MPST
mercaptopyruvate sulfurtransferase
Basic information
Region (hg38): 22:37019635-37029821
Links
Phenotypes
GenCC
Source:
- encephalopathy due to beta-mercaptolactate-cysteine disulfiduria (No Known Disease Relationship), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (50 variants)
- Encephalopathy_due_to_beta-mercaptolactate-cysteine_disulfiduria (1 variants)
- MPST-related_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the MPST gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021126.8. 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 | 0 | |||||
| missense | 50 | 52 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 50 | 2 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| MPST | protein_coding | protein_coding | ENST00000397129 | 3 | 10188 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000347 | 0.603 | 125688 | 0 | 24 | 125712 | 0.0000955 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.21 | 153 | 201 | 0.760 | 0.0000147 | 1983 |
| Missense in Polyphen | 40 | 56.56 | 0.70721 | 610 | ||
| Synonymous | 2.28 | 69 | 97.6 | 0.707 | 0.00000831 | 654 |
| Loss of Function | 0.769 | 8 | 10.7 | 0.746 | 6.99e-7 | 106 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000148 | 0.000148 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.0000590 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000134 | 0.000123 |
| Middle Eastern | 0.0000590 | 0.0000544 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.000173 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Transfer of a sulfur ion to cyanide or to other thiol compounds. Also has weak rhodanese activity. Detoxifies cyanide and is required for thiosulfate biosynthesis. Acts as an antioxidant. In combination with cysteine aminotransferase (CAT), contributes to the catabolism of cysteine and is an important producer of hydrogen sulfide in the brain, retina and vascular endothelial cells. Hydrogen sulfide H(2)S is an important synaptic modulator, signaling molecule, smooth muscle contractor and neuroprotectant. Its production by the 3MST/CAT pathway is regulated by calcium ions. {ECO:0000250|UniProtKB:P97532}.;
- Disease
- DISEASE: Note=Aberrant MPST activity is found in a few cases of mercaptolactate-cysteine disulfiduria (MCDU) characterized by the appearance of large quantaties of the sulfur-containing amino acid, beta-mercaptolactate-cysteine disulfide, in the urine (PubMed:4973015, PubMed:4690911 and PubMed:6945862). Some cases have associated mental retardation (PubMed:4973015 and PubMed:6945862).;
- Pathway
- Sulfur relay system - Homo sapiens (human);Cysteine and methionine metabolism - Homo sapiens (human);Sulfur metabolism - Homo sapiens (human);Beta-mercaptolactate-cysteine disulfiduria;Cysteine Metabolism;Cystinosis, ocular nonnephropathic;Trans-sulfuration pathway;Amino Acid metabolism;Degradation of cysteine and homocysteine;Metabolism of amino acids and derivatives;L-cysteine degradation II;Metabolism;Methionine Cysteine metabolism;Methionine and cysteine metabolism;Sulfur amino acid metabolism
(Consensus)
Haploinsufficiency Scores
- pHI
- 0.0827
- hipred
- N
- hipred_score
- 0.339
- ghis
- 0.447
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.749
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Mpst
- Phenotype
- reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- sulfur amino acid catabolic process;kidney development;liver development;cyanate catabolic process;response to toxic substance;transsulfuration;spinal cord development;hydrogen sulfide biosynthetic process
- Cellular component
- mitochondrial matrix;cytosol;cell junction;neuron projection;synapse;extracellular exosome
- Molecular function
- thiosulfate sulfurtransferase activity;3-mercaptopyruvate sulfurtransferase activity;identical protein binding