HSP90B1
heat shock protein 90 beta family member 1, the group of MicroRNA protein coding host genes|Heat shock 90kDa proteins
Basic information
Region (hg38): 12:103930107-103953931
Previous symbols: [ "TRA1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (72 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSP90B1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003299.3. 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 | 2 | |||||
| missense | 71 | 72 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 71 | 2 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HSP90B1 | protein_coding | protein_coding | ENST00000299767 | 18 | 23539 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.997 | 0.00280 | 125730 | 0 | 17 | 125747 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.12 | 307 | 431 | 0.712 | 0.0000226 | 5333 |
| Missense in Polyphen | 88 | 173.48 | 0.50725 | 2132 | ||
| Synonymous | 0.195 | 152 | 155 | 0.980 | 0.00000873 | 1437 |
| Loss of Function | 5.29 | 6 | 43.7 | 0.137 | 0.00000226 | 553 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000290 | 0.0000290 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000235 | 0.000217 |
| Finnish | 0.0000931 | 0.0000924 |
| European (Non-Finnish) | 0.0000645 | 0.0000615 |
| Middle Eastern | 0.000235 | 0.000217 |
| South Asian | 0.0000997 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Molecular chaperone that functions in the processing and transport of secreted proteins. When associated with CNPY3, required for proper folding of Toll-like receptors (By similarity). Functions in endoplasmic reticulum associated degradation (ERAD). Has ATPase activity. {ECO:0000250, ECO:0000269|PubMed:18264092}.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Thyroid hormone synthesis - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);Prostate cancer - Homo sapiens (human);Estrogen signaling pathway - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);ATF6 (ATF6-alpha) activates chaperone genes;Photodynamic therapy-induced unfolded protein response;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Prion disease pathway;Interleukin-4 and 13 signaling;PI3K-Akt Signaling Pathway;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Vesicle-mediated transport;Post-translational protein phosphorylation;Trafficking and processing of endosomal TLR;Toll-Like Receptors Cascades;Post-translational protein modification;Metabolism of proteins;Innate Immune System;Immune System;AndrogenReceptor;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Binding and Uptake of Ligands by Scavenger Receptors;Scavenging by Class A Receptors;IL6-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.429
Intolerance Scores
- loftool
- 0.297
- rvis_EVS
- -0.36
- rvis_percentile_EVS
- 29.31
Haploinsufficiency Scores
- pHI
- 0.858
- hipred
- Y
- hipred_score
- 0.736
- ghis
- 0.555
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.941
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hsp90b1
- Phenotype
- immune system phenotype; pigmentation phenotype; 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); 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); hematopoietic system phenotype; embryo phenotype; cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- hsp90b1
- Affected structure
- muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- disorganized
Gene ontology
- Biological process
- response to hypoxia;toll-like receptor signaling pathway;receptor-mediated endocytosis;protein transport;cytokine-mediated signaling pathway;ubiquitin-dependent ERAD pathway;retrograde protein transport, ER to cytosol;actin rod assembly;protein folding in endoplasmic reticulum;response to endoplasmic reticulum stress;ATF6-mediated unfolded protein response;negative regulation of apoptotic process;regulation of phosphoprotein phosphatase activity;post-translational protein modification;cellular protein metabolic process;sequestering of calcium ion;cellular response to ATP
- Cellular component
- extracellular region;nucleus;endoplasmic reticulum;endoplasmic reticulum lumen;endoplasmic reticulum membrane;cytosol;plasma membrane;focal adhesion;membrane;midbody;protein-containing complex;endoplasmic reticulum chaperone complex;melanosome;perinuclear region of cytoplasm;collagen-containing extracellular matrix;extracellular exosome;endocytic vesicle lumen
- Molecular function
- RNA binding;calcium ion binding;protein binding;ATP binding;protein phosphatase binding;low-density lipoprotein particle receptor binding;unfolded protein binding