TOR3A
protein-codingtorsin family 3 member A, the group of Torsins|Minor histocompatibility antigens
Gene summary
Enables ATP hydrolysis activity. Located in endoplasmic reticulum lumen. [provided by Alliance of Genome Resources, Jul 2025]
- ADIR
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.0 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 TOR3A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022371.4. 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 | 1 | 2 | |||
| missense | 73 | 3 | 76 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 77 | 4 | 0 | 81 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071766.2 | 6 | MANE Select | |
| Ensembl | ENSP00000356599.3 | 6 | MANE Select | |
| Ensembl | ENSP00000335351.6 | 6 | Standard | |
| Ensembl | ENSP00000335351.6 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- ATP binding
- ATPase activity
Cellular Component
- endoplasmic reticulum
- endoplasmic reticulum lumen
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000367627
- Coding exons
- 6
- Length
- 16647
- Individuals with no LoFs
- 125468
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 279
- Defined
- 125748
- p
- 0.00111
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.122 | 204 | 209 | 0.976 | 0.0000121 | 2543 |
| Missense (PolyPhen) | 64 | 66.555 | 0.96161 | 843 | ||
| Synonymous | -0.670 | 97 | 89.0 | 1.09 | 0.00000506 | 769 |
| Loss of Function | -0.357 | 17 | 15.5 | 1.10 | 6.67e-7 | 187 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0034 | 0.0033 | notable |
| Latino/Admixed American | 0.00021 | 0.00020 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.0032 | 0.0031 | notable |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00073 | 0.00072 | rare |
| South Asian | 0.0024 | 0.0024 | notable |
| Other | 0.00082 | 0.00081 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0955
Intolerance Scores
- LoFtool
- 0.868
- RVIS EVS
- -0.49
- RVIS percentile EVS
- 22.51
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |