HSPA2
heat shock protein family A (Hsp70) member 2, the group of Heat shock 70kDa proteins
Basic information
Region (hg38): 14:64535905-64546173
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (45 variants)
- not_provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSPA2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021979.4. 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 | 3 | |||||
| missense | 45 | 45 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 45 | 0 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HSPA2 | protein_coding | protein_coding | ENST00000247207 | 1 | 7333 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0486 | 0.947 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.72 | 219 | 438 | 0.500 | 0.0000285 | 4205 |
| Missense in Polyphen | 84 | 224.5 | 0.37416 | 2100 | ||
| Synonymous | 2.14 | 173 | 213 | 0.814 | 0.0000167 | 1325 |
| Loss of Function | 2.50 | 5 | 15.7 | 0.319 | 7.79e-7 | 182 |
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: Molecular chaperone implicated in a wide variety of cellular processes, including protection of the proteome from stress, folding and transport of newly synthesized polypeptides, activation of proteolysis of misfolded proteins and the formation and dissociation of protein complexes. Plays a pivotal role in the protein quality control system, ensuring the correct folding of proteins, the re-folding of misfolded proteins and controlling the targeting of proteins for subsequent degradation. This is achieved through cycles of ATP binding, ATP hydrolysis and ADP release, mediated by co-chaperones. The affinity for polypeptides is regulated by its nucleotide bound state. In the ATP-bound form, it has a low affinity for substrate proteins. However, upon hydrolysis of the ATP to ADP, it undergoes a conformational change that increases its affinity for substrate proteins. It goes through repeated cycles of ATP hydrolysis and nucleotide exchange, which permits cycles of substrate binding and release (PubMed:26865365). Plays a role in spermatogenesis. In association with SHCBP1L may participate in the maintenance of spindle integrity during meiosis in male germ cells (By similarity). {ECO:0000250|UniProtKB:P17156, ECO:0000303|PubMed:26865365}.;
- Pathway
- Antigen processing and presentation - Homo sapiens (human);Legionellosis - Homo sapiens (human);Endocytosis - Homo sapiens (human);Longevity regulating pathway - multiple species - Homo sapiens (human);Influenza A - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);Estrogen signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Toxoplasmosis - Homo sapiens (human);Spliceosome - Homo sapiens (human);Measles - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Parkin-Ubiquitin Proteasomal System pathway;MAPK Signaling Pathway;Attenuation phase;HSF1-dependent transactivation;Regulation of HSF1-mediated heat shock response;HSP90 chaperone cycle for steroid hormone receptors (SHR);Cellular responses to stress;Cellular responses to external stimuli;Cellular response to heat stress
(Consensus)
Intolerance Scores
- loftool
- 0.463
- rvis_EVS
- 0.13
- rvis_percentile_EVS
- 63.36
Haploinsufficiency Scores
- pHI
- 0.639
- hipred
- hipred_score
- ghis
- 0.389
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- 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
- Hspa2
- Phenotype
- reproductive system phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- positive regulation of protein phosphorylation;response to unfolded protein;male meiotic nuclear division;male meiosis I;spermatogenesis;spermatid development;response to heat;response to cold;positive regulation of G2/M transition of mitotic cell cycle;vesicle-mediated transport;cellular response to heat;cellular response to unfolded protein;protein refolding;chaperone cofactor-dependent protein refolding;synaptonemal complex disassembly;negative regulation of inclusion body assembly;positive regulation of calcium-transporting ATPase activity
- Cellular component
- synaptonemal complex;male germ cell nucleus;nucleus;cytoplasm;cytosol;plasma membrane;cell surface;membrane;CatSper complex;myelin sheath;extracellular exosome;blood microparticle;meiotic spindle
- Molecular function
- protein binding;ATP binding;ATPase activity;enzyme binding;heat shock protein binding;ATPase activity, coupled;protein folding chaperone;tau protein binding;unfolded protein binding;chaperone binding;misfolded protein binding;glycolipid binding;disordered domain specific binding