THNSL1
protein-codingthreonine synthase like 1
Gene summary
Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~10.1 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 THNSL1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024838.5. 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 | 2 | ||||
| missense | 109 | 4 | 113 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 109 | 6 | 0 | 115 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_079114.3 | 1 | MANE Select | |
| Ensembl | ENSP00000365534.4 | 1 | MANE Select | |
| Ensembl | ENSP00000434887.1 | 1 | Standard | |
| Ensembl | ENSP00000434887.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- biological_process
Molecular Function
- molecular_function
Cellular Component
- cellular_component
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000524413
- Coding exons
- 1
- Length
- 10007
- Individuals with no LoFs
- 125251
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 495
- Defined
- 125747
- p
- 0.00197
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.465 | 413 | 387 | 1.07 | 0.0000185 | 4896 |
| Missense (PolyPhen) | 164 | 150.57 | 1.0892 | 1937 | ||
| Synonymous | -0.485 | 148 | 141 | 1.05 | 0.00000713 | 1439 |
| Loss of Function | 0.0243 | 26 | 26.1 | 0.995 | 0.00000159 | 317 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0020 | 0.0020 | notable |
| Latino/Admixed American | 0.0025 | 0.0025 | notable |
| Ashkenazi Jewish | 0.0021 | 0.0021 | notable |
| East Asian | 0.0035 | 0.0035 | notable |
| Finnish | 0.00019 | 0.00018 | rare |
| European (Non-Finnish) | 0.0019 | 0.0019 | notable |
| South Asian | 0.0013 | 0.0013 | notable |
| Other | 0.0044 | 0.0044 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0977
Intolerance Scores
- LoFtool
- 0.588
- RVIS EVS
- 0.47
- RVIS percentile EVS
- 78.74
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.887
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |