UGT1A6
Basic information
Region (hg38): 2:233691607-233773300
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (22 variants)
- Crigler-Najjar syndrome type 1 (6 variants)
- Crigler-Najjar syndrome (4 variants)
- UGT1A1-related disorder (4 variants)
- Hyperbilirubinemia (2 variants)
- Gilbert syndrome (2 variants)
- Crigler-Najjar syndrome, type II (2 variants)
- Crigler-Najjar syndrome type 1;Gilbert syndrome;Crigler-Najjar syndrome, type II;Lucey-Driscoll syndrome (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the UGT1A6 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 | 19 | 27 | ||||
missense | 87 | 102 | ||||
nonsense | 7 | |||||
start loss | 0 | |||||
frameshift | 5 | |||||
inframe indel | 2 | |||||
splice donor/acceptor (+/-2bp) | 4 | |||||
splice region | 2 | 1 | 3 | |||
non coding | 15 | 11 | 125 | 38 | 17 | 206 |
Total | 26 | 23 | 223 | 58 | 23 |
Highest pathogenic variant AF is 0.0000919
Variants in UGT1A6
This is a list of pathogenic ClinVar variants found in the UGT1A6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
2-233693020-C-T | not specified | Uncertain significance (Nov 13, 2023) | ||
2-233693022-CT-TG | Likely benign (May 05, 2022) | |||
2-233693023-T-G | Benign (Nov 30, 2023) | |||
2-233693033-G-A | Uncertain significance (Apr 21, 2022) | |||
2-233693065-T-C | Uncertain significance (Oct 25, 2021) | |||
2-233693089-C-A | not specified | Uncertain significance (Oct 13, 2023) | ||
2-233693109-C-T | Benign (Mar 23, 2021) | |||
2-233693128-A-G | not specified | Uncertain significance (Jan 11, 2023) | ||
2-233693134-G-C | not specified | Uncertain significance (Jan 04, 2024) | ||
2-233693146-G-A | not specified | Uncertain significance (Mar 25, 2024) | ||
2-233693150-T-G | not specified | Uncertain significance (Feb 11, 2022) | ||
2-233693158-C-T | not specified | Uncertain significance (Apr 27, 2022) | ||
2-233693162-GT-G | Uncertain significance (Jul 23, 2021) | |||
2-233693210-A-G | not specified | Uncertain significance (Feb 06, 2023) | ||
2-233693218-T-C | Uncertain significance (Sep 26, 2019) | |||
2-233693233-A-G | not specified | Uncertain significance (Apr 07, 2023) | ||
2-233693267-A-G | Uncertain significance (Jan 09, 2023) | |||
2-233693272-C-T | not specified | Uncertain significance (Jun 06, 2023) | ||
2-233693273-G-A | Uncertain significance (Apr 26, 2022) | |||
2-233693297-A-G | not specified | Uncertain significance (Aug 08, 2022) | ||
2-233693319-A-G | Benign (Nov 30, 2023) | |||
2-233693352-G-C | Uncertain significance (Jun 15, 2017) | |||
2-233693375-T-A | not specified | Uncertain significance (Nov 17, 2022) | ||
2-233693437-G-C | not specified | Uncertain significance (Aug 12, 2021) | ||
2-233693458-G-A | not specified | Uncertain significance (Nov 23, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
UGT1A6 | protein_coding | protein_coding | ENST00000305139 | 5 | 81694 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.05e-7 | 0.777 | 125651 | 1 | 96 | 125748 | 0.000386 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.0280 | 294 | 295 | 0.995 | 0.0000166 | 3489 |
Missense in Polyphen | 146 | 142.85 | 1.022 | 1681 | ||
Synonymous | -0.399 | 120 | 115 | 1.05 | 0.00000676 | 1042 |
Loss of Function | 1.35 | 13 | 19.4 | 0.669 | 0.00000110 | 238 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000605 | 0.000604 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00120 | 0.00120 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000231 | 0.000229 |
Middle Eastern | 0.00120 | 0.00120 |
South Asian | 0.00111 | 0.00108 |
Other | 0.000490 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform has specificity for phenols. Isoform 3 lacks transferase activity but acts as a negative regulator of isoform 1 (By similarity). {ECO:0000250}.;
- Pathway
- Retinol metabolism - Homo sapiens (human);Steroid hormone biosynthesis - Homo sapiens (human);nicotine degradation III;Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human);Drug metabolism - other enzymes - Homo sapiens (human);Drug metabolism - cytochrome P450 - Homo sapiens (human);Porphyrin and chlorophyll metabolism - Homo sapiens (human);Chemical carcinogenesis - Homo sapiens (human);Ascorbate and aldarate metabolism - Homo sapiens (human);Pentose and glucuronate interconversions - Homo sapiens (human);Phenytoin Pathway, Pharmacokinetics;Valproic Acid Pathway, Pharmacokinetics;Pathway_PA165986194 -need delete;Acetaminophen Pathway, Pharmacokinetics;Irinotecan Pathway, Pharmacodynamics;Phenytoin (Antiarrhythmic) Action Pathway;Acetaminophen Metabolism Pathway;Codeine and Morphine Metabolism;Aryl Hydrocarbon Receptor Pathway;Constitutive Androstane Receptor Pathway;Pregnane X Receptor pathway;Nuclear Receptors Meta-Pathway;NRF2 pathway;Liver steatosis AOP;Oxidative Stress;Estrogen metabolism;Glucuronidation;Metapathway biotransformation Phase I and II;Glucuronidation;oxidative stress induced gene expression via nrf2;Phase II - Conjugation of compounds;Heme degradation;Metabolism of porphyrins;Tyrosine metabolism;Androgen and estrogen biosynthesis and metabolism;Biological oxidations;Metabolism;Linoleate metabolism;Vitamin A (retinol) metabolism;Xenobiotics metabolism;Porphyrin metabolism;nicotine degradation IV
(Consensus)
Recessive Scores
- pRec
- 0.581
Intolerance Scores
- loftool
- 0.915
- rvis_EVS
- -0.4
- rvis_percentile_EVS
- 26.85
Haploinsufficiency Scores
- pHI
- hipred
- N
- hipred_score
- 0.206
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.107
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ugt1a6b
- Phenotype
Gene ontology
- Biological process
- xenobiotic metabolic process;cellular glucuronidation;flavonoid glucuronidation;xenobiotic glucuronidation
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;intracellular membrane-bounded organelle
- Molecular function
- retinoic acid binding;UDP-glycosyltransferase activity;glucuronosyltransferase activity;protein homodimerization activity;protein heterodimerization activity