SULT2A1
protein-codingsulfotransferase family 2A member 1, the group of Sulfotransferases, cytosolic
Gene summary
This gene encodes a member of the sulfotransferase family. Sulfotransferases aid in the metabolism of drugs and endogenous compounds by converting these substances into more hydrophilic water-soluble sulfate conjugates that can be easily excreted. This protein catalyzes the sulfation of steroids and bile acids in the liver and adrenal glands, and may have a role in the inherited adrenal androgen excess in women with polycystic ovary syndrome. [provided by RefSeq, Mar 2010]
- STD
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~15.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SULT2A1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003167.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 24 | 4 | 1 | 29 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 26 | 4 | 2 | 32 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003158.2 | 6 | MANE Select | |
| Ensembl | ENSP00000222002.2 | 6 | MANE Select | |
| Ensembl | ENSP00000573294.1 | 4 | Standard | |
| Ensembl | ENSP00000573294.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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
Biological Process
- ethanol catabolic process
- steroid metabolic process
- lipid catabolic process
- regulation of lipid metabolic process
- bile acid catabolic process
Molecular Function
- aryl sulfotransferase activity
- estrone sulfotransferase activity
- protein binding
- sulfotransferase activity
- bile-salt sulfotransferase activity
Cellular Component
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000222002
- Coding exons
- 6
- Length
- 15932
- Individuals with no LoFs
- 125652
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 94
- Defined
- 125746
- p
- 0.000374
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.446 | 135 | 150 | 0.898 | 0.00000736 | 1899 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00052 | 0.00052 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00054 | 0.00054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00030 | 0.00030 | rare |
| South Asian | 0.00098 | 0.00098 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- 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.;
Recessive Scores
- pRec
- 0.359
Intolerance Scores
- LoFtool
- 0.615
- RVIS EVS
- 0.26
- RVIS percentile EVS
- 70.26
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.605
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |