MPST

mercaptopyruvate sulfurtransferase

Basic information

Region (hg38): 22:37019634-37029821

Links

ENSG00000128309 ∙ NCBI:4357 ∙ OMIM:602496 ∙ HGNC:7223 ∙ Uniprot:P25325 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• 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 ClinVar and linked to the MPST gene.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in MPST

This is a list of pathogenic ClinVar variants found in the MPST region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
22-37019867-A-G		not specified	Uncertain significance (Oct 14, 2023)
22-37024226-C-T		not specified	Uncertain significance (May 24, 2023)
22-37024253-C-T		not specified	Uncertain significance (Oct 06, 2021)
22-37024255-C-A		not specified	Uncertain significance (Jan 31, 2022)
22-37024257-A-C		not specified	Uncertain significance (May 28, 2024)
22-37024304-A-C		not specified	Uncertain significance (Jan 04, 2024)
22-37024363-G-C		not specified	Uncertain significance (Oct 12, 2021)
22-37024370-G-A		not specified	Uncertain significance (Oct 18, 2021)
22-37024382-G-T		MPST-related disorder	Likely benign (Jan 12, 2023)
22-37024417-C-A		not specified	Uncertain significance (Dec 15, 2022)
22-37024433-A-T		not specified	Uncertain significance (Aug 12, 2021)
22-37024463-C-A		not specified	Uncertain significance (Jan 02, 2024)
22-37024469-A-G		Encephalopathy due to beta-mercaptolactate-cysteine disulfiduria	not provided (-)
22-37024484-G-C		not specified	Uncertain significance (Jun 06, 2023)
22-37024544-C-T		not specified	Uncertain significance (Jan 26, 2023)
22-37024552-G-A		not specified	Uncertain significance (May 17, 2023)
22-37024612-C-A		not specified	Uncertain significance (Jun 03, 2022)
22-37024625-G-A		not specified	Uncertain significance (Jun 22, 2024)
22-37024674-G-C		not specified	Uncertain significance (Jan 20, 2023)
22-37024784-G-A		not specified	Uncertain significance (Sep 15, 2021)
22-37024790-C-T		not specified	Uncertain significance (Jun 05, 2024)
22-37029236-C-A		not specified	Uncertain significance (Dec 08, 2022)
22-37029245-G-C		not specified	Uncertain significance (Dec 08, 2023)
22-37029291-A-G		not specified	Uncertain significance (Dec 20, 2023)
22-37029323-G-A		not specified	Uncertain significance (May 10, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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