H2BC6

Summary

H2BC6 (H2B clustered histone 6, HGNC:4753) is a protein-coding gene on chromosome 6p22.2, encoding Histone H2B type 1-C/E/F/G/I (P62807). Core component of nucleosome. It is a common-essential gene (DepMap: required in 92.7% of cancer cell lines).

Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. The protein has antibacterial and antifungal antimicrobial activity. 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 but instead contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6.

Source: NCBI Gene 8344 — RefSeq curated summary.

At a glance

• GWAS associations: 38
• Clinical variants (ClinVar): 29 total
• Cancer dependency (DepMap): dependent in 92.7% of screened cell lines (common-essential)
• MANE Select transcript: NM_003523

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4753
Approved symbol	H2BC6
Name	H2B clustered histone 6
Location	6p22.2
Locus type	gene with protein product
Status	Approved
Aliases	H2B/h, H2B.h
Ensembl gene	ENSG00000274290
Ensembl biotype	protein_coding
OMIM	602805
Entrez	8344

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000614097, ENST00000634910

RefSeq mRNA: 1 — MANE Select: NM_003523 NM_003523

CCDS: CCDS4588

Canonical transcript exons

ENST00000614097 — 1 exons

Exon	Start	End
ENSE00003729177	26183761	26184230

Expression profiles

Bgee: expression breadth ubiquitous, 208 present calls, max score 89.75.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 149.6724 / max 4752.1263, expressed in 1762 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
66484	147.2496	1637
66482	2.4228	923

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adrenal tissue	UBERON:0018303	89.75	gold quality
tendon of biceps brachii	UBERON:0008188	89.31	gold quality
endometrium epithelium	UBERON:0004811	85.67	gold quality
bone marrow cell	CL:0002092	85.32	gold quality
tendon	UBERON:0000043	82.54	gold quality
heart right ventricle	UBERON:0002080	81.68	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.03	gold quality
calcaneal tendon	UBERON:0003701	80.89	gold quality
oocyte	CL:0000023	79.60	silver quality
colonic epithelium	UBERON:0000397	78.01	gold quality
cartilage tissue	UBERON:0002418	77.59	gold quality
bone marrow	UBERON:0002371	77.50	gold quality
thymus	UBERON:0002370	77.00	silver quality
medial globus pallidus	UBERON:0002477	76.82	silver quality
corpus epididymis	UBERON:0004359	76.54	gold quality
bronchial epithelial cell	CL:0002328	74.19	gold quality
amniotic fluid	UBERON:0000173	73.84	gold quality
jejunal mucosa	UBERON:0000399	73.35	gold quality
upper leg skin	UBERON:0004262	73.25	gold quality
oviduct epithelium	UBERON:0004804	72.77	silver quality
blood	UBERON:0000178	72.76	gold quality
oral cavity	UBERON:0000167	71.83	silver quality
secondary oocyte	CL:0000655	71.77	silver quality
decidua	UBERON:0002450	71.37	silver quality
globus pallidus	UBERON:0001875	71.29	silver quality
trabecular bone tissue	UBERON:0002483	70.98	silver quality
embryo	UBERON:0000922	70.96	gold quality
placenta	UBERON:0001987	70.96	gold quality
colonic mucosa	UBERON:0000317	70.76	silver quality
tonsil	UBERON:0002372	70.69	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.95

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 92.7% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 1)

• Histone H2B antimicrobial peptides participate in the colonic defense against bacteria and fungi. (PMID:12860195)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	H2bc4	ENSMUSG00000018102
mus_musculus	H2bc6	ENSMUSG00000047246
rattus_norvegicus	Hist1h2bc	ENSRNOG00000069373

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), H2BC17 (ENSG00000274641), H2BC9 (ENSG00000275713), H2BC3 (ENSG00000276410), H2BC7 (ENSG00000277224), H2BC10 (ENSG00000278588), H2BK1 (ENSG00000285480)

Protein

Protein identifiers

Histone H2B type 1-C/E/F/G/I — P62807 (reviewed: P62807)

Alternative names: Histone H2B.1 A, Histone H2B.a, Histone H2B.g, Histone H2B.h, Histone H2B.k, Histone H2B.l

All UniProt accessions (2): P62807, B2R4S9

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. Has broad antibacterial activity. May contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.

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. Interacts with VRK1; the interaction is mediated by the nucleosome acidic patch, a cluster of negatively charged residues of H2A and H2B forming a cleft within the nucleosome core.

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_003514* (*=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 (110 total): modified residue 91, helix 4, cross-link 4, sequence conflict 2, strand 2, initiator methionine 1, chain 1, sequence variant 1, mutagenesis site 1, region of interest 1, compositionally biased region 1, glycosylation site 1

Structure

Experimental structures (PDB)

76 structures, top 30 by resolution.

PDB	Method	Resolution (Å)
6ACO	X-RAY DIFFRACTION	1.71
7R5R	ELECTRON MICROSCOPY	2.44
8OX0	ELECTRON MICROSCOPY	2.52
9Y46	ELECTRON MICROSCOPY	2.59
10XZ	ELECTRON MICROSCOPY	2.6
7PII	ELECTRON MICROSCOPY	2.68
7U46	ELECTRON MICROSCOPY	2.68
10YA	ELECTRON MICROSCOPY	2.7
10YC	ELECTRON MICROSCOPY	2.7
8OOP	ELECTRON MICROSCOPY	2.7
8OX1	ELECTRON MICROSCOPY	2.7
9Y47	ELECTRON MICROSCOPY	2.74
10YB	ELECTRON MICROSCOPY	2.8
10YD	ELECTRON MICROSCOPY	2.8
8OO7	ELECTRON MICROSCOPY	2.8
5GT0	X-RAY DIFFRACTION	2.82
6X59	ELECTRON MICROSCOPY	2.98
7TAN	ELECTRON MICROSCOPY	3
8VWU	ELECTRON MICROSCOPY	3
6SEG	ELECTRON MICROSCOPY	3.1
7U51	ELECTRON MICROSCOPY	3.1
8QZM	ELECTRON MICROSCOPY	3.1
8VWS	ELECTRON MICROSCOPY	3.1
9DWF	ELECTRON MICROSCOPY	3.1
9EOZ	ELECTRON MICROSCOPY	3.1
7A08	ELECTRON MICROSCOPY	3.11
9NQU	ELECTRON MICROSCOPY	3.16
8OOA	ELECTRON MICROSCOPY	3.18
7UV9	ELECTRON MICROSCOPY	3.2
8X15	ELECTRON MICROSCOPY	3.2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P62807-F1	87.94	0.68

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

Mutagenesis-validated functional residues (1):

Position	Phenotype
114	no effect on interaction with vrk1.

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: 222 (showing top): REACTOME_MEIOTIC_RECOMBINATION, REACTOME_DNA_REPLICATION, REACTOME_SIGNALING_BY_NOTCH, GOBP_ANTIMICROBIAL_HUMORAL_RESPONSE, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_MEIOTIC_SYNAPSIS, REACTOME_G2_M_DNA_DAMAGE_CHECKPOINT, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_ORGAN_OR_TISSUE_SPECIFIC_IMMUNE_RESPONSE, REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS, GERY_CEBP_TARGETS, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM

GO Biological Process (6): innate immune response in mucosa (GO:0002227), nucleosome assembly (GO:0006334), antibacterial humoral response (GO:0019731), defense response to Gram-positive bacterium (GO:0050830), antimicrobial humoral immune response mediated by antimicrobial peptide (GO:0061844), defense response to bacterium (GO:0042742)

GO Molecular Function (5): DNA binding (GO:0003677), structural constituent of chromatin (GO:0030527), identical protein binding (GO:0042802), protein heterodimerization activity (GO:0046982), protein binding (GO:0005515)

GO Cellular Component (7): nucleosome (GO:0000786), obsolete extracellular space (GO:0005615), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829), extracellular exosome (GO:0070062), 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
antimicrobial humoral response	2
defense response to bacterium	2
chromatin	2
cellular anatomical structure	2
mucosal immune response	1
innate immune response	1
chromatin organization	1
nucleosome organization	1
protein-DNA complex assembly	1
defense response	1
response to bacterium	1
nucleic acid binding	1
structural molecule activity	1
protein binding	1
protein dimerization activity	1
binding	1
protein-DNA complex	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1
extracellular vesicle	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

113 interactions, top by confidence:

A	B	Type	Score
H2AZ1	ZNHIT1	psi-mi:“MI:0914”(association)	0.770
ANP32E	H2AZ1	psi-mi:“MI:0914”(association)	0.770
ANP32E	H2AZ1	psi-mi:“MI:0915”(physical association)	0.770
TP53BP1	H2AC11	psi-mi:“MI:0915”(physical association)	0.670
H2AC11	UBB	psi-mi:“MI:0915”(physical association)	0.650
MAPK7	PFDN6	psi-mi:“MI:0914”(association)	0.640
HIP1	HIP1R	psi-mi:“MI:0914”(association)	0.640
FH	H2AZ1	psi-mi:“MI:0914”(association)	0.620
H2BC10	TP53BP2	psi-mi:“MI:0915”(physical association)	0.560
H2BC10	AP2M1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (1779): HIST1H2BC (Two-hybrid), HIST1H2BG (Affinity Capture-RNA), HIST1H2BG (Affinity Capture-RNA), HIST1H2BD (Affinity Capture-MS), HIST1H2BD (Affinity Capture-MS), HIST1H2BD (Reconstituted Complex), HIST1H2BG (Reconstituted Complex), HIST1H2BF (Reconstituted Complex), HIST1H2BE (Reconstituted Complex), HIST1H2BI (Reconstituted Complex), HIST1H2BC (Reconstituted Complex), TPX2 (Proximity Label-MS), SMCHD1 (Proximity Label-MS), KIF23 (Proximity Label-MS), KIF4A (Proximity Label-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

2 interactions.

A	Effect	B	Mechanism
SLBP	“up-regulates quantity by expression”	H2BC4	“translation regulation”
“MSL acetyltransferase”	“down-regulates activity”	H2BC4	monoubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 101 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
Activation of NF-kappaB in B cells	5	12.6×	5e-03
Signaling by ALK fusions and activated point mutants	6	11.6×	2e-03
Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks	6	11.3×	2e-03
Deposition of new CENPA-containing nucleosomes at the centromere	5	10.2×	8e-03
B-WICH complex positively regulates rRNA expression	6	9.3×	5e-03
Oxidative Stress Induced Senescence	8	9.3×	1e-03
Senescence-Associated Secretory Phenotype (SASP)	7	8.9×	2e-03
Processing of DNA double-strand break ends	6	8.8×	5e-03

GO biological processes:

GO term	Partners	Fold	FDR
heterochromatin formation	5	15.0×	3e-03
chromatin remodeling	11	9.4×	1e-05
regulation of apoptotic process	9	8.8×	2e-04
negative regulation of apoptotic process	11	4.5×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	28
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

502 predictions. Top by Δscore:

Variant	Effect	Δscore
6:26183280:C:CA	acceptor_gain	0.9800
6:26172608:G:GT	donor_gain	0.9700
6:26183280:C:G	acceptor_gain	0.9700
6:26172231:A:AG	donor_gain	0.9600
6:26172783:GT:G	donor_gain	0.9600
6:26183279:AC:A	acceptor_gain	0.9600
6:26183780:GAACA:G	acceptor_gain	0.9600
6:26172173:G:GT	donor_gain	0.9500
6:26172601:GA:G	donor_gain	0.9500
6:26172700:A:G	donor_gain	0.9500
6:26183252:G:C	acceptor_gain	0.9400
6:26172533:C:T	donor_gain	0.9300
6:26172603:G:GG	donor_gain	0.9300
6:26183779:A:AG	acceptor_gain	0.9300
6:26183780:G:GG	acceptor_gain	0.9300
6:26183780:GAAC:G	acceptor_gain	0.9300
6:26172224:GCCT:G	donor_gain	0.9200
6:26172789:G:GG	donor_gain	0.9200
6:26172200:G:GT	donor_gain	0.9100
6:26172693:GCT:G	donor_gain	0.9100
6:26172092:G:GA	donor_gain	0.9000
6:26172777:G:T	donor_gain	0.9000
6:26183250:C:CA	acceptor_gain	0.9000
6:26172665:G:T	donor_gain	0.8900
6:26172326:G:GG	donor_gain	0.8800
6:26183780:GA:G	acceptor_gain	0.8800
6:26172217:G:GA	donor_gain	0.8700
6:26172665:G:GT	donor_gain	0.8700
6:26172785:GTAT:G	donor_gain	0.8700
6:26173622:T:G	donor_gain	0.8700

