H2BC1

Summary

H2BC1 (H2B clustered histone 1, HGNC:18730) is a protein-coding gene on chromosome 6p22.2, encoding Histone H2B type 1-A (Q96A08). Variant histone specifically required to direct the transformation of dissociating nucleosomes to protamine in male germ cells.

Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene is intronless and encodes a replication-dependent histone that is a testis/sperm-specific member of the histone H2B family. Transcripts from this gene contain a palindromic termination element.

Source: NCBI Gene 255626 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 37 total
• Druggable target: yes
• MANE Select transcript: NM_170610

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18730
Approved symbol	H2BC1
Name	H2B clustered histone 1
Location	6p22.2
Locus type	gene with protein product
Status	Approved
Aliases	bA317E16.3, STBP, TSH2B, H2BFU
Ensembl gene	ENSG00000146047
Ensembl biotype	protein_coding
OMIM	609904
Entrez	255626

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000274764

RefSeq mRNA: 1 — MANE Select: NM_170610 NM_170610

CCDS: CCDS4563

Canonical transcript exons

ENST00000274764 — 1 exons

Exon	Start	End
ENSE00000973630	25726777	25727345

Expression profiles

Bgee: expression breadth broad, 23 present calls, max score 94.24.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 23.8535 / max 17303.1689, expressed in 165 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
66444	23.8535	165

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	94.24	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.35	gold quality
left testis	UBERON:0004533	69.00	gold quality
right testis	UBERON:0004534	68.29	gold quality
testis	UBERON:0000473	67.98	gold quality
pancreatic ductal cell	CL:0002079	56.30	silver quality
sperm	CL:0000019	54.93	silver quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
epithelial cell of pancreas	CL:0000083	54.20	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
tibialis anterior	UBERON:0001385	53.83	silver quality
upper arm skin	UBERON:0004263	53.52	gold quality
myocardium	UBERON:0002349	50.25	gold quality
lower lobe of lung	UBERON:0008949	50.08	silver quality
ileal mucosa	UBERON:0000331	48.75	silver quality
deltoid	UBERON:0001476	48.67	gold quality
nasal cavity epithelium	UBERON:0005384	47.03	gold quality
quadriceps femoris	UBERON:0001377	46.74	gold quality
vastus lateralis	UBERON:0001379	45.40	gold quality
layer of synovial tissue	UBERON:0007616	43.55	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
colonic epithelium	UBERON:0000397	41.42	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
muscle tissue	UBERON:0002385	41.17	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
skeletal muscle tissue	UBERON:0001134	41.05	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
cartilage tissue	UBERON:0002418	40.77	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.99

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 4)

• Reconstituted TSH2B containing octamers are able to form nucleosome core particles which are structurally and dynamically indistinguishable from those reconstituted with octamers consisting of only native histones. (PMID:15709765)
• Data show that histone H2B of prostate cancer cell line DU-145 have hypoacetylation, hypomethylation, and dephosphorylation, suggesting there was an excessive histone deacetylase activity in the cells. (PMID:26759222)
• In a process of single-strand DNA repair, PARP3 mono-ADP-ribosylates nucleosomal histone H2B. (PMID:27716488)
• Data indicate that lactate dehydrogenase A (LDHA) is involved in the transcription of histone 2B gene. (PMID:28257841)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	H2bc1	ENSMUSG00000050799
rattus_norvegicus	H2bc1	ENSRNOG00000084925

Paralogs (21): H2BW2 (ENSG00000101812), H2BW1 (ENSG00000123569), H2BC11 (ENSG00000124635), H2BC5 (ENSG00000158373), H2BC4 (ENSG00000180596), H2BC21 (ENSG00000184678), H2BC13 (ENSG00000185130), H2BC26 (ENSG00000196890), H2BC12 (ENSG00000197903), H2BC18 (ENSG00000203814), H2BC15 (ENSG00000233822), H2BC12L (ENSG00000234289), H2BC14 (ENSG00000273703), H2BC8 (ENSG00000273802), H2BC6 (ENSG00000274290), H2BC17 (ENSG00000274641), H2BC9 (ENSG00000275713), H2BC3 (ENSG00000276410), H2BC7 (ENSG00000277224), H2BC10 (ENSG00000278588), H2BK1 (ENSG00000285480)

Protein

Protein identifiers

Histone H2B type 1-A — Q96A08 (reviewed: Q96A08)

Alternative names: Histone H2B, testis, Testis-specific histone H2B

All UniProt accessions (1): Q96A08

UniProt curated annotations — full annotation on UniProt →

Function. Variant histone specifically required to direct the transformation of dissociating nucleosomes to protamine in male germ cells. Entirely replaces classical histone H2B prior nucleosome to protamine transition and probably acts as a nucleosome dissociating factor that creates a more dynamic chromatin, facilitating the large-scale exchange of histones. Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. Also found in fat cells, its function and the presence of post-translational modifications specific to such cells are still unclear.

Subunit / interactions. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers.

Subcellular location. Nucleus. Chromosome.

Tissue specificity. Mainly expressed in testis, and the corresponding protein is also present in mature sperm (at protein level). Also found in some fat cells.

Post-translational modifications. Monoubiquitination at Lys-36 (H2BK34Ub) by the MSL1/MSL2 dimer is required for histone H3 ‘Lys-4’ (H3K4me) and ‘Lys-79’ (H3K79me) methylation and transcription activation at specific gene loci, such as HOXA9 and MEIS1 loci. Similarly, monoubiquitination at Lys-122 (H2BK120Ub) by the RNF20/40 complex gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 ‘Lys-4’ and ‘Lys-79’ methylation. It also functions cooperatively with the FACT dimer to stimulate elongation by RNA polymerase II. H2BK120Ub also acts as a regulator of mRNA splicing: deubiquitination by USP49 is required for efficient cotranscriptional splicing of a large set of exons. Crotonylation (Kcr) is specifically present in male germ cells and marks testis-specific genes in post-meiotic cells, including X-linked genes that escape sex chromosome inactivation in haploid cells. Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors. It is also associated with post-meiotically activated genes on autosomes. Acetylated during spermatogenesis. Acetylated form is most abundant in spermatogonia compared to spermatocytes and round spermatids. Phosphorylated at Thr-117 in spermatogonia, spermatocytes and round spermatids. Methylated at Lys-118 in spermatogonia, spermatocytes and round spermatids. Lactylated in macrophages by EP300/P300 by using lactoyl-CoA directly derived from endogenous or exogenous lactate, leading to stimulates gene transcription.

Similarity. Belongs to the histone H2B family.

RefSeq proteins (1): NP_733759* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000558	Histone_H2B	Family
IPR007125	H2A/H2B/H3	Domain
IPR009072	Histone-fold	Homologous_superfamily
IPR055333	HISTONE_H2B_site	Conserved_site

Pfam: PF00125

UniProt features (72 total): modified residue 57, cross-link 4, helix 4, sequence conflict 3, initiator methionine 1, chain 1, region of interest 1, strand 1

Structure

Experimental structures (PDB)

5 structures.

PDB	Method	Resolution (Å)
6BIY	X-RAY DIFFRACTION	2.05
8VLR	ELECTRON MICROSCOPY	2.6
3WKJ	X-RAY DIFFRACTION	2.8
5GT3	X-RAY DIFFRACTION	2.91
5GSU	X-RAY DIFFRACTION	3.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96A08-F1	84.88	0.70

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 (61): 13, 13, 13, 13, 14, 14, 17, 17, 17, 17, 18, 18, 18, 18, 18, 22, 22, 22, 22, 22 …

Function

Pathways and Gene Ontology

Reactome pathways

58 pathways

ID	Pathway
R-HSA-110328	Recognition and association of DNA glycosylase with site containing an affected pyrimidine
R-HSA-110329	Cleavage of the damaged pyrimidine
R-HSA-110330	Recognition and association of DNA glycosylase with site containing an affected purine
R-HSA-110331	Cleavage of the damaged purine
R-HSA-1221632	Meiotic synapsis
R-HSA-171306	Packaging Of Telomere Ends
R-HSA-1912408	Pre-NOTCH Transcription and Translation
R-HSA-201722	Formation of the beta-catenin:TCF transactivating complex
R-HSA-212300	PRC2 methylates histones and DNA
R-HSA-2299718	Condensation of Prophase Chromosomes
R-HSA-2559580	Oxidative Stress Induced Senescence
R-HSA-2559582	Senescence-Associated Secretory Phenotype (SASP)
R-HSA-2559586	DNA Damage/Telomere Stress Induced Senescence
R-HSA-3214815	HDACs deacetylate histones
R-HSA-3214847	HATs acetylate histones
R-HSA-427359	SIRT1 negatively regulates rRNA expression
R-HSA-427389	ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
R-HSA-427413	NoRC negatively regulates rRNA expression
R-HSA-5250924	B-WICH complex positively regulates rRNA expression
R-HSA-5334118	DNA methylation
R-HSA-5578749	Transcriptional regulation by small RNAs
R-HSA-5617472	Activation of anterior HOX genes in hindbrain development during early embryogenesis
R-HSA-5625886	Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
R-HSA-5689880	Ub-specific processing proteases
R-HSA-5693565	Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
R-HSA-5693571	Nonhomologous End-Joining (NHEJ)
R-HSA-5693607	Processing of DNA double-strand break ends
R-HSA-606279	Deposition of new CENPA-containing nucleosomes at the centromere
R-HSA-68616	Assembly of the ORC complex at the origin of replication
R-HSA-69473	G2/M DNA damage checkpoint

MSigDB gene sets: 187 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, REACTOME_MEIOTIC_RECOMBINATION, GOBP_CHROMOSOME_ORGANIZATION, REACTOME_DNA_REPLICATION, REACTOME_SIGNALING_BY_NOTCH, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_MEIOTIC_SYNAPSIS, GOBP_INFLAMMATORY_RESPONSE, REACTOME_G2_M_DNA_DAMAGE_CHECKPOINT, GOCC_CELL_SURFACE, MEF2_02, GOBP_MALE_GAMETE_GENERATION, REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS, GOBP_LEUKOCYTE_MIGRATION, GOBP_PROTEIN_MATURATION

GO Biological Process (8): nucleosome assembly (GO:0006334), nucleosome disassembly (GO:0006337), inflammatory response (GO:0006954), plasminogen activation (GO:0031639), sperm DNA condensation (GO:0035092), chromosome organization (GO:0051276), mononuclear cell migration (GO:0071674), chromatin organization (GO:0006325)

GO Molecular Function (4): DNA binding (GO:0003677), structural constituent of chromatin (GO:0030527), histone binding (GO:0042393), protein heterodimerization activity (GO:0046982)

GO Cellular Component (7): chromosome, telomeric region (GO:0000781), nucleosome (GO:0000786), female germ cell nucleus (GO:0001674), nucleus (GO:0005634), nucleoplasm (GO:0005654), cell surface (GO:0009986), chromosome (GO:0005694)

Reactome top-level categories

Rollup of top-12 pathways:

Category	Pathways
Cellular Senescence	3
Depyrimidination	2
Depurination	2
Epigenetic regulation of gene expression	2
Chromatin modifying enzymes	2
Negative epigenetic regulation of rRNA expression	2
Positive epigenetic regulation of rRNA expression	2
Meiosis	1
Telomere Maintenance	1
Pre-NOTCH Expression and Processing	1
TCF dependent signaling in response to WNT	1
Mitotic Prophase	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
chromatin organization	2
nucleosome organization	2
chromatin	2
cellular anatomical structure	2
protein-DNA complex assembly	1
protein-DNA complex disassembly	1
defense response	1
zymogen activation	1
spermatid nucleus differentiation	1
organelle organization	1
leukocyte migration	1
cellular component organization	1
nucleic acid binding	1
structural molecule activity	1
protein binding	1
protein dimerization activity	1
chromosomal region	1
protein-DNA complex	1
germ cell nucleus	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

2364 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
H2BC1	PLG	P00747	867
H2BC1	RNF20	Q5VTR2	833
H2BC1	H3C1	P02295	825
H2BC1	H3-4	Q16695	817
H2BC1	H3-5	Q6NXT2	816
H2BC1	H3-3A	P06351	815
H2BC1	H3C14	Q71DI3	815
H2BC1	H3-7	Q5TEC6	813
H2BC1	RNF40	O75150	772
H2BC1	H2AC19	P20670	772
H2BC1	H2AC20	Q16777	772
H2BC1	H2AC1	Q96QV6	767
H2BC1	H4C7	Q99525	751
H2BC1	H4C16	P02304	747
H2BC1	DET1	Q7L5Y6	730

IntAct

36 interactions, top by confidence:

