TPST1

tyrosylprotein sulfotransferase 1, the group of Sulfotransferases, membrane bound

Basic information

Region (hg38): 7:66205317-66420543

Links

ENSG00000169902 ∙ NCBI:8460 ∙ OMIM:603125 ∙ HGNC:12020 ∙ Uniprot:O60507 ∙ 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 TPST1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPST1 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in TPST1

This is a list of pathogenic ClinVar variants found in the TPST1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-66240430-T-C		not specified	Uncertain significance (May 11, 2022)
7-66240526-G-A		not specified	Uncertain significance (Jul 14, 2023)
7-66240537-C-T		not specified	Uncertain significance (Apr 04, 2023)
7-66240538-G-A		not specified	Uncertain significance (Sep 26, 2022)
7-66240550-T-A		not specified	Uncertain significance (Sep 16, 2021)
7-66240562-G-A		not specified	Uncertain significance (Sep 28, 2022)
7-66240627-G-T		not specified	Uncertain significance (Jul 05, 2022)
7-66240706-A-G		not specified	Uncertain significance (Dec 20, 2023)
7-66240793-G-A		not specified	Uncertain significance (Dec 12, 2023)
7-66240802-A-T		not specified	Uncertain significance (Dec 26, 2023)
7-66240952-A-G		not specified	Uncertain significance (Aug 04, 2023)
7-66240969-A-G		not specified	Uncertain significance (Dec 14, 2021)
7-66240984-C-T		not specified	Uncertain significance (Mar 19, 2024)
7-66240985-G-A		not specified	Uncertain significance (Dec 15, 2022)
7-66241012-G-A		not specified	Uncertain significance (Dec 28, 2022)
7-66241074-C-T		not specified	Uncertain significance (Aug 12, 2021)
7-66241168-G-A		not specified	Uncertain significance (Jun 04, 2024)
7-66286519-G-A		not specified	Uncertain significance (Feb 28, 2023)
7-66286566-A-G		not specified	Uncertain significance (Sep 22, 2023)
7-66286585-C-T		not specified	Uncertain significance (Aug 02, 2021)
7-66352539-T-C		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPST1	protein_coding	protein_coding	ENST00000304842	4	215345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.292	0.707	125731	0	16	125747	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.36	155	210	0.737	0.0000111	2407
Missense in Polyphen		49	82.842	0.59149		892
Synonymous	0.844	64	73.2	0.875	0.00000350	730
Loss of Function	2.90	4	16.8	0.238	0.00000101	195

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000153
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000970	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000338	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the O-sulfation of tyrosine residues within acidic motifs of polypeptides, using 3'-phosphoadenylyl sulfate (PAPS) as cosubstrate. {ECO:0000269|PubMed:28821720, ECO:0000269|PubMed:9501187, ECO:0000269|PubMed:9733778}.
• Pathway: Phase II - Conjugation of compounds;Biological oxidations;Metabolism;Cytosolic sulfonation of small molecules (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.360
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.321
• ghis: 0.497

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.561

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tpst1
• Phenotype: growth/size/body region phenotype; reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: peptidyl-tyrosine sulfation;inflammatory response;3'-phosphoadenosine 5'-phosphosulfate metabolic process
• Cellular component: Golgi membrane;Golgi apparatus;membrane;integral component of Golgi membrane
• Molecular function: protein-tyrosine sulfotransferase activity;protein homodimerization activity