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1002852454 (6:26182959 A>C), RS1002911379 (6:26183954 C>G,T), RS1005520740 (6:26184464 A>G), RS1007404959 (6:26181973 G>C), RS1007478573 (6:26182537 CCT>C), RS1007776448 (6:26182304 G>A,C), RS1008186138 (6:26184507 G>A), RS1008443564 (6:26184351 ACT>A), RS1008826790 (6:26183615 A>G), RS1009036890 (6:26183541 C>G,T), RS1009468740 (6:26181782 G>A), RS1009807805 (6:26183508 G>A,C), RS1009862251 (6:26183279 A>C), RS1010377939 (6:26182878 G>A), RS1010471436 (6:26183199 G>C)

Disease associations

OMIM: gene MIM:602805 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

38 associations (top):

Study	Trait	p-value
GCST004212_19	Height	3.000000e-13
GCST004521_113	Autism spectrum disorder or schizophrenia	3.000000e-19
GCST004521_142	Autism spectrum disorder or schizophrenia	2.000000e-09
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
GCST005146_45	Birth weight	1.000000e-08
GCST006426_3	Serum urate levels in chronic kidney disease	9.000000e-07
GCST007294_143	Body fat distribution (trunk fat ratio)	5.000000e-29
GCST007294_82	Body fat distribution (trunk fat ratio)	1.000000e-48
GCST007295_120	Body fat distribution (leg fat ratio)	2.000000e-46
GCST007295_91	Body fat distribution (leg fat ratio)	1.000000e-26
GCST007325_267	General risk tolerance (MTAG)	9.000000e-14
GCST008163_299	Height	1.000000e-18
GCST008163_41	Height	5.000000e-06
GCST008362_109	Birth weight	2.000000e-06
GCST008362_151	Birth weight	1.000000e-13
GCST008363_111	Offspring birth weight	2.000000e-08
GCST010002_50	Refractive error	4.000000e-34
GCST010141_1	Beef consumption	7.000000e-13
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
GCST010143_19	Meat-related diet	5.000000e-13
GCST010143_31	Meat-related diet	7.000000e-09
GCST010143_5	Meat-related diet	4.000000e-09
GCST010702_75	Subcortical volume (MOSTest)	3.000000e-11

EFO canonical traits (10, from GWAS)

EFO ID	Trait name
EFO:0004344	birth weight
EFO:0004531	urate measurement
EFO:0004341	body fat distribution
EFO:0008579	risk-taking behaviour
EFO:0005939	parental genotype effect measurement
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement
EFO:0007789	BMI-adjusted waist circumference
EFO:0008039	BMI-adjusted hip circumference
EFO:0004980	appendicular lean mass

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
propionaldehyde	decreases expression, increases methylation	2
bisphenol A	decreases expression, increases expression	2
Silicon Dioxide	increases expression	2
Aflatoxin B1	increases methylation, increases expression	2
Copper Sulfate	increases expression, decreases expression	2
nonanal	increases methylation	1
n-hexanal	increases methylation	1
butyraldehyde	increases methylation	1
caprylic aldehyde	increases methylation	1
N,N,N’,N’-tetrakis(2-pyridylmethyl)ethylenediamine	increases expression	1
pentanal	increases methylation	1
heptanal	increases methylation	1
licochalcone B	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
NSC 689534	increases expression, affects binding	1
(+)-JQ1 compound	increases expression	1
Resveratrol	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Amiodarone	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Berberine	decreases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Copper	affects binding, increases expression	1
Coumestrol	decreases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Demecolcine	increases expression	1
Dimethyl Sulfoxide	affects expression	1
Doxorubicin	decreases expression	1
Formaldehyde	increases expression	1

Clinical trials (associated diseases)

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