A	B	Type	Score
H2BC1	PPM1G	psi-mi:“MI:0914”(association)	0.640
SFMBT1	H4C16	psi-mi:“MI:0914”(association)	0.460
H2BC1	H2BC21	psi-mi:“MI:0915”(physical association)	0.400
	H4C16	psi-mi:“MI:0915”(physical association)	0.400
	H2AC7	psi-mi:“MI:0915”(physical association)	0.400
H2BC1	BRD7	psi-mi:“MI:0915”(physical association)	0.400
CREB1	NFIX	psi-mi:“MI:0914”(association)	0.350
MEF2A	REV3L	psi-mi:“MI:0914”(association)	0.350
NFATC1	SMARCA5	psi-mi:“MI:0914”(association)	0.350
NFKB1	NFKB1	psi-mi:“MI:0914”(association)	0.350
JUN		psi-mi:“MI:0914”(association)	0.350
JUN	TPM3	psi-mi:“MI:0914”(association)	0.350
COX15	SNRPGP15	psi-mi:“MI:0914”(association)	0.350
PDHA1		psi-mi:“MI:0914”(association)	0.350
COX15	MYO1C	psi-mi:“MI:0914”(association)	0.350
COX15	SAP18	psi-mi:“MI:0914”(association)	0.350
RMND5A	HTRA2	psi-mi:“MI:0914”(association)	0.350
CRY1	IGKV2D-30	psi-mi:“MI:0914”(association)	0.350
ELK4	MYO1C	psi-mi:“MI:0914”(association)	0.350
P		psi-mi:“MI:0914”(association)	0.350
CBX8	IGF2BP3	psi-mi:“MI:0914”(association)	0.350
	HNRNPDL	psi-mi:“MI:0914”(association)	0.350
	POLR3A	psi-mi:“MI:0914”(association)	0.350

BioGRID (483): HIST1H2BA (Affinity Capture-MS), HDAC1 (Reconstituted Complex), HDAC2 (Reconstituted Complex), HDAC3 (Reconstituted Complex), NAP1L1 (Affinity Capture-MS), RUVBL1 (Affinity Capture-MS), MIER1 (Affinity Capture-MS), HDAC1 (Affinity Capture-MS), EP400 (Affinity Capture-MS), GON4L (Affinity Capture-MS), MEAF6 (Affinity Capture-MS), H2AFY2 (Affinity Capture-MS), H2AFY (Affinity Capture-MS), SUPT16H (Affinity Capture-MS), LIG3 (Affinity Capture-MS)

ESM2 similar proteins: O97484, P02283, P02284, P02285, P02286, P02287, P02288, P02289, P04255, P04913, P08993, P08994, P0C1H4, P16888, P16889, P16890, P17271, P21897, P27795, P33778, P35067, P35068, P35069, P48557, P57053, P59781, P59782, P70696, P82887, P83863, Q00729, Q27442, Q27876, Q27894, Q41575, Q64524, Q6PC60, Q76FD7, Q76FE5, Q76FE9

Diamond homologs: A0A2R8Y619, A2WKT1, A2WKT4, A2WWU2, A2XF66, A2YWI3, A3AGM4, O22582, O60814, O65819, P02281, P02283, P02284, P02285, P02286, P02287, P02288, P02289, P02290, P04255, P06145, P06899, P06900, P07794, P07795, P0C1H3, P0C1H4, P0C1H5, P10853, P10854, P14001, P16888, P16889, P16890, P17271, P19374, P21897, P23527, P27326, P27807

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
SLBP	“up-regulates quantity by expression”	H2BC1	“translation regulation”
“MSL acetyltransferase”	“down-regulates activity”	H2BC1	monoubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 37 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:

Pathway	Partners	Fold	FDR
B-WICH complex positively regulates rRNA expression	5	21.7×	6e-04
Regulation of PD-L1(CD274) transcription	5	19.4×	6e-04
NoRC negatively regulates rRNA expression	5	18.7×	6e-04
Senescence-Associated Secretory Phenotype (SASP)	5	17.7×	6e-04
Oxidative Stress Induced Senescence	5	16.2×	7e-04
HCMV Early Events	5	14.5×	8e-04
HATs acetylate histones	5	14.2×	8e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	36
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

122 predictions. Top by Δscore:

Variant	Effect	Δscore
6:25726987:G:GT	donor_gain	0.8800
6:25727018:A:T	donor_gain	0.8700
6:25727007:GACCC:G	donor_gain	0.8300
6:25727087:C:G	donor_gain	0.8300
6:25727012:G:GG	donor_gain	0.8200
6:25727017:G:GT	donor_gain	0.8000
6:25726951:GGCTT:G	donor_gain	0.7900
6:25727022:T:G	donor_gain	0.7700
6:25726988:A:T	donor_gain	0.7600
6:25727009:CCC:C	donor_gain	0.7600
6:25727270:C:CG	donor_gain	0.7200
6:25727086:GCTA:G	donor_gain	0.6700
6:25727010:CC:C	donor_gain	0.6600
6:25727289:G:GG	donor_gain	0.6600
6:25727089:A:G	donor_gain	0.6300
6:25726952:GCTT:G	donor_gain	0.6200
6:25727007:G:GT	donor_gain	0.6000
6:25726987:G:T	donor_gain	0.5700
6:25727096:T:TG	donor_gain	0.5500
6:25727270:C:G	donor_gain	0.5500
6:25726970:T:G	donor_gain	0.5400
6:25726934:C:CG	donor_gain	0.5300
6:25727008:ACCCG:A	donor_loss	0.5300
6:25727011:CG:C	donor_loss	0.5300
6:25727012:GTAA:G	donor_loss	0.5300
6:25727013:TAA:T	donor_loss	0.5300
6:25727014:A:C	donor_loss	0.5300
6:25727015:AGG:A	donor_loss	0.5200
6:25727016:G:C	donor_loss	0.5200
6:25727058:C:A	donor_gain	0.5200

AlphaMissense

821 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:25727048:T:C	L47P	0.999
6:25727143:G:C	A79P	0.999
6:25727203:G:C	A99P	0.999
6:25727204:C:A	A99E	0.999
6:25727213:T:C	L102S	0.999
6:25727239:C:G	H111D	0.999
6:25727241:T:A	H111Q	0.999
6:25727241:T:G	H111Q	0.999
6:25727243:C:A	A112D	0.999
6:25727254:G:C	G116R	0.999
6:25727255:G:A	G116D	0.999
6:25727263:G:C	A119P	0.999
6:25727054:A:C	Q49P	0.998
6:25727129:G:C	R74P	0.998
6:25727153:T:C	L82S	0.998
6:25727209:C:A	R101S	0.998
6:25727210:G:C	R101P	0.998
6:25727225:G:A	G106E	0.998
6:25727231:T:A	L108Q	0.998
6:25727231:T:C	L108P	0.998
6:25727239:C:A	H111N	0.998
6:25727240:A:C	H111P	0.998
6:25727242:G:C	A112P	0.998
6:25727254:G:T	G116C	0.998
6:25727262:G:C	K118N	0.998
6:25727262:G:T	K118N	0.998
6:25727264:C:A	A119D	0.998
6:25727267:T:A	V120D	0.998
6:25727104:T:C	S66P	0.997
6:25727144:C:A	A79E	0.997

dbSNP variants (sampled 300 via entrez): RS1000483009 (6:25726835 A>C,G), RS1001893748 (6:25725930 G>A,C), RS1002155579 (6:25727382 A>C,G,T), RS1002647352 (6:25725867 C>T), RS1002664843 (6:25726026 G>A,C), RS1005764806 (6:25726955 T>A,C), RS1006907826 (6:25727473 G>A,C), RS1007182920 (6:25727667 G>A), RS1007632076 (6:25726429 A>G), RS1008162172 (6:25725205 A>G), RS1008738577 (6:25727549 A>C,T), RS1009145881 (6:25725966 T>A,G), RS1009661299 (6:25725103 G>A), RS1009935320 (6:25727691 A>G), RS1010526241 (6:25727016 G>A)

Disease associations

OMIM: gene MIM:609904 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST004521_169	Autism spectrum disorder or schizophrenia	4.000000e-14
GCST004521_69	Autism spectrum disorder or schizophrenia	8.000000e-24
GCST004521_83	Autism spectrum disorder or schizophrenia	1.000000e-13

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5724670 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression	2
sodium arsenite	increases expression	1
epigallocatechin gallate	increases expression	1
Arsenic	affects methylation	1
Methylcholanthrene	affects binding, increases reaction	1
Valproic Acid	increases methylation	1
Copper Sulfate	affects expression	1
Nanotubes, Carbon	affects expression	1

ChEMBL screening assays

6 unique, capped per target: 6 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5697172	Binding	Inhibition of HIST1H2BA (unknown origin) assessed as fold change at 10 uM incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysis	Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. — Nature

Clinical trials (associated diseases)

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