H1-5
Basic information
Region (hg38): 6:27866792-27867588
Previous symbols: [ "H1F5", "HIST1H1B" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (52 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the H1-5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005322.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 52 | 52 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 52 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| H1-5 | protein_coding | protein_coding | ENST00000331442 | 1 | 790 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.575 | 0.384 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -3.54 | 232 | 122 | 1.90 | 0.00000549 | 1412 |
| Missense in Polyphen | 26 | 21.618 | 1.2027 | 286 | ||
| Synonymous | -7.13 | 118 | 52.4 | 2.25 | 0.00000258 | 489 |
| Loss of Function | 1.50 | 0 | 2.63 | 0.00 | 1.09e-7 | 66 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Histone H1 protein binds to linker DNA between nucleosomes forming the macromolecular structure known as the chromatin fiber. Histones H1 are necessary for the condensation of nucleosome chains into higher-order structured fibers. Acts also as a regulator of individual gene transcription through chromatin remodeling, nucleosome spacing and DNA methylation (By similarity). {ECO:0000250}.;
- Pathway
- Formation of Senescence-Associated Heterochromatin Foci (SAHF);DNA Damage/Telomere Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;Activation of DNA fragmentation factor;Apoptosis induced DNA fragmentation;Apoptotic execution phase;Apoptosis;Programmed Cell Death;Cellular responses to external stimuli
(Consensus)
Recessive Scores
- pRec
- 0.206
Intolerance Scores
- loftool
- 0.153
- rvis_EVS
- 0.58
- rvis_percentile_EVS
- 82.17
Haploinsufficiency Scores
- pHI
- 0.276
- hipred
- Y
- hipred_score
- 0.663
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.989
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hist1h1b
- Phenotype
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;chromatin organization;nucleosome assembly;regulation of transcription, DNA-templated;nucleosome positioning;chromosome condensation;positive regulation of cell growth;negative regulation of chromatin silencing;negative regulation of DNA recombination;protein stabilization;positive regulation of histone H3-K9 methylation;establishment of protein localization to chromatin
- Cellular component
- nucleosome;nuclear chromatin;nucleus;nuclear heterochromatin
- Molecular function
- double-stranded DNA binding;RNA binding;protein binding;chromatin DNA binding;nucleosomal DNA binding;histone deacetylase binding