TARS3
protein-codingthreonyl-tRNA synthetase 3
Gene summary
Predicted to enable threonine-tRNA ligase activity. Predicted to be involved in threonyl-tRNA aminoacylation. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jun 2026]
- TARSL2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~70.9 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 TARS3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_152334.3. 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 | 1 | 3 | |||
| missense | 132 | 2 | 134 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 139 | 3 | 0 | 142 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_689547.2 | 19 | MANE Select | |
| Ensembl | ENSP00000338093.3 | 19 | MANE Select | |
| Ensembl | ENSP00000439899.1 | 19 | Standard | |
| Ensembl | ENSP00000452740.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Aminoacyl-tRNA biosynthesis - Homo sapiens (human)
- tRNA charging
Biological Process
- threonyl-tRNA aminoacylation
- biological_process
Molecular Function
- molecular_function
- threonine-tRNA ligase activity
- protein binding
- ATP binding
Cellular Component
- cellular_component
- nucleus
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000335968
- Coding exons
- 19
- Length
- 71007
- Individuals with no LoFs
- 125621
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 127
- Defined
- 125748
- p
- 0.000505
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.310 | 400 | 418 | 0.957 | 0.0000212 | 5302 |
| Missense (PolyPhen) | 104 | 119.12 | 0.87311 | 1491 | ||
| Synonymous | -1.07 | 169 | 152 | 1.11 | 0.00000832 | 1415 |
| Loss of Function | 2.11 | 30 | 45.3 | 0.662 | 0.00000235 | 543 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00062 | 0.00061 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00076 | 0.00076 | rare |
| Finnish | 0.00023 | 0.00023 | rare |
| European (Non-Finnish) | 0.00052 | 0.00052 | rare |
| South Asian | 0.00082 | 0.00082 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.128
Intolerance Scores
- LoFtool
- 0.304
- RVIS EVS
- -1.53
- RVIS percentile EVS
- 3.37
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.116
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |