TOR2A
protein-codingtorsin family 2 member A, the group of Torsins
Gene summary
This gene encodes a member of the AAA family of adenosine triphosphatases with similarity to Clp proteases and heat shock proteins. Alternative splicing at this locus results in the translation of multiple isoforms of the encoded protein, some of which contain salusin peptides in the C-terminal region. These peptides may play roles in hypotension, myocardial growth and the induction of mitogenesis, and may also be involved in the pathogenesis of atherosclerosis. The antimicrobial peptide salusin-beta has antibacterial activity. [provided by RefSeq, Nov 2014]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.8 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 TOR2A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001085347.3. 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 | 1 | 9 | 10 | |||
| missense | 63 | 2 | 1 | 66 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 65 | 11 | 1 | 77 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001078816.2 | 5 | MANE Select | |
| Ensembl | ENSP00000362381.5 | 5 | MANE Select | |
| RefSeq | NP_001127902.1 | 4 | Standard | |
| RefSeq | NP_001127903.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- chaperone cofactor-dependent protein refolding
- protein homooligomerization
Molecular Function
- ATP binding
Cellular Component
- endoplasmic reticulum lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000373284
- Coding exons
- 5
- Length
- 3802
- Individuals with no LoFs
- 125661
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 8
- Defined
- 125670
- p
- 0.0000358
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.247 | 181 | 191 | 0.950 | 0.0000128 | 2037 |
| Missense (PolyPhen) | 70 | 67.359 | 1.0392 | 741 | ||
| Synonymous | 0.167 | 85 | 87.0 | 0.977 | 0.00000587 | 694 |
| Loss of Function | 2.03 | 3 | 9.90 | 0.303 | 4.23e-7 | 120 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000062 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0.00020 | 0.000099 | rare |
| East Asian | 0.000056 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Salusins -alpha and -beta may be endocrine and/or paracrine factors able to increase intracellular calcium concentrations and induce cell mitogenesis. Salusins may also be potent hypotensive peptides. {ECO:0000269|PubMed:12910263}.;
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- LoFtool
- 0.491
- RVIS EVS
- 0.6
- RVIS percentile EVS
- 82.66
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.471
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |