BAHD1

gene
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Also known as KIAA0945

Summary

BAHD1 (bromo adjacent homology domain containing 1, HGNC:29153) is a protein-coding gene on chromosome 15q15.1, encoding Bromo adjacent homology domain-containing 1 protein (Q8TBE0). Heterochromatin protein that acts as a transcription repressor and has the ability to promote the formation of large heterochromatic domains.

Enables chromatin binding activity. Involved in heterochromatin formation and negative regulation of DNA-templated transcription. Located in nucleoplasm. Part of chromatin silencing complex.

Source: NCBI Gene 22893 — RefSeq curated summary.

At a glance

  • GWAS associations: 6
  • Clinical variants (ClinVar): 135 total
  • MANE Select transcript: NM_014952

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29153
Approved symbolBAHD1
Namebromo adjacent homology domain containing 1
Location15q15.1
Locus typegene with protein product
StatusApproved
AliasesKIAA0945
Ensembl geneENSG00000140320
Ensembl biotypeprotein_coding
OMIM613880
Entrez22893

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 21 protein_coding, 1 retained_intron

ENST00000416165, ENST00000560846, ENST00000561234, ENST00000561464, ENST00000852443, ENST00000852444, ENST00000852445, ENST00000852446, ENST00000852447, ENST00000918911, ENST00000918912, ENST00000918913, ENST00000918914, ENST00000918915, ENST00000918916, ENST00000918917, ENST00000959369, ENST00000959370, ENST00000959371, ENST00000959372, ENST00000959373, ENST00000959374

RefSeq mRNA: 3 — MANE Select: NM_014952 NM_001301132, NM_001411044, NM_014952

CCDS: CCDS10058, CCDS73705, CCDS91980

Canonical transcript exons

ENST00000416165 — 7 exons

ExonStartEnd
ENSE000009424254046191240462294
ENSE000009424264046386140464020
ENSE000009424274046447140464547
ENSE000009424284046533540465435
ENSE000013775714045845140459896
ENSE000014929664044095340441268
ENSE000016298234046594140468236

Expression profiles

Bgee: expression breadth ubiquitous, 274 present calls, max score 91.57.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.7170 / max 109.8383, expressed in 1782 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
1461146.78731744
1461162.23751204
1461170.6444381
1461150.6311380
1461130.2017101
1461110.160763
1461120.054331

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
olfactory bulbUBERON:000226491.57silver quality
granulocyteCL:000009488.93gold quality
left adrenal gland cortexUBERON:003582588.15gold quality
right adrenal glandUBERON:000123388.11gold quality
left adrenal glandUBERON:000123488.03gold quality
type B pancreatic cellCL:000016988.01gold quality
upper arm skinUBERON:000426387.79gold quality
right lobe of thyroid glandUBERON:000111987.75gold quality
right ovaryUBERON:000211887.69gold quality
adrenal cortexUBERON:000123587.65gold quality
vena cavaUBERON:000408787.48gold quality
left ovaryUBERON:000211987.41gold quality
adrenal glandUBERON:000236987.23gold quality
left lobe of thyroid glandUBERON:000112087.21gold quality
mucosa of transverse colonUBERON:000499187.17gold quality
right adrenal gland cortexUBERON:003582787.12gold quality
apex of heartUBERON:000209886.73gold quality
thyroid glandUBERON:000204686.54gold quality
cardia of stomachUBERON:000116286.08gold quality
ovaryUBERON:000099285.59gold quality
right testisUBERON:000453485.40gold quality
left uterine tubeUBERON:000130385.08gold quality
lower esophagus mucosaUBERON:003583484.92gold quality
nippleUBERON:000203084.90gold quality
body of stomachUBERON:000116184.69gold quality
body of pancreasUBERON:000115084.67gold quality
left testisUBERON:000453384.60gold quality
adenohypophysisUBERON:000219684.54gold quality
thymusUBERON:000237084.51gold quality
adrenal tissueUBERON:001830384.48gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.95
E-MTAB-6058no39.61

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

137 targeting BAHD1, 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-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-8485100.0077.574731
HSA-MIR-9-5P100.0072.282361
HSA-MIR-6748-5P100.0065.811057
HSA-MIR-4455100.0065.481587
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-6740-5P100.0065.64932
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-302E99.9670.742669
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-141-3P99.9472.792421
HSA-MIR-200A-3P99.9472.682420
HSA-MIR-454-3P99.9174.011925
HSA-MIR-106A-5P99.9073.942683
HSA-MIR-130A-3P99.9073.311861
HSA-MIR-130B-3P99.9073.271850
HSA-MIR-301A-3P99.9073.151839
HSA-MIR-301B-3P99.9073.191836
HSA-MIR-366699.9073.241833
HSA-MIR-429599.9073.111838
HSA-MIR-17-5P99.8973.832665

Literature-anchored findings (GeneRIF, showing 11)

  • BAHD1 acts as a silencer by recruiting at specific promoters a set of proteins that coordinate heterochromatin assembly (PMID:19666599)
  • findings show a Listeria virulence factor, lmo0438/lntA, could target the chromatin repressor BAHD1 in host cell nucleus to activate interferon-stimulated genes; LntA-BAHD1 interplay may modulate IFN-lambda-mediated immune response to control host colonization (PMID:21252314)
  • Authors identified a dilysine motif (K180/K181) in the elbow region of Listeria monocytogenes LntA and a central proline-rich region in human BAHD1 as crucial for the direct LntA-BAHD1 interaction. (PMID:24449750)
  • computational approaches leveraging public gene expression data can be used to infer potential genes or proteins for diseases, and BAHD1 might act as an indispensable factor in regulating the cellular inflammatory response in UC. (PMID:26183847)
  • The BAH domain of BAHD1 is a histone H3K27me3 reader. (PMID:26850261)
  • Biochemical analysis of the BAHD1-associated multiprotein complex identifies MIER proteins as novel partners of BAHD1 and suggests that BAHD1-MIER interaction forms a hub for histone deacetylases and methyltransferases (PMID:26938916)
  • EFNA5, BAHD1 and PPP2R5E were particularly good candidates for novel disease loci (PMID:30352868)
  • The effect of partial BAHD1 deficiency on behavior was then evaluated on Bahd1 heterozygous male mice, which have no lethal or metabolic phenotypes. Bahd1+/- mice showed anxiety-like behavior and reduced prepulse inhibition (PPI) of the startle response. (PMID:32407325)
  • FBXO11-mediated proteolysis of BAHD1 relieves PRC2-dependent transcriptional repression in erythropoiesis. (PMID:33156908)
  • A conserved BAH module within mammalian BAHD1 connects H3K27me3 to Polycomb gene silencing. (PMID:33823544)
  • BAHD1 serves as a critical regulator of breast cancer cell proliferation and invasion. (PMID:35048286)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriobahd1ENSDARG00000086789
danio_rerioENSDARG00000102965
mus_musculusBahd1ENSMUSG00000040007
rattus_norvegicusBahd1ENSRNOG00000010428
drosophila_melanogasterwgeFBGN0051151

Paralogs (2): TNRC18 (ENSG00000182095), BAHCC1 (ENSG00000266074)

Protein

Protein identifiers

Bromo adjacent homology domain-containing 1 proteinQ8TBE0 (reviewed: Q8TBE0)

All UniProt accessions (1): Q8TBE0

UniProt curated annotations — full annotation on UniProt →

Function. Heterochromatin protein that acts as a transcription repressor and has the ability to promote the formation of large heterochromatic domains. May act by recruiting heterochromatin proteins such as CBX5 (HP1 alpha), HDAC5 and MBD1. Represses IGF2 expression by binding to its CpG-rich P3 promoter and recruiting heterochromatin proteins. At specific stages of Listeria infection, in complex with TRIM28, corepresses interferon-stimulated genes, including IFNL1, IFNL2 and IFNL3.

Subunit / interactions. Interacts with CBX5 (HP1 alpha), HDAC5, MBD1 and SP1. Forms a transcription silencing complex with at least CBX3 (HP1 gamma), HDAC1, HDAC2 and TRIM28. Interacts with L.monocytogenes LntA; this interaction, occurring at a late Listeria infection stage, relieves transcription repression, mostly that of interferon-stimulated genes. Interacts with FBXO11.

Subcellular location. Nucleus. Chromosome.

Post-translational modifications. Ubiquitinated in a FBXO11-dependent manner; leading to degradation.

Domain organisation. The BAH domain is required for localization at H3K27me3.

Isoforms (3)

UniProt IDNamesCanonical?
Q8TBE0-11yes
Q8TBE0-22
Q8TBE0-33

RefSeq proteins (3): NP_001288061, NP_001397973, NP_055767* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001025BAH_domDomain
IPR043151BAH_sfHomologous_superfamily
IPR053032BAH_domain-containingFamily

Pfam: PF01426

UniProt features (28 total): compositionally biased region 10, modified residue 6, region of interest 5, sequence variant 3, splice variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8TBE0-F151.190.12

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 (6): 8, 101, 121, 184, 206, 588

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 254 (showing top): MORF_RAGE, GGGACCA_MIR133A_MIR133B, RNGTGGGC_UNKNOWN, RRAGTTGT_UNKNOWN, GCM_GSPT1, TGCACTT_MIR519C_MIR519B_MIR519A, LFA1_Q6, GCANCTGNY_MYOD_Q6, MORF_ATRX, GGGTGGRR_PAX4_03, CAGCTG_AP4_Q5, SP1_Q2_01, CEBPB_01, NFKB_C, GOBP_NEGATIVE_REGULATION_OF_GENE_EXPRESSION_EPIGENETIC

GO Biological Process (3): heterochromatin formation (GO:0031507), negative regulation of DNA-templated transcription (GO:0045892), chromatin organization (GO:0006325)

GO Molecular Function (3): transcription cis-regulatory region binding (GO:0000976), chromatin binding (GO:0003682), protein binding (GO:0005515)

GO Cellular Component (4): nucleoplasm (GO:0005654), chromatin silencing complex (GO:0005677), chromosome (GO:0005694), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
cellular component assembly1
heterochromatin boundary formation1
negative regulation of gene expression, epigenetic1
heterochromatin organization1
DNA-templated transcription1
regulation of DNA-templated transcription1
negative regulation of RNA biosynthetic process1
cellular component organization1
transcription regulatory region nucleic acid binding1
sequence-specific double-stranded DNA binding1
nuclear lumen1
cellular anatomical structure1
nuclear protein-containing complex1
intracellular membraneless organelle1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1084 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BAHD1HDAC5Q9UQL6684
BAHD1SETDB1Q15047553
BAHD1MIER1Q8N108535
BAHD1PPP1R35Q8TAP8493
BAHD1MIER3Q7Z3K6488
BAHD1TRIM28Q13263474
BAHD1PDXDC1Q6P996441
BAHD1NAA30Q147X3437
BAHD1MRPL47Q9HD33434
BAHD1PHF20L1A8MW92413
BAHD1FBXL5Q9UKA1412
BAHD1RPUSD2Q8IZ73404
BAHD1PIK3IP1Q96FE7400
BAHD1TATDN2Q93075398
BAHD1TMEM43Q9BTV4394

IntAct

244 interactions, top by confidence:

ABTypeScore
MDFIBAHD1psi-mi:“MI:0915”(physical association)0.780
BAHD1LZTS2psi-mi:“MI:0915”(physical association)0.780
LZTS2BAHD1psi-mi:“MI:0915”(physical association)0.780
BAHD1MDFIpsi-mi:“MI:0915”(physical association)0.780
TRAF4BAHD1psi-mi:“MI:0915”(physical association)0.720
BAHD1TRAF4psi-mi:“MI:0915”(physical association)0.720
KHDRBS3BAHD1psi-mi:“MI:0915”(physical association)0.670
BAHD1KHDRBS3psi-mi:“MI:0915”(physical association)0.670
TRAF2BAHD1psi-mi:“MI:0915”(physical association)0.670
BAHD1DVL3psi-mi:“MI:0915”(physical association)0.670
BAHD1psi-mi:“MI:0915”(physical association)0.560
BAHD1psi-mi:“MI:0915”(physical association)0.560
BAHD1KRTAP10-7psi-mi:“MI:0915”(physical association)0.560
TLE5BAHD1psi-mi:“MI:0915”(physical association)0.560
GOLGA2BAHD1psi-mi:“MI:0915”(physical association)0.560
CALCOCO2BAHD1psi-mi:“MI:0915”(physical association)0.560
BAHD1KRT40psi-mi:“MI:0915”(physical association)0.560
KRTAP10-7BAHD1psi-mi:“MI:0915”(physical association)0.560
BAHD1CALCOCO2psi-mi:“MI:0915”(physical association)0.560

BioGRID (83): BAHD1 (Two-hybrid), BAHD1 (Two-hybrid), BAHD1 (Two-hybrid), BAHD1 (Two-hybrid), BAHD1 (Two-hybrid), BAHD1 (Two-hybrid), LZTS2 (Two-hybrid), KRT40 (Two-hybrid), KRTAP10-7 (Two-hybrid), KRTAP10-1 (Two-hybrid), KRTAP10-3 (Two-hybrid), BAHD1 (Affinity Capture-MS), BAHD1 (Two-hybrid), BAHD1 (Two-hybrid), BEGAIN (Two-hybrid)

ESM2 similar proteins: A0JNJ4, A2APT9, A6NEL2, A6NP61, B1ASB6, B1WBS3, B2RXF5, F6WEQ6, O15015, O43918, O88282, O88286, O95785, P98168, P98169, Q2M3G4, Q2MHN3, Q2QGD7, Q3U1J1, Q3U381, Q497V6, Q5SW24, Q5SXM2, Q6YND2, Q6ZMQ8, Q6ZMY3, Q7TN08, Q7TSX9, Q80SU3, Q80YE4, Q811H0, Q8BG26, Q8BZW2, Q8C8V1, Q8IX07, Q8IY92, Q8N143, Q8N1G0, Q8NC74, Q8TBE0

Diamond homologs: O15417, Q3LHL9, Q497V6, Q80WC3, Q8TBE0, F4JGB7, F4JL28, Q3UHR0, Q9FEN9, Q9P281

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 64 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
Keratinization78.9×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance131
Likely benign2
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

939 predictions. Top by Δscore:

VariantEffectΔscore
15:40463851:T:TAacceptor_gain1.0000
15:40463858:TA:Tacceptor_loss1.0000
15:40463859:A:AGacceptor_gain1.0000
15:40463859:AG:Aacceptor_gain1.0000
15:40463860:G:GTacceptor_gain1.0000
15:40463860:GG:Gacceptor_gain1.0000
15:40463860:GGAT:Gacceptor_gain1.0000
15:40464017:TCAGG:Tdonor_loss1.0000
15:40464018:CAG:Cdonor_loss1.0000
15:40464021:G:GAdonor_loss1.0000
15:40464022:T:Gdonor_loss1.0000
15:40464466:TCCA:Tacceptor_loss1.0000
15:40464469:A:AGacceptor_gain1.0000
15:40464469:AGG:Aacceptor_loss1.0000
15:40464470:G:GGacceptor_gain1.0000
15:40464470:GGA:Gacceptor_gain1.0000
15:40464547:GGT:Gdonor_loss1.0000
15:40464548:GT:Gdonor_loss1.0000
15:40464549:T:Gdonor_loss1.0000
15:40465331:T:TAacceptor_gain1.0000
15:40465333:A:AGacceptor_gain1.0000
15:40465334:G:GGacceptor_gain1.0000
15:40465432:GCAG:Gdonor_gain1.0000
15:40465433:CAGG:Cdonor_loss1.0000
15:40465436:G:GAdonor_loss1.0000
15:40465436:G:GGdonor_gain1.0000
15:40465940:GGTTC:Gacceptor_gain1.0000
15:40462292:TTGGT:Tdonor_loss0.9900
15:40462293:TGG:Tdonor_loss0.9900
15:40462294:GGT:Gdonor_loss0.9900

AlphaMissense

4977 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:40462250:T:AW591R1.000
15:40462250:T:CW591R1.000
15:40462251:G:CW591S1.000
15:40462252:G:CW591C1.000
15:40462252:G:TW591C1.000
15:40463891:T:GY616D1.000
15:40463933:G:CD630H1.000
15:40463934:A:CD630A1.000
15:40463934:A:TD630V1.000
15:40463940:T:AV632D1.000
15:40463943:T:CL633P1.000
15:40463946:T:AL634H1.000
15:40463946:T:CL634P1.000
15:40463985:C:AA647D1.000
15:40463989:G:CK648N1.000
15:40463989:G:TK648N1.000
15:40463991:T:AI649N1.000
15:40463991:T:GI649S1.000
15:40463996:G:CA651P1.000
15:40464000:T:CL652P1.000
15:40464002:T:AW653R1.000
15:40464002:T:CW653R1.000
15:40464003:G:CW653S1.000
15:40464004:G:CW653C1.000
15:40464004:G:TW653C1.000
15:40464485:A:CS664R1.000
15:40464487:C:AS664R1.000
15:40464487:C:GS664R1.000
15:40464489:T:AL665H1.000
15:40464489:T:CL665P1.000

dbSNP variants (sampled 300 via entrez): RS1000050417 (15:40454025 A>G), RS1000063701 (15:40441912 C>A,G,T), RS1000281142 (15:40437985 G>A), RS1000285592 (15:40450374 T>C), RS1000437327 (15:40455694 C>A,G,T), RS1000482275 (15:40467750 C>G,T), RS1000552674 (15:40437601 C>A), RS1000615673 (15:40439890 G>T), RS1000701201 (15:40467434 G>A,C), RS1000725808 (15:40456468 C>T), RS1000732444 (15:40444732 G>A), RS1000964166 (15:40445659 G>A), RS1000995268 (15:40445937 G>C), RS1000998898 (15:40461357 G>C,T), RS1001085831 (15:40460720 A>C,G)

Disease associations

OMIM: gene MIM:613880 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

StudyTraitp-value
GCST010002_167Refractive error3.000000e-11
GCST010242_81HDL cholesterol levels2.000000e-08
GCST010725_23Malaria2.000000e-06
GCST010725_38Malaria3.000000e-06
GCST010725_80Malaria7.000000e-06
GCST90002396_631Mean reticulocyte volume2.000000e-16

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0010701mean reticulocyte volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs3803357BAHD10.000

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression4
Arsenicdecreases expression, decreases methylation, increases abundance, affects cotreatment, increases expression3
Benzo(a)pyrenedecreases methylation, increases methylation, increases mutagenesis2
Valproic Aciddecreases methylation, increases expression2
FR900359increases phosphorylation1
dicrotophosincreases expression1
methylmercuric chlorideincreases expression1
triphenyl phosphateaffects expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
2-palmitoylglycerolincreases expression1
Doxorubicindecreases expression1
Manganeseaffects cotreatment, increases abundance, increases expression1
Ouabaindecreases expression1
Smokedecreases expression1
Thiramincreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethaneincreases expression1
Cyclosporineincreases expression1
Metals, Heavyincreases abundance, decreases methylation1
Copper Sulfateincreases expression1
Lactic Acidincreases expression1
Acrylamideincreases expression1
Vitamin K 3affects expression1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_D6BHHyCyte HeLa KO-hBAHD1Cancer cell lineFemale
CVCL_D9YGUbigene HeLa BAHD1 KOCancer cell lineFemale

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.