UGT1A9

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

Basic information

Region (hg38): 2:233671898-233773300

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 (291 variants)
• not_specified (246 variants)
• UGT1A1-related_disorder (91 variants)
• Gilbert_syndrome (91 variants)
• Lucey-Driscoll_syndrome (75 variants)
• Crigler-Najjar_syndrome_type_1 (64 variants)
• Crigler-Najjar_syndrome,_type_II (56 variants)
• Crigler-Najjar_syndrome (39 variants)
• BILIRUBIN,_SERUM_LEVEL_OF,_QUANTITATIVE_TRAIT_LOCUS_1 (38 variants)
• Inborn_genetic_diseases (23 variants)
• Hyperbilirubinemia (16 variants)
• UGT1A9-related_disorder (11 variants)
• Irinotecan_response (3 variants)
• UGT1A4-related_disorder (2 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. These statistics are base on transcript: NM_000021027.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			3	32	1	36
missense	5	17	107	5	1	135
nonsense	4	3	1			8
start loss						0
frameshift	6	5				11
splice donor/acceptor (+/-2bp)	2	4				6
Total	17	29	111	37	2

Highest pathogenic variant AF is 0.00048507

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