H2BW1
protein-codingH2B.W histone 1, the group of H2B histones
Gene summary
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. This gene encodes a replication-independent histone that is a member of the H2B histone family that is specifically expressed in sperm nuclei. A polymorphism in the 5' UTR of this gene is associated with male infertility.[provided by RefSeq, Oct 2015]
- H2BFWT
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~2.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to H2BW1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001002916.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 3 | ||||
| missense | 27 | 3 | 30 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 27 | 7 | 0 | 34 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001002916.4 | 2 | MANE Select | |
| Ensembl | ENSP00000354723.5 | 2 | MANE Select | |
| Ensembl | ENSP00000774551.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Systemic lupus erythematosus - Homo sapiens (human)
- Viral carcinogenesis - Homo sapiens (human)
- Alcoholism - Homo sapiens (human)
Biological Process
- nucleosome assembly
Molecular Function
- DNA binding
- protein heterodimerization activity
Cellular Component
- nucleosome
- nuclear membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000217926
- Coding exons
- 2
- Length
- 2541
- Individuals with no LoFs
- 124403
- Homozygous LoFs
- 36
- Heterozygous LoFs
- 54
- Defined
- 124493
- p
- 0.000362
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.602 | 110 | 93.6 | 1.18 | 0.00000912 | 1110 |
| Missense (PolyPhen) | 21 | 18.685 | 1.1239 | 293 | ||
| Synonymous | 0.965 | 29 | 36.4 | 0.796 | 0.00000330 | 387 |
| Loss of Function | 0.288 | 4 | 4.67 | 0.856 | 3.69e-7 | 64 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00084 | 0.00068 | rare |
| Latino/Admixed American | 0.00011 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00070 | 0.00050 | rare |
| South Asian | 0.0010 | 0.00062 | rare |
| Other | 0.00022 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Atypical histone H2B. Nucleosomes containing it are structurally and dynamically indistinguishable from those containing conventional H2B. However, unlike conventional H2B, does not recruit chromosome condensation factors and does not participate in the assembly of mitotic chromosomes. May be important for telomere function. {ECO:0000269|PubMed:16449661}.;
Recessive Scores
- pRec
- 0.0929
Intolerance Scores
- RVIS EVS
- 0.24
- RVIS percentile EVS
- 69.21
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |