CADD 24.80
- S71T (p.Ser71Thr), Ensembl rs2147281664
- M72I (p.Met72Ile), Ensembl rs2147281408, REVEL 0.21, CADD 23.00
- M72K (p.Met72Lys), Ensembl rs2147281455
- M72L (p.Met72Leu), gnomAD rs1339230290
- M72R (p.Met72Arg), Ensembl rs2147281455
- M72V (p.Met72Val), gnomAD rs1339230290, REVEL 0.24, CADD 22.80
- D73E (p.Asp73Glu), Ensembl rs2147281276
- D73H (p.Asp73His), Ensembl rs2147281350
- R74C (p.Arg74Cys), cosmic curated COSV60719, ExAC rs747350059, gnomAD rs747350059, REVEL 0.72, CADD 27.10
- R74G (p.Arg74Gly), ExAC rs747350059, gnomAD rs747350059
- R74H (p.Arg74His), rs1434826738, ClinGen CA412749189, cosmic curated COSV60713, ClinVar RCV000519315, REVEL 0.54, CADD 24.20, Uncertain significance, not provided; Oculofaciocardiodental syndrome
- R74P (p.Arg74Pro), TOPMed rs1434826738, gnomAD rs1434826738, Uncertain significance
- T75I (p.Thr75Ile), Ensembl rs2147280910
- T75S (p.Thr75Ser), Ensembl rs2147280910, REVEL 0.04, CADD 6.94, Likely benign, Oculofaciocardiodental syndrome
- G76A (p.Gly76Ala), Ensembl rs2147280841, REVEL 0.23, CADD 22.80
- G76D (p.Gly76Asp), Ensembl rs2147280841
- G76V (p.Gly76Val), Ensembl rs2147280841
- L77P (p.Leu77Pro), Ensembl rs2147280693
- L77Q (p.Leu77Gln), Ensembl rs2147280693
- L77V (p.Leu77Val), ExAC rs375552814, TOPMed rs375552814, gnomAD rs375552814
- I78F (p.Ile78Phe), TOPMed rs920090586, gnomAD rs920090586
- I78L (p.Ile78Leu), TOPMed rs920090586, gnomAD rs920090586
- I78M (p.Ile78Met), Ensembl rs2147280408
- I78N (p.Ile78Asn), Ensembl rs2147280491
- I78S (p.Ile78Ser), Ensembl rs2147280491
- I78T (p.Ile78Thr), Ensembl rs2147280491
- I78V (p.Ile78Val), TOPMed rs920090586, gnomAD rs920090586, REVEL 0.06, CADD 15.80
- R79G (p.Arg79Gly), TOPMed rs1462787258, gnomAD rs1462787258, REVEL 0.46, CADD 24.10, Uncertain significance
- R79L (p.Arg79Leu), cosmic curated COSV60720, 1000Genomes rs746635655, ExAC rs746635655, gnomAD rs746635655, REVEL 0.43, CADD 24.80
- R79Q (p.Arg79Gln), 1000Genomes rs746635655, ExAC rs746635655, gnomAD rs746635655, REVEL 0.22, CADD 23.40
- R79W (p.Arg79Trp), rs1462787258, ClinGen CA412749163, ClinVar RCV001952805, TOPMed rs1462787258, REVEL 0.64, CADD 28.60, Uncertain significance, Oculofaciocardiodental syndrome
- E80* (p.Glu80Ter), Ensembl rs2147280061
- E80D (p.Glu80Asp), gnomAD rs1172322701
- E80G (p.Glu80Gly), Ensembl rs2147279978
- E80K (p.Glu80Lys), Ensembl rs2147280061
- E80Q (p.Glu80Gln), Ensembl rs2147280061
- E80V (p.Glu80Val), Ensembl rs2147279978
- G81E (p.Gly81Glu), rs144450053, ClinGen CA10387069, ClinVar RCV002174936, ClinVar RCV002553686, REVEL 0.45, CADD 23.30, Benign/Likely benign, Inborn genetic diseases; Oculofaciocardiodental syndrome
- L82P (p.Leu82Pro), Ensembl rs2147279590
- L82Q (p.Leu82Gln), Ensembl rs2147279590
- L82R (p.Leu82Arg), Ensembl rs2147279590
- L82V (p.Leu82Val), Ensembl rs2147279686
- R83G (p.Arg83Gly), TOPMed rs1420747737, gnomAD rs1420747737
- R83L (p.Arg83Leu), Ensembl rs1321289860
- R83Q (p.Arg83Gln), cosmic curated COSV10590, Ensembl rs1321289860, REVEL 0.29, CADD 24.60
- R83W (p.Arg83Trp), cosmic curated COSV60722, TOPMed rs1420747737, gnomAD rs1420747737, REVEL 0.52, CADD 24.50
- V84A (p.Val84Ala), cosmic curated COSV60712, 1000Genomes rs61744882, ESP rs61744882, ExAC rs61744882, Likely benign
- V84D (p.Val84Asp), Ensembl rs2147279111
- V84G (p.Val84Gly), Ensembl rs2147279111
- V84I (p.Val84Ile), ExAC rs747983005, TOPMed rs747983005, gnomAD rs747983005
- V84L (p.Val84Leu), ExAC rs747983005, TOPMed rs747983005, gnomAD rs747983005, REVEL 0.17, CADD 21.70
- P85L (p.Pro85Leu), cosmic curated COSV10065
- P85S (p.Pro85Ser), cosmic curated COSV10742
Public BCOR analysis runs
- BCOR analysis run — BCOR (3,236 variants) — completed 2026-08-20