H2BN1

Summary

H2BN1 (H2B.N variant histone 1, HGNC:56200) is a protein-coding gene on chromosome 17q11.2, encoding Histone H2B.N (P0DW85). 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 124188214 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001401340

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:56200
Approved symbol	H2BN1
Name	H2B.N variant histone 1
Location	17q11.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000290320
Ensembl biotype	protein_coding
Entrez	124188214

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000704639

RefSeq mRNA: 1 — MANE Select: NM_001401340 NM_001401340

CCDS: CCDS92289

Canonical transcript exons

ENST00000704639 — 2 exons

Exon	Start	End
ENSE00003992029	32895433	32895606
ENSE00003992030	32906191	32906586

Expression profiles

Top tissues by expression

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

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Histone H2B.N — P0DW85 (reviewed: P0DW85)

Alternative names: H2B.N variant histone 1

All UniProt accessions (1): P0DW85

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.

Tissue specificity. Expressed in germline. Predominantly expressed in oocytes.

Similarity. Belongs to the histone H2B family.

RefSeq proteins (1): NP_001388269* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000558	Histone_H2B	Family
IPR009072	Histone-fold	Homologous_superfamily

UniProt features (4 total): modified residue 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0DW85-F1	72.00	0.23

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 (3): 24, 24, 54

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 8 (showing top): chr17q11, GOCC_PROTEIN_DNA_COMPLEX, GOMF_PROTEIN_HETERODIMERIZATION_ACTIVITY, GOMF_PROTEIN_DIMERIZATION_ACTIVITY, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, GOCC_NUCLEOSOME, GOMF_STRUCTURAL_CONSTITUENT_OF_CHROMATIN, GOCC_CHROMATIN

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

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1W2PP81, A0A1W2PPE2, A0A1W2PPH5, A0A1W2PPL8, A0A1W2PR64, A0A1W2PRV1, A0A3B3IU63, A4QVR2, A5DQL2, A9UMV8, F4HR03, O35216, P06898, P0C1H6, P0C5Y9, P0C5Z0, P0DW11, P0DW12, P0DW13, P0DW14, P0DW85, P35061, P48003, P49450, Q00728, Q3SZB8, Q3ZBX9, Q4IMD1, Q5M8Q2, Q5TKR9, Q64522, Q64598, Q7Z2G1, Q803H4, Q873G4, Q8BRB7, Q8BZ21, Q8CGP5, Q8IUE6, Q8R1M2

Diamond homologs: A0A2R8Y619, A1CJ09, A1D8G9, A2QY49, L7I1W3, O22582, O60814, O65819, P02281, P02283, P02284, P02285, P02286, P02287, P02290, P04255, P04913, P06145, P06899, P06900, P07794, P07795, P0C1H4, P0C1H5, P0CO02, P0CO03, P0CT13, P0DW85, P10853, P10854, P16889, P16890, P17271, P21897, P23527, P23754, P33778, P35067, P35068, P35069

SIGNOR signaling

0 interactions.

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

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000384442 (17:32895929 G>A,T), RS1000721973 (17:32897702 G>A), RS1000800854 (17:32902042 C>A,T), RS1001602537 (17:32905764 G>C), RS1001676248 (17:32905513 G>GTT), RS1002127038 (17:32893984 A>G), RS1002416248 (17:32901286 T>C), RS1002688514 (17:32901489 C>A), RS1002914758 (17:32896864 A>C,G), RS1003089971 (17:32905022 C>A), RS1003138685 (17:32897346 C>T), RS1003142282 (17:32905357 A>G), RS1003282759 (17:32900429 A>G), RS1003355716 (17:32898294 G>A), RS1003474908 (17:32907064 C>G,T)

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)

Clinical trials (associated diseases)

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