TOR1A
protein-codingtorsin family 1 member A, the group of Torsins
Gene summary
The protein encoded by this gene is a member of the AAA family of adenosine triphosphatases (ATPases), is related to the Clp protease/heat shock family and is expressed prominently in the substantia nigra pars compacta. Mutations in this gene result in the autosomal dominant disorder, torsion dystonia 1. [provided by RefSeq, Jul 2008]
- DYT1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~11.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0007492
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0100218
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0007492
Submitter: Illumina
Inheritance Pattern: AR
Disease ID:MONDO:0100218
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0007492
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0007492
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0100218
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0100218
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0007492
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0007492
Submitter: Genomics England PanelApp
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Musculoskeletal; Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TOR1A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000113.3. 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 | 2 | 44 | 1 | 47 | ||
| missense | 2 | 2 | 112 | 9 | 125 | |
| nonsense | 3 | 6 | 2 | 11 | ||
| start loss | 0 | |||||
| frameshift | 3 | 6 | 9 | |||
| splice donor/acceptor (+/-2bp) | 2 | 1 | 3 | |||
| Total | 5 | 13 | 123 | 53 | 1 | 195 |
Highest pathogenic variant AF is 0.000095412164
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000104.1 | 5 | MANE Select | |
| Ensembl | ENSP00000345719.4 | 5 | MANE Select | |
| Ensembl | ENSP00000498222.1 | 5 | Standard | |
| Ensembl | ENSP00000498222.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vesicle-mediated transport
- Membrane Trafficking
- Clathrin-mediated endocytosis
- Cargo recognition for clathrin-mediated endocytosis
- Alpha-synuclein signaling
Biological Process
- protein deneddylation
- response to oxidative stress
- organelle organization
- nuclear envelope organization
- cell adhesion
Molecular Function
- protein binding
- ATP binding
- cytoskeletal protein binding
- ATPase activity
- kinesin binding
Cellular Component
- nuclear envelope
- endoplasmic reticulum
- endoplasmic reticulum lumen
- cytosol
- cytoskeleton
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000351698
- Coding exons
- 5
- Length
- 11191
- Individuals with no LoFs
- 125724
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 24
- Defined
- 125748
- p
- 0.0000954
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.535 | 160 | 180 | 0.888 | 0.00000992 | 2198 |
| Missense (PolyPhen) | 60 | 71.364 | 0.84076 | 896 | ||
| Synonymous | -0.0862 | 77 | 76.0 | 1.01 | 0.00000481 | 626 |
| Loss of Function | 1.43 | 7 | 12.4 | 0.563 | 7.25e-7 | 149 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00016 | 0.00016 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Protein with chaperone functions important for the control of protein folding, processing, stability and localization as well as for the reduction of misfolded protein aggregates. Involved in the regulation of synaptic vesicle recycling, controls STON2 protein stability in collaboration with the COP9 signalosome complex (CSN). In the nucleus, may link the cytoskeleton with the nuclear envelope, this mechanism seems to be crucial for the control of nuclear polarity, cell movement and, specifically in neurons, nuclear envelope integrity. Participates in the cellular trafficking and may regulate the subcellular location of multipass membrane proteins such as the dopamine transporter SLC6A3, leading to the modulation of dopamine neurotransmission. In the endoplasmic reticulum, plays a role in the quality control of protein folding by increasing clearance of misfolded proteins such as SGCE variants or holding them in an intermediate state for proper refolding. May have a redundant function with TOR1B in non- neural tissues. {ECO:0000269|PubMed:15505207, ECO:0000269|PubMed:16361107, ECO:0000269|PubMed:17428918, ECO:0000269|PubMed:18167355, ECO:0000269|PubMed:18827015, ECO:0000269|PubMed:19339278, ECO:0000269|PubMed:20169475, ECO:0000269|PubMed:23569223}.;
- Disease
- DISEASE: Dystonia 1, torsion, autosomal dominant (DYT1) [MIM:128100]: A primary torsion dystonia, and the most common and severe form. Dystonia is defined by the presence of sustained involuntary muscle contractions, often leading to abnormal postures. Dystonia type 1 is characterized by involuntary, repetitive, sustained muscle contractions or postures involving one or more sites of the body, in the absence of other neurological symptoms. Typically, symptoms develop first in an arm or leg in middle to late childhood and progress in approximately 30% of patients to other body regions (generalized dystonia) within about five years. 'Torsion' refers to the twisting nature of body movements observed in DYT1, often affecting the trunk. Distribution and severity of symptoms vary widely between affected individuals, ranging from mild focal dystonia to severe generalized dystonia, even within families. {ECO:0000269|PubMed:14970196, ECO:0000269|PubMed:15505207, ECO:0000269|PubMed:16361107, ECO:0000269|PubMed:17428918, ECO:0000269|PubMed:18167355, ECO:0000269|PubMed:18477710, ECO:0000269|PubMed:18827015, ECO:0000269|PubMed:19955557, ECO:0000269|PubMed:20169475, ECO:0000269|PubMed:21102408, ECO:0000269|PubMed:27490483, ECO:0000269|PubMed:9288096}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.328
Intolerance Scores
- LoFtool
- 0.524
- RVIS EVS
- -0.18
- RVIS percentile EVS
- 39.95
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.991
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |