TST

thiosulfate sulfurtransferase

Basic information

Region (hg38): 22:37010858-37020183

Links

ENSG00000128311 ∙ NCBI:7263 ∙ OMIM:180370 ∙ HGNC:12388 ∙ Uniprot:Q16762 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TST gene.

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.

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				1		1
missense			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	23	2	0

Variants in TST

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

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

Position	Type	Phenotype	Significance	ClinVar
22-37011067-G-T		not specified	Uncertain significance (May 17, 2024)
22-37011077-G-A		not specified	Uncertain significance (Oct 25, 2022)
22-37011110-C-T		not specified	Uncertain significance (Aug 23, 2021)
22-37011128-C-T		not specified	Uncertain significance (Feb 27, 2023)
22-37011152-C-T		not specified	Uncertain significance (Dec 21, 2022)
22-37011181-G-A		not specified	Uncertain significance (Jan 27, 2022)
22-37011199-G-A		not specified	Uncertain significance (Oct 06, 2021)
22-37011214-T-G		not specified	Uncertain significance (Feb 08, 2023)
22-37011232-C-T		not specified	Uncertain significance (Oct 14, 2023)
22-37011233-G-A		not specified	Uncertain significance (May 02, 2024)
22-37011290-T-G		not specified	Uncertain significance (Jan 26, 2023)
22-37018129-G-A			Likely benign (Aug 22, 2018)
22-37018149-G-A		not specified	Uncertain significance (May 16, 2023)
22-37018155-G-T		not specified	Uncertain significance (Aug 26, 2022)
22-37018176-C-T		not specified	Uncertain significance (Jul 05, 2022)
22-37018242-G-A		not specified	Uncertain significance (Mar 12, 2024)
22-37018279-C-A		not specified	Uncertain significance (Jul 11, 2023)
22-37018280-G-C			Likely benign (Jul 02, 2018)
22-37018285-G-A		not specified	Uncertain significance (Jul 19, 2023)
22-37018335-T-C		not specified	Uncertain significance (Sep 14, 2023)
22-37018344-C-G		not specified	Uncertain significance (Nov 15, 2021)
22-37018363-C-T		not specified	Uncertain significance (Feb 14, 2023)
22-37018502-G-C		not specified	Uncertain significance (Sep 26, 2023)
22-37018519-C-T		not specified	Uncertain significance (May 23, 2024)
22-37018570-C-T		not specified	Uncertain significance (Mar 30, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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