UGT1A9

UDP glucuronosyltransferase family 1 member A9, the group of UDP glucuronosyltransferases

Basic information

Region (hg38): 2:233671897-233773300

Links

ENSG00000241119 ∙ NCBI:54600 ∙ OMIM:606434 ∙ HGNC:12541 ∙ Uniprot:O60656 ∙ 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 UGT1A9 gene.

• not provided (268 variants)
• Inborn genetic diseases (90 variants)
• Gilbert syndrome (60 variants)
• Crigler-Najjar syndrome (49 variants)
• Lucey-Driscoll syndrome (45 variants)
• UGT1A1-related condition (20 variants)
• not specified (17 variants)
• Crigler-Najjar syndrome, type II (17 variants)
• Hyperbilirubinemia (16 variants)
• Crigler-Najjar syndrome type 1 (14 variants)
• Irinotecan response (5 variants)
• UGT1A1-Related Disorders (4 variants)
• Bilirubin, serum level of, quantitative trait locus 1 (2 variants)
• Gilbert syndrome;Crigler-Najjar syndrome type 1;Crigler-Najjar syndrome, type II;Bilirubin, serum level of, quantitative trait locus 1;Lucey-Driscoll syndrome (2 variants)
• Bilirubin, serum level of, quantitative trait locus 1;Crigler-Najjar syndrome type 1;Lucey-Driscoll syndrome;Crigler-Najjar syndrome, type II;Gilbert syndrome (2 variants)
• irinotecan response - Toxicity (1 variants)
• UGT1A1-related disorder (1 variants)
• Lucey-Driscoll syndrome;Crigler-Najjar syndrome, type II;Gilbert syndrome;Crigler-Najjar syndrome type 1;Bilirubin, serum level of, quantitative trait locus 1 (1 variants)
• Bilirubin, serum level of, quantitative trait locus 1;Crigler-Najjar syndrome type 1;Crigler-Najjar syndrome, type II;Lucey-Driscoll syndrome;Gilbert syndrome (1 variants)
• Crigler-Najjar syndrome, type II;Lucey-Driscoll syndrome;Crigler-Najjar syndrome type 1;Bilirubin, serum level of, quantitative trait locus 1;Gilbert syndrome (1 variants)
• Gilbert syndrome, susceptibility to (1 variants)
• Bilirubin, serum level of, quantitative trait locus 1;Lucey-Driscoll syndrome;Crigler-Najjar syndrome, type II;Gilbert syndrome;Crigler-Najjar syndrome type 1 (1 variants)
• Lucey-Driscoll syndrome;Crigler-Najjar syndrome, type II;Bilirubin, serum level of, quantitative trait locus 1;Gilbert syndrome;Crigler-Najjar syndrome type 1 (1 variants)
• Crigler-Najjar syndrome type 1;Gilbert syndrome;Crigler-Najjar syndrome, type II;Lucey-Driscoll syndrome (1 variants)
• Crigler-Najjar syndrome, type II;Gilbert syndrome;Lucey-Driscoll syndrome;Crigler-Najjar syndrome type 1;Bilirubin, serum level of, quantitative trait locus 1 (1 variants)
• Gilbert syndrome;Bilirubin, serum level of, quantitative trait locus 1;Crigler-Najjar syndrome type 1;Lucey-Driscoll syndrome;Crigler-Najjar syndrome, type II (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UGT1A9 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			7	10		17
missense	3	8	64		1	76
nonsense	4		2			6
start loss						0
frameshift	4					4
inframe indel			2			2
splice donor/acceptor (+/-2bp)	1	3				4
splice region			2	1		3
non coding	15	10	167	34	32	258
Total	27	21	242	44	33

Highest pathogenic variant AF is 0.0000919

Variants in UGT1A9

This is a list of pathogenic ClinVar variants found in the UGT1A9 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-233672004-G-A		not specified	Uncertain significance (Aug 23, 2021)
2-233672032-T-C			Benign (Feb 01, 2023)
2-233672035-A-G		not specified	Uncertain significance (Jan 22, 2024)
2-233672062-C-T		not specified	Uncertain significance (Jan 03, 2024)
2-233672119-T-C		not specified	Uncertain significance (Feb 13, 2024)
2-233672130-C-T		UGT1A9-related disorder	Benign (Nov 25, 2019)
2-233672151-A-G		not specified	Uncertain significance (Jun 05, 2023)
2-233672158-A-G		not specified	Uncertain significance (Jul 14, 2023)
2-233672159-G-A		not specified	Benign/Likely benign (Jul 19, 2023)
2-233672311-G-A		not specified	Uncertain significance (Mar 01, 2023)
2-233672331-T-A		not specified	Uncertain significance (Aug 09, 2021)
2-233672351-G-A		UGT1A9-related disorder	Likely benign (Oct 30, 2020)
2-233672357-T-G		UGT1A9-related disorder	Likely benign (May 14, 2019)
2-233672363-T-G		not specified	Uncertain significance (Mar 05, 2024)
2-233672366-A-G		UGT1A9-related disorder	Likely benign (May 28, 2019)
2-233672397-T-G		not specified	Uncertain significance (Nov 18, 2022)
2-233672434-T-C		UGT1A9-related disorder	Likely benign (Aug 09, 2022)
2-233672446-G-T		not specified	Uncertain significance (Jun 16, 2023)
2-233672458-A-G		not specified	Uncertain significance (Jan 31, 2023)
2-233672487-G-A		not specified	Uncertain significance (Jan 30, 2024)
2-233672550-A-G		not specified	Uncertain significance (Apr 17, 2023)
2-233672596-A-G		not specified	Uncertain significance (Jan 04, 2022)
2-233672614-C-T		not specified	Uncertain significance (Sep 22, 2023)
2-233672698-C-T		not specified	Uncertain significance (Dec 26, 2023)
2-233672703-T-G		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UGT1A9	protein_coding	protein_coding	ENST00000354728	5	101448

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.36e-8	0.648	125625	0	123	125748	0.000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.937	346	300	1.15	0.0000173	3471
Missense in Polyphen		153	139.65	1.0956		1653
Synonymous	-2.38	149	116	1.28	0.00000724	1035
Loss of Function	1.19	14	19.7	0.711	0.00000111	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000399	0.000398
Ashkenazi Jewish	0.00	0.00
East Asian	0.00228	0.00229
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000462	0.000431
Middle Eastern	0.00228	0.00229
South Asian	0.000621	0.000621
Other	0.000655	0.000652

dbNSFP

Source: dbNSFP

• 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 2 lacks transferase activity but acts as a negative regulator of isoform 1. {ECO:0000269|PubMed:19545173}.
• Pathway: Artemisinin and Derivatives Pathway, Pharmacokinetics;Benzodiazepine Pathway, Pharmacokinetics;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);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;Estrogen Metabolism Pathway;Sorafenib Pharmacokinetics;Valproic Acid Pathway, Pharmacokinetics;Mycophenolic acid Pathway, Pharmacokinetics;Mycophenolic acid Pathway, Pharmacokinetics/Pharmacodynamics;Pathway_PA165986194 -need delete;Acetaminophen Pathway, Pharmacokinetics;Ibuprofen Pathway, Pharmacokinetics;Irinotecan Pathway, Pharmacokinetics;Nicotine Pathway, Pharmacokinetics;Irinotecan Pathway, Pharmacodynamics;Ibuprofen Action Pathway;Phenytoin (Antiarrhythmic) Action Pathway;Artemether Metabolism Pathway;Mycophenolic Acid Metabolism Pathway;Ibuprofen Metabolism Pathway;Nicotine Metabolism Pathway;Nicotine Action Pathway;Irinotecan Action Pathway;Sorafenib Metabolism Pathway;Acetaminophen Metabolism Pathway;Irinotecan Metabolism Pathway;Nicotine Metabolism;Codeine and Morphine Metabolism;Irinotecan Pathway;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Aryl Hydrocarbon Receptor Pathway;Constitutive Androstane Receptor Pathway;Pregnane X Receptor pathway;PPAR Alpha Pathway;Nuclear Receptors Meta-Pathway;NRF2 pathway;Liver steatosis AOP;Arylamine metabolism;Estrogen metabolism;Glucuronidation;Metapathway biotransformation Phase I and II;Glucuronidation;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 (Consensus)

Recessive Scores

• pRec: 0.581

Intolerance Scores

• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.27

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0872

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ugt1a9

Gene ontology

• Biological process: xenobiotic metabolic process;regulation of lipid metabolic process;retinoic acid metabolic process;flavone 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