H2BC3

Summary

H2BC3 (H2B clustered histone 3, HGNC:4751) is a protein-coding gene on chromosome 6p22.2, encoding Histone H2B type 1-B (P33778). Core component of nucleosome. It is a selective cancer dependency (DepMap: 12.8% of cell lines).

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 member of the histone H2B family. Transcripts from this gene lack polyA tails; instead, they contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6p22-p21.3.

Source: NCBI Gene 3018 — RefSeq curated summary.

At a glance

• GWAS associations: 14
• Clinical variants (ClinVar): 24 total
• Cancer dependency (DepMap): dependent in 12.8% of screened cell lines
• MANE Select transcript: NM_021062

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4751
Approved symbol	H2BC3
Name	H2B clustered histone 3
Location	6p22.2
Locus type	gene with protein product
Status	Approved
Aliases	H2B/f
Ensembl gene	ENSG00000276410
Ensembl biotype	protein_coding
OMIM	602803
Entrez	3018

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000615966, ENST00000850571

RefSeq mRNA: 1 — MANE Select: NM_021062 NM_021062

CCDS: CCDS4575

Canonical transcript exons

ENST00000615966 — 1 exons

Exon	Start	End
ENSE00004282155	26043227	26043713

Expression profiles

Bgee: expression breadth broad, 94 present calls, max score 97.94.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 79.7016 / max 2515.5944, expressed in 1559 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
72300	79.7016	1559

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bone marrow cell	CL:0002092	97.94	gold quality
adrenal tissue	UBERON:0018303	91.65	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.63	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.07	gold quality
calcaneal tendon	UBERON:0003701	80.58	gold quality
colonic epithelium	UBERON:0000397	75.78	gold quality
tendon	UBERON:0000043	65.39	gold quality
heart right ventricle	UBERON:0002080	61.58	gold quality
hair follicle	UBERON:0002073	61.06	gold quality
bone marrow	UBERON:0002371	61.03	gold quality
decidua	UBERON:0002450	58.67	gold quality
corpus callosum	UBERON:0002336	57.98	gold quality
oocyte	CL:0000023	57.64	silver quality
cartilage tissue	UBERON:0002418	55.51	gold quality
pons	UBERON:0000988	54.77	gold quality
amniotic fluid	UBERON:0000173	51.48	gold quality
sural nerve	UBERON:0015488	50.53	gold quality
tonsil	UBERON:0002372	50.50	gold quality
lower lobe of lung	UBERON:0008949	50.45	silver quality
thymus	UBERON:0002370	50.19	silver quality
left testis	UBERON:0004533	49.40	gold quality
blood vessel layer	UBERON:0004797	49.29	gold quality
choroid plexus epithelium	UBERON:0003911	48.89	gold quality
testis	UBERON:0000473	48.54	gold quality
mammalian vulva	UBERON:0000997	48.05	gold quality
ventricular zone	UBERON:0003053	48.05	gold quality
right testis	UBERON:0004534	47.62	gold quality
granulocyte	CL:0000094	47.58	silver quality
periodontal ligament	UBERON:0008266	47.14	gold quality
vastus lateralis	UBERON:0001379	46.93	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.24

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 12.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 5)

• RNF20-mediated H2B ubiquitination at DSBs plays a critical role in HRR through chromatin remodeling (PMID:21362548)
• RNF20 and H2Bub1 promotes chronic colonic inflammation and inflammation-associated colorectal cancer in mice and humans, partly by augmenting NF-kappaB activity and attenuating the antitumoral T cell response. (PMID:26854224)
• Monoubiquitination of histone H2B blocks eviction of histone variant H2A.Z from inducible enhancers. (PMID:27692985)
• Functional crosstalk between histone H2B ubiquitylation and H2A modifications and variants has been uncovered. (PMID:29643390)
• HIST1H2BB and MAGI2 Methylation and Somatic Mutations as Precision Medicine Biomarkers for Diagnosis and Prognosis of High-grade Serous Ovarian Cancer. (PMID:32581010)

Cross-species orthologs

0 orthologs

Paralogs (21): H2BW2 (ENSG00000101812), H2BW1 (ENSG00000123569), H2BC11 (ENSG00000124635), H2BC1 (ENSG00000146047), 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), H2BC7 (ENSG00000277224), H2BC10 (ENSG00000278588), H2BK1 (ENSG00000285480)

Protein

Protein identifiers

Histone H2B type 1-B — P33778 (reviewed: P33778)

Alternative names: H2B-clustered histone 3, Histone H2B.1, Histone H2B.f

All UniProt accessions (1): P33778

UniProt curated annotations — full annotation on UniProt →

Function. 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.

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. The octamer wraps approximately 147 bp of DNA.

Subcellular location. Nucleus. Chromosome.

Post-translational modifications. Monoubiquitination at Lys-35 (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-121 (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. Phosphorylation at Ser-37 (H2BS36ph) by AMPK in response to stress promotes transcription. Phosphorylated on Ser-15 (H2BS14ph) by STK4/MST1 during apoptosis; which facilitates apoptotic chromatin condensation. Also phosphorylated on Ser-15 in response to DNA double strand breaks (DSBs), and in correlation with somatic hypermutation and immunoglobulin class-switch recombination. GlcNAcylation at Ser-113 promotes monoubiquitination of Lys-121. It fluctuates in response to extracellular glucose, and associates with transcribed genes. ADP-ribosylated by PARP1 or PARP2 on Ser-7 (H2BS6ADPr) in response to DNA damage. H2BS6ADPr promotes recruitment of CHD1L. Mono-ADP-ribosylated on Glu-3 (H2BE2ADPr) by PARP3 in response to single-strand breaks. Poly ADP-ribosylation on Glu-36 (H2BE35ADPr) by PARP1 regulates adipogenesis: it inhibits phosphorylation at Ser-37 (H2BS36ph), thereby blocking expression of pro-adipogenetic genes. 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. 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_066406* (*=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 (105 total): modified residue 91, helix 4, cross-link 4, initiator methionine 1, chain 1, strand 1, region of interest 1, compositionally biased region 1, glycosylation site 1

Structure

Experimental structures (PDB)

6 structures.

PDB	Method	Resolution (Å)
9FGQ	ELECTRON MICROSCOPY	2.5
3X1S	X-RAY DIFFRACTION	2.81
3X1U	X-RAY DIFFRACTION	3.25
9GE5	ELECTRON MICROSCOPY	3.35
8YJM	X-RAY DIFFRACTION	4.15
9C62	ELECTRON MICROSCOPY	5.28

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P33778-F1	87.89	0.69

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 (95): 6, 6, 6, 6, 7, 12, 12, 12, 12, 12, 12, 13, 13, 13, 15, 16, 16, 16, 16, 17 …

Glycosylation sites (1): 113

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: 214 (showing top): REACTOME_MEIOTIC_RECOMBINATION, REACTOME_DNA_REPLICATION, REACTOME_SIGNALING_BY_NOTCH, GOBP_ANTIMICROBIAL_HUMORAL_RESPONSE, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_MEIOTIC_SYNAPSIS, REACTOME_G2_M_DNA_DAMAGE_CHECKPOINT, CAGCTG_AP4_Q5, GOBP_ORGAN_OR_TISSUE_SPECIFIC_IMMUNE_RESPONSE, REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM, GOBP_INNATE_IMMUNE_RESPONSE_IN_MUCOSA, GOBP_HUMORAL_IMMUNE_RESPONSE, HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP, POU3F2_02

GO Biological Process (1): nucleosome assembly (GO:0006334)

GO Molecular Function (4): DNA binding (GO:0003677), structural constituent of chromatin (GO:0030527), protein heterodimerization activity (GO:0046982), protein binding (GO:0005515)

GO Cellular Component (6): chromosome, telomeric region (GO:0000781), nucleosome (GO:0000786), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829), 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	2
cellular anatomical structure	2
chromatin organization	1
nucleosome organization	1
protein-DNA complex assembly	1
nucleic acid binding	1
structural molecule activity	1
protein dimerization activity	1
binding	1
chromosomal region	1
protein-DNA complex	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

2498 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
H2BC3	PLG	P00747	867
H2BC3	RNF20	Q5VTR2	842
H2BC3	H3C1	P02295	817
H2BC3	H3C14	Q71DI3	813
H2BC3	H3-3A	P06351	809
H2BC3	H3-5	Q6NXT2	809
H2BC3	H3-4	Q16695	809
H2BC3	H3-7	Q5TEC6	809
H2BC3	RNF40	O75150	772
H2BC3	H2AC19	P20670	758
H2BC3	H4C16	P02304	747
H2BC3	H4C7	Q99525	745
H2BC3	H2AC20	Q16777	744
H2BC3	DET1	Q7L5Y6	727
H2BC3	USP22	Q9UPT9	722

IntAct

41 interactions, top by confidence:

A	B	Type	Score
FH	H2AZ1	psi-mi:“MI:0914”(association)	0.620
H2BC3	RHBDD2	psi-mi:“MI:0915”(physical association)	0.560
PPM1G	COPE	psi-mi:“MI:0914”(association)	0.530
CBX6	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
CBX1	KPNA3	psi-mi:“MI:0914”(association)	0.530
SYNGAP1	IGF2BP3	psi-mi:“MI:0914”(association)	0.530
DAXX	MACF1	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
CHD1L	H2BC12	psi-mi:“MI:0914”(association)	0.350
PRNP	MBP	psi-mi:“MI:0914”(association)	0.350
SMARCB1	H2BC3	psi-mi:“MI:0914”(association)	0.350
PRKCB	HNRNPDL	psi-mi:“MI:0914”(association)	0.350
RPS6KA3	BAG2	psi-mi:“MI:0914”(association)	0.350
PRKCB	CHEK1	psi-mi:“MI:0914”(association)	0.350
P		psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
CTBP1	TAF15	psi-mi:“MI:0914”(association)	0.350
SLC16A11	ESYT2	psi-mi:“MI:0914”(association)	0.350
SLC16A11	PABPC4	psi-mi:“MI:0914”(association)	0.350
BMI1	HMGB1P1	psi-mi:“MI:0914”(association)	0.350
BMI1	MEIS3P1	psi-mi:“MI:0914”(association)	0.350
HOXA2	SYNJ1	psi-mi:“MI:0914”(association)	0.350
	BANF1	psi-mi:“MI:0914”(association)	0.350
CBX8	IGF2BP3	psi-mi:“MI:0914”(association)	0.350
GPC3	PXDNL	psi-mi:“MI:0914”(association)	0.350
NS	IGF2BP3	psi-mi:“MI:0914”(association)	0.350

BioGRID (675): HIST1H2BB (Biochemical Activity), HIST1H2BB (Biochemical Activity), HIST1H2BB (Biochemical Activity), HIST1H2BB (Biochemical Activity), HIST1H2BB (Biochemical Activity), HIST1H2BB (Reconstituted Complex), HIST1H2BB (Biochemical Activity), HIST1H2BB (Biochemical Activity), HIST1H2BB (Affinity Capture-MS), HIST1H2BB (Biochemical Activity), HIST1H2BB (Biochemical Activity), HIST1H2BB (Affinity Capture-MS), HIST1H2BB (Affinity Capture-MS), HIST1H2BB (Affinity Capture-Western), HIST1H2BB (Affinity Capture-MS)

ESM2 similar proteins: A0A2R8Y619, O97484, P02284, P02285, P02286, P02287, P02288, P04255, P04913, P07794, P07795, P0C1H4, P16888, P16889, P16890, P19374, P21897, P23527, P27326, P30757, P33778, P35067, P35068, P35069, P48557, P57053, P62807, P62808, P70696, P83863, Q00715, Q00729, Q16778, Q27894, Q32L48, Q5QNW6, Q5R893, Q5RCP8, Q64475, Q64478

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

5 interactions.

A	Effect	B	Mechanism
MST1	unknown	H2BC3	phosphorylation
STK4	unknown	H2BC3	phosphorylation
RPS6KA3	unknown	H2BC3	phosphorylation
SLBP	“up-regulates quantity by expression”	H2BC3	“translation regulation”
“MSL acetyltransferase”	“down-regulates activity”	H2BC3	monoubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 51 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
Transcriptional regulation by RUNX1	5	20.3×	6e-04
Cellular Senescence	5	19.1×	6e-04
Oxidative Stress Induced Senescence	5	12.6×	2e-03
Cellular responses to stress	6	6.1×	1e-02

GO biological processes:

GO term	Partners	Fold	FDR
response to oxidative stress	5	15.2×	4e-03
chromatin remodeling	6	10.2×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	24
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

107 predictions. Top by Δscore:

Variant	Effect	Δscore
6:26043569:CGCTT:C	donor_gain	0.8900
6:26043519:TCAGA:T	donor_gain	0.8500
6:26043569:CG:C	donor_gain	0.8200
6:26043613:AGAAC:A	donor_gain	0.8200
6:26043551:T:A	donor_gain	0.7900
6:26043310:AGTGC:A	donor_gain	0.7100
6:26043577:ACCAT:A	donor_gain	0.7100
6:26043578:CCATC:C	donor_gain	0.7100
6:26043568:A:AC	donor_gain	0.7000
6:26043569:C:CC	donor_gain	0.7000
6:26043297:TGGTA:T	donor_gain	0.6700
6:26043430:G:A	donor_gain	0.6700
6:26043581:T:TA	donor_gain	0.5700
6:26043498:CGG:C	acceptor_gain	0.5600
6:26043612:TAGA:T	donor_gain	0.5600
6:26043613:AGAA:A	donor_gain	0.5600
6:26043485:T:TG	acceptor_gain	0.5400
6:26043335:G:C	donor_gain	0.5200
6:26043479:ATGG:A	donor_gain	0.5200
6:26043523:A:T	donor_gain	0.5100
6:26043570:G:C	donor_gain	0.5100
6:26043573:TCTTA:T	donor_loss	0.5000
6:26043574:CTTAC:C	donor_loss	0.5000
6:26043576:TACCA:T	donor_loss	0.5000
6:26043577:A:AG	donor_loss	0.5000
6:26043578:CCA:C	donor_loss	0.5000
6:26043334:AG:A	donor_gain	0.4800
6:26043571:CTTCT:C	donor_loss	0.4800
6:26043572:TTCTT:T	donor_loss	0.4800
6:26043527:T:C	acceptor_gain	0.4700

AlphaMissense

814 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:26043302:A:T	V119D	1.000
6:26043306:C:G	A118P	1.000
6:26043307:C:A	K117N	1.000
6:26043307:C:G	K117N	1.000
6:26043314:C:A	G115V	1.000
6:26043314:C:T	G115D	1.000
6:26043315:C:A	G115C	1.000
6:26043315:C:G	G115R	1.000
6:26043326:G:T	A111D	1.000
6:26043327:C:G	A111P	1.000
6:26043328:A:C	H110Q	1.000
6:26043328:A:T	H110Q	1.000
6:26043330:G:C	H110D	1.000
6:26043335:G:T	A108D	1.000
6:26043338:A:G	L107P	1.000
6:26043338:A:T	L107Q	1.000
6:26043344:C:A	G105V	1.000
6:26043344:C:T	G105E	1.000
6:26043345:C:A	G105W	1.000
6:26043356:A:G	L101P	1.000
6:26043356:A:T	L101Q	1.000
6:26043360:G:T	R100S	1.000
6:26043365:G:T	A98D	1.000
6:26043366:C:G	A98P	1.000
6:26043370:C:A	Q96H	1.000
6:26043370:C:G	Q96H	1.000
6:26043378:C:T	E94K	1.000
6:26043379:C:A	R93S	1.000
6:26043379:C:G	R93S	1.000
6:26043380:C:A	R93M	1.000

dbSNP variants (sampled 300 via entrez): RS1000064690 (6:26044480 G>C,T), RS1001071216 (6:26045591 C>G,T), RS1002040428 (6:26044760 C>T), RS1002091133 (6:26045001 G>A,C), RS1003497669 (6:26043198 T>C), RS1006835270 (6:26045060 T>C), RS1006882858 (6:26044764 C>G,T), RS1007664292 (6:26043169 CAG>C), RS1009865249 (6:26045308 C>A), RS1010298248 (6:26043870 A>C,G,T), RS1011575529 (6:26045096 TACTG>T), RS1011792603 (6:26043278 T>A,C,G), RS1012793288 (6:26044006 G>A,T), RS1013933616 (6:26044542 T>C), RS1014408471 (6:26043838 A>G,T)

Disease associations

OMIM: gene MIM:602803 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

14 associations (top):

Study	Trait	p-value
GCST004521_113	Autism spectrum disorder or schizophrenia	3.000000e-19
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
GCST010002_50	Refractive error	4.000000e-34
GCST010142_16	Fish- and plant-related diet	2.000000e-10
GCST010142_19	Fish- and plant-related diet	4.000000e-10
GCST010142_34	Fish- and plant-related diet	7.000000e-09
GCST010142_35	Fish- and plant-related diet	8.000000e-09
GCST010142_42	Fish- and plant-related diet	1.000000e-08
GCST010142_7	Fish- and plant-related diet	3.000000e-12
GCST010702_75	Subcortical volume (MOSTest)	3.000000e-11
GCST010703_272	Brain morphology (MOSTest)	7.000000e-16
GCST90002404_247	Red cell distribution width	1.000000e-10

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement
EFO:0009188	Red cell distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

44 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Particulate Matter	decreases expression, increases abundance, increases expression	3
sodium arsenite	increases expression, decreases expression	2
Air Pollutants	decreases expression, increases abundance, increases expression	2
Benzo(a)pyrene	affects methylation, decreases expression, decreases methylation	2
Aflatoxin B1	decreases expression, decreases methylation	2
methyleugenol	decreases expression	1
bisphenol A	decreases expression	1
2-methyl-4-isothiazolin-3-one	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
potassium chromate(VI)	decreases expression	1
bicalutamide	increases expression	1
deguelin	increases expression	1
fenpyroximate	increases expression	1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamide	increases expression	1
dimethylarsinous acid	increases expression	1
pyrimidifen	increases expression	1
thifluzamide	increases expression	1
abrine	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Dasatinib	decreases expression	1
Acetaminophen	decreases expression	1
Antimycin A	increases expression	1
Catechin	increases expression, affects cotreatment	1
Cisplatin	decreases expression	1
Citrulline	decreases expression	1
Demecolcine	increases expression	1
Drugs, Chinese Herbal	increases expression	1
Folic Acid	affects cotreatment, decreases expression	1
Formaldehyde	increases expression	1

Clinical trials (associated diseases)

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