SULT2A1

sulfotransferase family 2A member 1, the group of Sulfotransferases, cytosolic

Basic information

Region (hg38): 19:47870467-47886315

Previous symbols: [ "STD" ]

Links

ENSG00000105398 ∙ NCBI:6822 ∙ OMIM:125263 ∙ HGNC:11458 ∙ Uniprot:Q06520 ∙ 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 SULT2A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SULT2A1 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			6	2	1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	2	2

Variants in SULT2A1

This is a list of pathogenic ClinVar variants found in the SULT2A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-47874723-T-C			Likely benign (Apr 13, 2018)
19-47879074-T-C		not specified	Likely benign (Apr 25, 2023)
19-47882102-A-C		not specified	Uncertain significance (Jun 21, 2021)
19-47883590-C-A		not specified	Uncertain significance (Jan 25, 2023)
19-47883641-C-T		not specified	Uncertain significance (Aug 19, 2023)
19-47883664-T-G			Benign (Jun 10, 2018)
19-47883701-C-T		not specified	Uncertain significance (Mar 01, 2024)
19-47883735-C-G			Benign (Jun 10, 2018)
19-47883774-A-C		not specified	Uncertain significance (Jul 05, 2023)
19-47886166-A-G		not specified	Uncertain significance (Apr 23, 2024)
19-47886201-T-A		not specified	Uncertain significance (Jun 05, 2024)
19-47886208-C-T		not specified	Uncertain significance (Aug 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SULT2A1	protein_coding	protein_coding	ENST00000222002	6	15932

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.25e-15	0.00161	125652	0	94	125746	0.000374

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.446	135	150	0.898	0.00000736	1899
Missense in Polyphen		38	50.634	0.75048		672
Synonymous	-0.702	60	53.5	1.12	0.00000276	481
Loss of Function	-1.15	20	15.2	1.32	7.23e-7	181

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000521	0.000521
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000299	0.000299
Middle Eastern	0.000544	0.000544
South Asian	0.000981	0.000980
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the sulfonation of steroids and bile acids in the liver and adrenal glands.
• Pathway: Bile secretion - Homo sapiens (human);Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human);Chemical carcinogenesis - Homo sapiens (human);Estrogen Metabolism Pathway;Tamoxifen Pathway, Pharmacokinetics;Pathway_PA165986194 -need delete;Acetaminophen Pathway, Pharmacokinetics;Acetaminophen Metabolism Pathway;Drug Induction of Bile Acid Pathway;Corticotropin-releasing hormone signaling pathway;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Constitutive Androstane Receptor Pathway;Pregnane X Receptor pathway;Vitamin D Receptor Pathway;Farnesoid X Receptor Pathway;Nuclear Receptors Meta-Pathway;Liver steatosis AOP;Tamoxifen metabolism;Sulfation Biotransformation Reaction;Metapathway biotransformation Phase I and II;Phase II - Conjugation of compounds;Biological oxidations;Metabolism;Cytosolic sulfonation of small molecules;E2F transcription factor network (Consensus)

Recessive Scores

• pRec: 0.359

Intolerance Scores

• loftool: 0.615
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

• pHI: 0.0700
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.605

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sult2a6

Gene ontology

• Biological process: ethanol catabolic process;steroid metabolic process;lipid catabolic process;regulation of lipid metabolic process;bile acid catabolic process;3'-phosphoadenosine 5'-phosphosulfate metabolic process;sulfation
• Cellular component: cytosol
• Molecular function: aryl sulfotransferase activity;estrone sulfotransferase activity;protein binding;sulfotransferase activity;bile-salt sulfotransferase activity;steroid sulfotransferase activity