HIRA
histone cell cycle regulator, the group of WD repeat domain containing|HIRA histone chaperone complex subunits
Basic information
Region (hg38): 22:19330698-19447450
Previous symbols: [ "TUPLE1" ]
Links
Phenotypes
GenCC
Source:
- neurodevelopmental disorder (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (94 variants)
- not_provided (40 variants)
- HIRA-related_disorder (24 variants)
- Prostate_cancer (1 variants)
- Fanconi_anemia_complementation_group_T (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HIRA gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003325.4. 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 | 22 | 30 | ||||
| missense | 91 | 99 | ||||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 0 | 94 | 29 | 9 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HIRA | protein_coding | protein_coding | ENST00000263208 | 25 | 117004 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 1.35e-7 | 125742 | 0 | 5 | 125747 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.71 | 352 | 610 | 0.578 | 0.0000371 | 6603 |
| Missense in Polyphen | 86 | 234.29 | 0.36707 | 2454 | ||
| Synonymous | -0.423 | 260 | 251 | 1.03 | 0.0000163 | 2058 |
| Loss of Function | 6.63 | 3 | 57.1 | 0.0526 | 0.00000303 | 619 |
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 | 0.0000925 | 0.0000924 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Cooperates with ASF1A to promote replication-independent chromatin assembly. Required for the periodic repression of histone gene transcription during the cell cycle. Required for the formation of senescence-associated heterochromatin foci (SAHF) and efficient senescence-associated cell cycle exit. {ECO:0000269|PubMed:12370293, ECO:0000269|PubMed:14718166, ECO:0000269|PubMed:15621527}.;
- Pathway
- Formation of Senescence-Associated Heterochromatin Foci (SAHF);DNA Damage/Telomere Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;Cellular responses to external stimuli
(Consensus)
Recessive Scores
- pRec
- 0.232
Intolerance Scores
- loftool
- 0.0158
- rvis_EVS
- -1.37
- rvis_percentile_EVS
- 4.43
Haploinsufficiency Scores
- pHI
- 0.942
- hipred
- Y
- hipred_score
- 0.816
- ghis
- 0.541
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hira
- Phenotype
- hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; skeleton phenotype; immune system phenotype; muscle phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype;
Gene ontology
- Biological process
- mitotic sister chromatid segregation;osteoblast differentiation;DNA replication-independent nucleosome assembly;transcription, DNA-templated;regulation of transcription by RNA polymerase II;gastrulation;anatomical structure morphogenesis;chromatin silencing at centromere;regulation of chromatin silencing;muscle cell differentiation
- Cellular component
- HIR complex;chromosome, centromeric region;nuclear chromatin;nucleus;nucleoplasm;PML body;protein-containing complex;extracellular exosome
- Molecular function
- DNA binding;DNA-binding transcription factor activity;transcription corepressor activity;protein binding;nucleosome binding