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Atlas / Gene / BACC1

BACC1

gene
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Also known as MGC49942BAP18HEPIS

Summary

BACC1 (BPTF associated chromatin complex component 1, HGNC:28737) is a protein-coding gene on chromosome 17p13.1, encoding BPTF-associated chromatin complex component 1 (Q8IXM2). Component of chromatin complexes such as the MLL1/MLL and NURF complexes. It is a selective cancer dependency (DepMap: 17.0% of cell lines).

Enables identical protein binding activity. Predicted to be involved in chromatin organization. Located in cytosol and nucleoplasm. Part of MLL1 complex and NURF complex.

Source: NCBI Gene 124944 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 4 total — 1 pathogenic
  • Cancer dependency (DepMap): dependent in 17.0% of screened cell lines
  • MANE Select transcript: NM_174893

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28737
Approved symbolBACC1
NameBPTF associated chromatin complex component 1
Location17p13.1
Locus typegene with protein product
StatusApproved
AliasesMGC49942, BAP18, HEPIS
Ensembl geneENSG00000258315
Ensembl biotypeprotein_coding
OMIM617215
Entrez124944

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 11 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000439424, ENST00000546495, ENST00000546760, ENST00000547709, ENST00000547747, ENST00000549857, ENST00000550038, ENST00000552402, ENST00000552775, ENST00000857273, ENST00000913091, ENST00000913092, ENST00000913093, ENST00000913094, ENST00000913095

RefSeq mRNA: 3 — MANE Select: NM_174893 NM_001142798, NM_001142799, NM_174893

CCDS: CCDS32542, CCDS45595, CCDS45596

Canonical transcript exons

ENST00000439424 — 6 exons

ExonStartEnd
ENSE0000241574070147827014878
ENSE0000346824870164957016685
ENSE0000347999470157747015875
ENSE0000352142970169107017014
ENSE0000355169270172617017520
ENSE0000360118870150627015156

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 97.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 71.9335 / max 443.1374, expressed in 1827 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
15909341.04081823
15909512.94441796
15909210.73581784
1590966.11901640
1590940.5832324
1590970.5103124

Top tissues by expression

134 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009497.99gold quality
ganglionic eminenceUBERON:000402397.64gold quality
cortical plateUBERON:000534397.30gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099197.13gold quality
ventricular zoneUBERON:000305396.85gold quality
lymph nodeUBERON:000002996.84gold quality
bone marrowUBERON:000237196.49gold quality
amygdalaUBERON:000187696.47gold quality
temporal lobeUBERON:000187196.38gold quality
spleenUBERON:000210696.29gold quality
leukocyteCL:000073896.26gold quality
vermiform appendixUBERON:000115496.26gold quality
putamenUBERON:000187496.25gold quality
monocyteCL:000057696.14gold quality
prefrontal cortexUBERON:000045196.08gold quality
stromal cell of endometriumCL:000225596.05gold quality
bone marrow cellCL:000209296.04gold quality
Ammon’s hornUBERON:000195496.02gold quality
right lungUBERON:000216795.95gold quality
hypothalamusUBERON:000189895.88gold quality
substantia nigraUBERON:000203895.82gold quality
cerebral cortexUBERON:000095695.67gold quality
frontal cortexUBERON:000187095.66gold quality
anterior cingulate cortexUBERON:000983595.65gold quality
olfactory segment of nasal mucosaUBERON:000538695.62gold quality
caudate nucleusUBERON:000187395.58gold quality
skin of legUBERON:000151195.57gold quality
dorsolateral prefrontal cortexUBERON:000983495.53gold quality
nucleus accumbensUBERON:000188295.52gold quality
subcutaneous adipose tissueUBERON:000219095.46gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes7.40
E-CURD-112no2.47

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

25 targeting BACC1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3163100.0077.238605
HSA-MIR-4533100.0069.482758
HSA-MIR-56899.9869.862084
HSA-MIR-3912-5P99.9566.11925
HSA-MIR-368699.9070.532432
HSA-MIR-449399.9066.48977
HSA-MIR-10393-3P99.7266.56961
HSA-MIR-6801-5P99.7266.50981
HSA-MIR-320299.6667.702737
HSA-MIR-613499.6365.681537
HSA-MIR-4743-3P99.6268.122095
HSA-MIR-24-3P99.5969.971934
HSA-MIR-4652-3P99.3370.022742
HSA-MIR-429199.2068.882969
HSA-MIR-92299.0267.231838
HSA-MIR-3619-5P99.0068.872308
HSA-MIR-6770-5P98.9766.761853
HSA-MIR-4742-3P98.7369.821803
HSA-MIR-214-3P98.7168.122128
HSA-MIR-76198.7168.072051
HSA-MIR-4722-5P98.4666.341611
HSA-MIR-1245B-3P98.0168.911387
HSA-MIR-425797.8668.051190
HSA-MIR-493-3P97.5066.44731
HSA-MIR-990096.0665.48557

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 17.0% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 6)

  • BAP18 as an epigenetic modifier regulates AR-induced transactivation and the function of BAP18 might be targeted in human prostate cancer to promote tumor growth and progression to castration-resistance. (PMID:27226492)
  • BAP18 is involved in upregulation of CCND1/2 transcription to promote cell growth in oral squamous cell carcinoma. (PMID:32113162)
  • An H3K4me3 reader, BAP18 as an adaptor of COMPASS-like core subunits co-activates ERalpha action and associates with the sensitivity of antiestrogen in breast cancer. (PMID:32986841)
  • BAP18 induces growth of non-small-cell lung carcinoma through upregulating transcriptional level of CCND1/2. (PMID:35587057)
  • BAP18 facilitates CTCF-mediated chromatin accessible to regulate enhancer activity in breast cancer. (PMID:36828916)
  • BAP18 acting as a novel peroxisome proliferator-activated receptor alpha co-regulator contributes to hepatocellular carcinoma progression. (PMID:38042310)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_rerioBACC1ENSDARG00000015161
danio_rerioBACC1ENSDARG00000099273
mus_musculusBacc1ENSMUSG00000020831
rattus_norvegicusC10h17orf49ENSRNOG00000018829
drosophila_melanogasterCG33695FBGN0052831
caenorhabditis_elegansWBGENE00012828
caenorhabditis_elegansWBGENE00012829

Protein

Protein identifiers

BPTF-associated chromatin complex component 1 — Q8IXM2 (reviewed: Q8IXM2)

Alternative names: BPTF-associated protein of 18 kDa, Chromatin complexes subunit BAP18

All UniProt accessions (4): Q8IXM2, F8W038, F8W1H0, K7ES76

UniProt curated annotations — full annotation on UniProt →

Function. Component of chromatin complexes such as the MLL1/MLL and NURF complexes.

Subunit / interactions. Component of some MLL1/MLL complex, at least composed of the core components KMT2A/MLL1, ASH2L, HCFC1/HCF1, WDR5 and RBBP5, as well as the facultative components BACC1, CHD8, E2F6, HSP70, INO80C, KANSL1, LAS1L, MAX, MCRS1, MGA, KAT8/MOF, PELP1, PHF20, PRP31, RING2, RUVB1/TIP49A, RUVB2/TIP49B, SENP3, TAF1, TAF4, TAF6, TAF7, TAF9 and TEX10. Component of the nucleosome-remodeling factor (NURF) complex.

Subcellular location. Nucleus.

Isoforms (3)

UniProt IDNamesCanonical?
Q8IXM2-11yes
Q8IXM2-22
Q8IXM2-33

RefSeq proteins (3): NP_001136270, NP_001136271, NP_777553* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001005SANT/MybDomain
IPR009057Homeodomain-like_sfHomologous_superfamily

UniProt features (8 total): compositionally biased region 2, splice variant 2, chain 1, domain 1, region of interest 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8IXM2-F170.360.30

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 96

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 62 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, SHEPARD_BMYB_MORPHOLINO_DN, WANG_LMO4_TARGETS_DN, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, GUO_HEX_TARGETS_DN, SHEPARD_BMYB_TARGETS, GOCC_TRANSFERASE_COMPLEX, CTGAGCC_MIR24, GOCC_HISTONE_METHYLTRANSFERASE_COMPLEX, GOCC_MLL1_2_COMPLEX, GOCC_METHYLTRANSFERASE_COMPLEX, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOCC_ATPASE_COMPLEX, SANSOM_APC_TARGETS_REQUIRE_MYC, MATSUDA_NATURAL_KILLER_DIFFERENTIATION

GO Biological Process (1): chromatin organization (GO:0006325)

GO Molecular Function (3): DNA binding (GO:0003677), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (5): nucleoplasm (GO:0005654), cytosol (GO:0005829), NURF complex (GO:0016589), MLL1 complex (GO:0071339), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
cellular component organization1
nucleic acid binding1
protein binding1
binding1
nuclear lumen1
cytoplasm1
ISWI-type complex1
MLL1/2 complex1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

356 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BACC1DPY30Q9C005697
BACC1BPTFQ12830680
BACC1ASH2LQ9UBL3401
BACC1ACTR8Q9H981392
BACC1AKAP8O43823383
BACC1SETD4Q9NVD3368
BACC1ACTR5Q9H9F9343
BACC1PHF10Q8WUB8321
BACC1SETD1AO15047318
BACC1CHD5Q8TDI0313
BACC1SGF29Q96ES7311
BACC1HMGXB4Q9UGU5300
BACC1ZBTB35P52739290
BACC1WDR5P61964277
BACC1LRTM1Q9HBL6271

IntAct

61 interactions, top by confidence:

ABTypeScore
RBBP4CDK2AP1psi-mi:“MI:0914”(association)0.790
MAGEA3BACC1psi-mi:“MI:0915”(physical association)0.670
DPY30BACC1psi-mi:“MI:0407”(direct interaction)0.640
KPNA1TCERG1psi-mi:“MI:0914”(association)0.640
RPL10ARRP8psi-mi:“MI:0914”(association)0.640
DPY30AKAP8psi-mi:“MI:0914”(association)0.610
YY1YY2psi-mi:“MI:0914”(association)0.570
BACC1BACC1psi-mi:“MI:0915”(physical association)0.560
BACC1GRNpsi-mi:“MI:0915”(physical association)0.560
BACC1NEFLpsi-mi:“MI:0915”(physical association)0.560
BACC1WFS1psi-mi:“MI:0915”(physical association)0.560
BACC1KIF1Bpsi-mi:“MI:0915”(physical association)0.560
BACC1RNF11psi-mi:“MI:0915”(physical association)0.560
DPY30BPTFpsi-mi:“MI:0914”(association)0.530
TRIM44ODAD3psi-mi:“MI:0914”(association)0.530
SMARCA5RBBP4psi-mi:“MI:0914”(association)0.530
RBBP4TNRC18psi-mi:“MI:0914”(association)0.530
BACC1SMARCA1psi-mi:“MI:0914”(association)0.530

BioGRID (133): C17orf49 (Protein-peptide), RBBP4 (Affinity Capture-MS), HMGXB4 (Affinity Capture-MS), BPTF (Affinity Capture-MS), SMARCA5 (Affinity Capture-MS), SMARCA1 (Affinity Capture-MS), RBBP7 (Affinity Capture-MS), HSPA1A (Affinity Capture-MS), HSPA9 (Affinity Capture-MS), LMNB1 (Affinity Capture-MS), HSPA8 (Affinity Capture-MS), LMNA (Affinity Capture-MS), C17orf49 (Affinity Capture-MS), C17orf49 (Affinity Capture-MS), C17orf49 (Proximity Label-MS)

ESM2 similar proteins: A0A0G2K0D3, A0JPM9, A2AQ19, A2VDN6, B2GV05, O43395, O75391, O75822, P29540, P50478, P52756, P82979, Q02614, Q0VCU8, Q13123, Q15459, Q15650, Q1RMU5, Q2KIA6, Q2KJF9, Q32LD1, Q3UGC7, Q498U4, Q5NVI3, Q5R4V4, Q5R5F1, Q5R8D1, Q5RAD5, Q5ZJ85, Q5ZK25, Q5ZKA4, Q66HG8, Q66JS6, Q6GR00, Q6P320, Q7TNE3, Q8IXM2, Q8K4Z5, Q91YE7, Q922U1

Diamond homologs: Q32LD1, Q8IXM2, Q9DCT6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 58 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
RNA Polymerase III Abortive And Retractive Initiation537.6×1e-05
Negative epigenetic regulation of rRNA expression535.1×1e-05
Activation of anterior HOX genes in hindbrain development during early embryogenesis1127.2×4e-11
B-WICH complex positively regulates rRNA expression826.3×8e-08
Influenza Infection523.7×4e-05
Transcriptional regulation by small RNAs623.4×1e-05
Inhibition of DNA recombination at telomere522.7×5e-05
HIV Life Cycle521.7×6e-05

GO biological processes:

GO termPartnersFoldFDR
nucleosome assembly512.5×5e-03
chromatin remodeling810.4×3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

4 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance0
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
980123GRCh37/hg19 17p13.1(chr17:6650649-8040151)x3Pathogenic

SpliceAI

1207 predictions. Top by Δscore:

VariantEffectΔscore
17:7014874:CAAAG:Cdonor_loss1.0000
17:7014875:AAAG:Adonor_loss1.0000
17:7015152:GCGGG:Gdonor_gain1.0000
17:7015154:GGG:Gdonor_gain1.0000
17:7015155:GG:Gdonor_gain1.0000
17:7015155:GGG:Gdonor_gain1.0000
17:7015155:GGGTA:Gdonor_loss1.0000
17:7015156:GG:Gdonor_gain1.0000
17:7015157:GTAC:Gdonor_loss1.0000
17:7015239:G:Tdonor_gain1.0000
17:7015852:C:Gdonor_gain1.0000
17:7015865:G:GTdonor_gain1.0000
17:7015866:A:Tdonor_gain1.0000
17:7015871:A:Tdonor_gain1.0000
17:7015874:G:GGdonor_gain1.0000
17:7015874:GT:Gdonor_gain1.0000
17:7015876:G:GGdonor_gain1.0000
17:7015881:G:GTdonor_gain1.0000
17:7015882:G:Tdonor_gain1.0000
17:7016491:TCA:Tacceptor_loss1.0000
17:7016493:A:AGacceptor_gain1.0000
17:7016493:AG:Aacceptor_gain1.0000
17:7016493:AGG:Aacceptor_gain1.0000
17:7016494:G:Aacceptor_gain1.0000
17:7016494:G:GAacceptor_loss1.0000
17:7016494:G:GCacceptor_gain1.0000
17:7016494:G:GGacceptor_gain1.0000
17:7016494:GGG:Gacceptor_gain1.0000
17:7016557:C:Gdonor_gain1.0000
17:7016909:GAT:Gacceptor_gain1.0000

AlphaMissense

1110 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:7015074:T:CF12L1.000
17:7015075:T:CF12S1.000
17:7015076:C:AF12L1.000
17:7015076:C:GF12L1.000
17:7015084:C:AA15D1.000
17:7015086:G:CG16R1.000
17:7015087:G:AG16D1.000
17:7015095:T:CF19L1.000
17:7015096:T:CF19S1.000
17:7015097:C:AF19L1.000
17:7015097:C:GF19L1.000
17:7015105:T:AL22H1.000
17:7015105:T:CL22P1.000
17:7015107:G:AG23R1.000
17:7015107:G:CG23R1.000
17:7015107:G:TG23W1.000
17:7015108:G:AG23E1.000
17:7015114:T:CL25P1.000
17:7015126:T:CL29P1.000
17:7015781:T:AW42R1.000
17:7015781:T:CW42R1.000
17:7015783:G:CW42C1.000
17:7015783:G:TW42C1.000
17:7015806:T:CL50P1.000
17:7015826:T:CF57L1.000
17:7015827:T:CF57S1.000
17:7015828:T:AF57L1.000
17:7015828:T:GF57L1.000
17:7015839:T:AL61H1.000
17:7015839:T:CL61P1.000

dbSNP variants (sampled 300 via entrez): RS1000296550 (17:7012914 G>A,C), RS1001139790 (17:7015996 T>A,C), RS1001337651 (17:7017410 G>A), RS1001397642 (17:7017139 C>G,T), RS1001828550 (17:7015363 A>C,G), RS1001872040 (17:7017629 G>C), RS1001930551 (17:7013152 G>A), RS1001987045 (17:7015720 G>A,T), RS1003843299 (17:7013170 G>A), RS1003969414 (17:7015567 G>A,C), RS1004257647 (17:7015298 C>A), RS1006066314 (17:7017306 T>C), RS1007762344 (17:7014018 A>C,G,T), RS1007981173 (17:7014803 C>A,G,T), RS1008095763 (17:7014995 G>A)

Disease associations

OMIM: gene MIM:617215 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, affects expression, increases methylation7
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression, decreases expression2
bisphenol Faffects cotreatment, increases expression1
triphenyl phosphateaffects expression1
bisphenol Aincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
bisphenol Saffects cotreatment, increases expression1
jinfukangincreases expression1
LDN 193189affects cotreatment, increases expression1
Decitabineaffects expression1
Atrazineincreases expression1
Cisplatinaffects expression1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Estradioldecreases expression1
Indomethacinaffects cotreatment, increases expression1
Ivermectindecreases expression1
Smokedecreases expression1
Tretinoindecreases expression1
Tunicamycindecreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Cyclosporineincreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot