H2BK1

Summary

H2BK1 (H2B.K variant histone 1, HGNC:53833) is a protein-coding gene on chromosome 7q36.1, encoding Histone H2B type 2-K1 (A0A2R8Y619). Core component of nucleosome.

Predicted to enable DNA binding activity and protein heterodimerization activity. Predicted to be a structural constituent of chromatin. Predicted to be located in chromosome and nucleus. Predicted to be part of nucleosome.

Source: NCBI Gene 114483833 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001369125

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53833
Approved symbol	H2BK1
Name	H2B.K variant histone 1
Location	7q36.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000285480
Ensembl biotype	protein_coding
Entrez	114483833

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000644661

RefSeq mRNA: 1 — MANE Select: NM_001369125 NM_001369125

CCDS: CCDS94232

Canonical transcript exons

ENST00000644661 — 2 exons

Exon	Start	End
ENSE00003815570	151210187	151210488
ENSE00003819028	151207837	151208107

Expression profiles

Bgee: expression breadth ubiquitous, 122 present calls, max score 91.55.

Top tissues by expression

132 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	91.55	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.41	gold quality
lower esophagus mucosa	UBERON:0035834	69.08	gold quality
tibial nerve	UBERON:0001323	68.11	gold quality
right coronary artery	UBERON:0001625	67.57	gold quality
skin of abdomen	UBERON:0001416	67.17	gold quality
zone of skin	UBERON:0000014	66.37	gold quality
skin of leg	UBERON:0001511	66.21	gold quality
granulocyte	CL:0000094	66.20	gold quality
ascending aorta	UBERON:0001496	65.67	gold quality
left coronary artery	UBERON:0001626	65.59	gold quality
thoracic aorta	UBERON:0001515	65.40	gold quality
endocervix	UBERON:0000458	64.16	gold quality
tibial artery	UBERON:0007610	63.82	gold quality
popliteal artery	UBERON:0002250	63.61	gold quality
subcutaneous adipose tissue	UBERON:0002190	63.27	gold quality
left uterine tube	UBERON:0001303	63.05	gold quality
monocyte	CL:0000576	62.84	gold quality
descending thoracic aorta	UBERON:0002345	62.66	gold quality
ectocervix	UBERON:0012249	62.39	gold quality
gastrocnemius	UBERON:0001388	62.30	gold quality
leukocyte	CL:0000738	62.07	gold quality
adipose tissue	UBERON:0001013	62.02	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	61.97	gold quality
body of uterus	UBERON:0009853	61.51	gold quality
omental fat pad	UBERON:0010414	61.20	gold quality
muscle layer of sigmoid colon	UBERON:0035805	60.75	gold quality
lower esophagus muscularis layer	UBERON:0035833	60.74	gold quality
lower esophagus	UBERON:0013473	60.73	gold quality
spleen	UBERON:0002106	60.67	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.23

Regulation

Is transcription factor: no

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), H2BC3 (ENSG00000276410), H2BC7 (ENSG00000277224), H2BC10 (ENSG00000278588)

Protein

Protein identifiers

Histone H2B type 2-K1 — A0A2R8Y619 (reviewed: A0A2R8Y619)

Alternative names: Histone H2B type 2-E1

All UniProt accessions (1): A0A2R8Y619

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. Chromosome. Nucleus.

Similarity. Belongs to the histone H2B family.

RefSeq proteins (1): NP_001356054* (*=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 (49 total): modified residue 42, cross-link 2, initiator methionine 1, chain 1, region of interest 1, compositionally biased region 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A2R8Y619-F1	84.34	0.72

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 (44): 40, 40, 40, 40, 43, 43, 43, 43, 54, 54, 54, 54, 76, 81, 83, 89, 105, 105, 105, 105 …

Glycosylation sites (1): 109

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 13 (showing top): PEREZ_TP63_TARGETS, GOCC_PROTEIN_DNA_COMPLEX, GOMF_PROTEIN_HETERODIMERIZATION_ACTIVITY, GOMF_PROTEIN_DIMERIZATION_ACTIVITY, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, GOCC_NUCLEOSOME, GOMF_STRUCTURAL_CONSTITUENT_OF_CHROMATIN, GOBP_CHROMATIN_ORGANIZATION, GSE6269_STAPH_AUREUS_VS_STREP_PNEUMO_INF_PBMC_UP, GOCC_CHROMATIN, chr7q36, MOOTHA_HUMAN_MITODB_6_2002, MOOTHA_MITOCHONDRIA

GO Biological Process (0):

GO Molecular Function (3): DNA binding (GO:0003677), structural constituent of chromatin (GO:0030527), protein heterodimerization activity (GO:0046982)

GO Cellular Component (3): nucleosome (GO:0000786), nucleus (GO:0005634), chromosome (GO:0005694)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
chromatin	2
nucleic acid binding	1
structural molecule activity	1
protein dimerization activity	1
protein-DNA complex	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1716 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
H2BK1	PLG	P00747	867
H2BK1	RNF20	Q5VTR2	843
H2BK1	H3C14	Q71DI3	815
H2BK1	H3-5	Q6NXT2	815
H2BK1	H3C1	P02295	815
H2BK1	H3-4	Q16695	815
H2BK1	H3-7	Q5TEC6	815
H2BK1	H3-3A	P06351	813
H2BK1	RNF40	O75150	772
H2BK1	H4C7	Q99525	746
H2BK1	H4C16	P02304	742
H2BK1	H2AC19	P20670	729
H2BK1	USP22	Q9UPT9	728
H2BK1	H2AC20	Q16777	728
H2BK1	DET1	Q7L5Y6	728

IntAct

0 interactions, top by confidence:

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

1 interactions.

A	Effect	B	Mechanism
SLBP	“up-regulates quantity by expression”	H2BE1	“translation regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

776 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:151207920:G:T	A107D	0.984
7:151207921:C:G	A107P	0.983
7:151207909:C:G	G111R	0.982
7:151207900:C:G	A114P	0.981
7:151207901:C:A	K113N	0.981
7:151207901:C:G	K113N	0.981
7:151207960:C:G	A94P	0.979
7:151207959:G:T	A94D	0.975
7:151210194:A:G	L42P	0.974
7:151207968:A:T	V91D	0.973
7:151207908:C:T	G111D	0.971
7:151207896:A:T	V115D	0.966
7:151207974:C:G	R89P	0.966
7:151210190:C:A	K43N	0.966
7:151210190:C:G	K43N	0.966
7:151207925:C:A	K105N	0.964
7:151207925:C:G	K105N	0.964
7:151207964:C:A	Q92H	0.964
7:151207964:C:G	Q92H	0.964
7:151207950:A:G	L97P	0.963
7:151208020:C:G	A74P	0.961
7:151207929:G:T	A104D	0.959
7:151208104:G:C	H46D	0.956
7:151207953:C:G	R96P	0.955
7:151208059:A:G	S61P	0.955
7:151207915:A:G	S109P	0.954
7:151208088:A:G	I51T	0.954
7:151208019:G:T	A74D	0.952
7:151207922:G:C	H106Q	0.951
7:151207922:G:T	H106Q	0.951

dbSNP variants (sampled 300 via entrez): RS1000169109 (7:151209356 C>T), RS1000307528 (7:151209484 TG>T), RS1000374572 (7:151211129 C>T), RS1000640058 (7:151208216 C>A,T), RS1001438379 (7:151211902 C>T), RS1001842396 (7:151208543 C>G), RS1002909461 (7:151207841 G>C,T), RS1004559891 (7:151211462 T>C), RS1004586159 (7:151207379 A>T), RS1004980142 (7:151210972 A>G), RS1005012757 (7:151210729 GAA>G), RS1005157631 (7:151210240 G>A), RS1005388340 (7:151209812 A>G), RS1005537920 (7:151210422 G>A,C,T), RS1005770206 (7:151209993 T>C)

Disease associations

OMIM: gene `` | 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

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Furaldehyde	affects cotreatment, increases expression	1
Sodium Chloride	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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