TPST2

tyrosylprotein sulfotransferase 2, the group of Sulfotransferases, membrane bound|MicroRNA protein coding host genes

Basic information

Region (hg38): 22:26521995-26596717

Links

ENSG00000128294 ∙ NCBI:8459 ∙ OMIM:603126 ∙ HGNC:12021 ∙ Uniprot:O60704 ∙ 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 TPST2 gene.

• Inborn genetic diseases (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPST2 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in TPST2

This is a list of pathogenic ClinVar variants found in the TPST2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-26536289-C-T		not specified	Uncertain significance (Jul 26, 2022)
22-26536290-G-A		not specified	Uncertain significance (Jul 13, 2022)
22-26536340-T-A		not specified	Uncertain significance (Jan 16, 2024)
22-26536431-T-G		not specified	Uncertain significance (Jul 20, 2022)
22-26536439-G-A		not specified	Uncertain significance (Oct 26, 2021)
22-26536461-T-C		not specified	Uncertain significance (Aug 04, 2023)
22-26536475-G-A		not specified	Uncertain significance (Feb 06, 2023)
22-26536482-C-T		not specified	Uncertain significance (Jan 05, 2022)
22-26540844-C-A		not specified	Uncertain significance (Jun 27, 2022)
22-26540862-C-T		not specified	Uncertain significance (Dec 18, 2023)
22-26540882-T-C		not specified	Uncertain significance (Oct 24, 2023)
22-26540892-G-A		not specified	Uncertain significance (Aug 30, 2021)
22-26540985-T-C		not specified	Uncertain significance (Oct 27, 2023)
22-26541354-C-G		not specified	Uncertain significance (Aug 03, 2022)
22-26541501-C-T		not specified	Uncertain significance (Feb 06, 2023)
22-26541507-G-A		not specified	Uncertain significance (Mar 29, 2023)
22-26541524-G-A		not specified	Uncertain significance (Feb 23, 2023)
22-26541558-C-T		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TPST2	protein_coding	protein_coding	ENST00000338754	4	71224

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.271	0.724	125742	0	5	125747	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	204	259	0.788	0.0000184	2391
Missense in Polyphen		44	77.79	0.56563		743
Synonymous	-0.520	122	115	1.06	0.00000855	794
Loss of Function	2.43	3	12.2	0.247	5.16e-7	143

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000381	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000180	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:9733778}.
• Pathway: Phase II - Conjugation of compounds;Biological oxidations;Metabolism;Cytosolic sulfonation of small molecules (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.113
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.18

Haploinsufficiency Scores

• pHI: 0.224
• hipred: Y
• hipred_score: 0.593
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.300

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tpst2
• Phenotype: reproductive system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

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