TOR1A

protein-coding

torsin 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]

Previous symbols:
  • DYT1

MANE transcript

NM_000113.3

Inheritance

AD, AR

ClinVar variants

P:18U:123B:54

Top phenotype

Dystonia 1, torsion; Arthrogryposis multiplex congenita 5

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr9:129,812,942-129,824,244

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~11.3 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

early-onset generalized limb-onset dystoniaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007492

Submitter: Orphanet

arthrogryposis multiplex congenita 5STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0100218

Submitter: PanelApp Australia

early-onset generalized limb-onset dystoniaDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007492

Submitter: Illumina

arthrogryposis multiplex congenita 5STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0100218

Submitter: Labcorp Genetics (formerly Invitae)

early-onset generalized limb-onset dystoniaSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007492

Submitter: Labcorp Genetics (formerly Invitae)

early-onset generalized limb-onset dystoniaSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007492

Submitter: PanelApp Australia

arthrogryposis multiplex congenita 5DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0100218

Submitter: G2P

arthrogryposis multiplex congenita 5MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0100218

Submitter: Ambry Genetics

early-onset generalized limb-onset dystoniaMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0007492

Submitter: Ambry Genetics

early-onset generalized limb-onset dystoniaSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007492

Submitter: Genomics England PanelApp

Clinical Genomic Database (CGD)

Dystonia 1, torsion; Arthrogryposis multiplex congenita 5AD/AR

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

Refs: 9288096; 10541594; 10435508; 11523564; 12391355; 11973627; 12481989; 12402271; 12975293; 15326234; 16275837; 17503336; 18519876; 19955557; 20925076; 21515903; 22132914; 28516161; 29053766; 30244176Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TOR1A variants in ClinVar

11 Conditions Cataloged
Dystonic disorderTotal: 125
not providedTotal: 69
Inborn genetic diseasesTotal: 43
Early-onset generalized limb-onset dystoniaTotal: 30
Arthrogryposis multiplex congenita 5Total: 18
not specifiedTotal: 14
TOR1A-related disorderTotal: 11
Dystonia, early-onset atypical, with myoclonic featuresTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
44
clinvar
1
clinvar
47
missense
2
clinvar
2
clinvar
112
clinvar
9
clinvar
125
nonsense
3
clinvar
6
clinvar
2
clinvar
11
start loss
0
frameshift
3
clinvar
6
clinvar
9
splice donor/acceptor (+/-2bp)
2
clinvar
1
clinvar
3
Total513123531195

Highest pathogenic variant AF is 0.000095412164

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000113.3RefSeqNP_000104.15MANE Select
ENST00000351698.5EnsemblENSP00000345719.45MANE Select
ENST00000651202.1EnsemblENSP00000498222.15Standard
ENST00000651202.2EnsemblENSP00000498222.15Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.5351601800.8880.000009922198
Missense (PolyPhen)6071.3640.84076896
Synonymous-0.08627776.01.010.00000481626
Loss of Function1.43712.40.5637.25e-7149

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000870.000087rare
Ashkenazi Jewish00.0absent
East Asian0.000110.00011rare
Finnish00.0absent
European (Non-Finnish)0.000160.00016rare
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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