TST
Basic information
Region (hg38): 22:37010859-37020183
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (43 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TST gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003312.6. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 42 | 43 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 42 | 2 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TST | protein_coding | protein_coding | ENST00000403892 | 2 | 8782 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000787 | 0.540 | 125687 | 0 | 20 | 125707 | 0.0000796 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.589 | 174 | 197 | 0.882 | 0.0000139 | 1878 |
| Missense in Polyphen | 71 | 83.763 | 0.84763 | 858 | ||
| Synonymous | 0.244 | 85 | 87.9 | 0.967 | 0.00000654 | 632 |
| Loss of Function | 0.562 | 7 | 8.80 | 0.795 | 4.21e-7 | 99 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000145 | 0.000145 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000545 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000126 | 0.000123 |
| Middle Eastern | 0.0000545 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Formation of iron-sulfur complexes, cyanide detoxification or modification of sulfur-containing enzymes. Other thiol compounds, besides cyanide, can act as sulfur ion acceptors. Also has weak mercaptopyruvate sulfurtransferase (MST) activity (By similarity). Together with MRPL18, acts as a mitochondrial import factor for the cytosolic 5S rRNA. Only the nascent unfolded cytoplasmic form is able to bind to the 5S rRNA. {ECO:0000250, ECO:0000269|PubMed:20663881, ECO:0000269|PubMed:21685364}.;
- Pathway
- Sulfur relay system - Homo sapiens (human);Cysteine and methionine metabolism - Homo sapiens (human);Sulfur metabolism - Homo sapiens (human);Sulfide oxidation to sulfate;Degradation of cysteine and homocysteine;Metabolism of amino acids and derivatives;thiosulfate disproportionation III (rhodanese);Metabolism;Sulfur amino acid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.355
Intolerance Scores
- loftool
- 0.598
- rvis_EVS
- 0.13
- rvis_percentile_EVS
- 63.36
Haploinsufficiency Scores
- pHI
- 0.0574
- hipred
- N
- hipred_score
- 0.297
- ghis
- 0.432
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.975
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tst
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- sulfur amino acid catabolic process;cyanate catabolic process;epithelial cell differentiation;rRNA import into mitochondrion;rRNA transport
- Cellular component
- extracellular space;mitochondrion;mitochondrial matrix
- Molecular function
- thiosulfate sulfurtransferase activity;5S rRNA binding