UGT2A1
protein-codingUDP glucuronosyltransferase family 2 member A1 complex locus, the group of UDP glucuronosyltransferases
Gene summary
The protein encoded by this gene belongs to the UDP-glycosyltransferase family. Members of this protein family play a role in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. The encoded enzyme is expressed in the olfactory neuroepithelium, which lines the posterior nasal cavity and is exposed to a wide range of odorants and airborne toxic compounds. Hence, this protein has been suggested to be involved in clearing lipophilic odorant molecules from the sensory epithelium. This gene shares exon structure with the UDP glucuronosyltransferase 2A2 family member, which encodes N-terminally distinct isoforms. Polymorphisms in this gene may be associated with the loss of taste and smell that is reported by some individuals during SARS-CoV-2 infection. [provided by RefSeq, Jan 2022]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~64.8 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 UGT2A1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001252275.3. 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 | 2 | 1 | 3 | |||
| missense | 35 | 4 | 1 | 40 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 35 | 7 | 2 | 44 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001239204.2 | 6 | MANE Select | |
| Ensembl | ENSP00000286604.4 | 6 | MANE Select | |
| RefSeq | NP_001239203.2 | 6 | Standard | |
| RefSeq | NP_001288168.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Retinol metabolism - Homo sapiens (human)
- Steroid hormone biosynthesis - Homo sapiens (human)
- Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human)
- Drug metabolism - other enzymes - Homo sapiens (human)
- Drug metabolism - cytochrome P450 - Homo sapiens (human)
Biological Process
- sensory perception of smell
- detection of chemical stimulus
- cellular glucuronidation
Molecular Function
- UDP-glycosyltransferase activity
- glucuronosyltransferase activity
Cellular Component
- integral component of membrane
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000503640
- Coding exons
- 6
- Length
- 64831
- Individuals with no LoFs
- 117512
- Homozygous LoFs
- 193
- Heterozygous LoFs
- 8040
- Defined
- 125745
- p
- 0.0333
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.40 | 340 | 275 | 1.24 | 0.0000131 | 3453 |
| Missense (PolyPhen) | 115 | 93.338 | 1.2321 | 1258 | ||
| Synonymous | -0.800 | 107 | 97.0 | 1.10 | 0.00000498 | 993 |
| Loss of Function | -0.398 | 24 | 22.0 | 1.09 | 0.00000118 | 268 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.011 | 0.011 | notable |
| Latino/Admixed American | 0.025 | 0.025 | notable |
| Ashkenazi Jewish | 0.067 | 0.067 | notable |
| East Asian | 0.00098 | 0.00098 | rare |
| Finnish | 0.036 | 0.036 | notable |
| European (Non-Finnish) | 0.046 | 0.046 | notable |
| South Asian | 0.013 | 0.013 | notable |
| Other | 0.046 | 0.045 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: UDP-glucuronosyltransferases catalyze phase II biotransformation reactions in which lipophilic substrates are conjugated with glucuronic acid to increase water solubility and enhance excretion. They are of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. Active on odorants and seems to be involved in olfaction; it could help clear lipophilic odorant molecules from the sensory epithelium. {ECO:0000269|PubMed:19858781}.;
Intolerance Scores
- LoFtool
- 0.903
- RVIS EVS
- 0.98
- RVIS percentile EVS
- 90.46
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0490
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |