UGT1A10

UDP glucuronosyltransferase family 1 member A10, the group of UDP glucuronosyltransferases

Basic information

Region (hg38): 2:233636447-233773300

Links

ENSG00000242515 ∙ NCBI:54575 ∙ OMIM:606435 ∙ HGNC:12531 ∙ Uniprot:Q9HAW8 ∙ 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 UGT1A10 gene.

• not provided (270 variants)
• Inborn genetic diseases (101 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 UGT1A10 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	9	1	17
missense	3	8	64			75
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	178	35	34	272
Total	27	21	253	44	35

Highest pathogenic variant AF is 0.0000919

Variants in UGT1A10

This is a list of pathogenic ClinVar variants found in the UGT1A10 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-233636550-G-A		not specified	Uncertain significance (Jul 14, 2021)
2-233636553-C-G		not specified	Uncertain significance (Oct 26, 2021)
2-233636575-T-C		not specified	Uncertain significance (Sep 01, 2021)
2-233636584-G-C		not specified	Uncertain significance (May 17, 2023)
2-233636599-G-A		not specified	Uncertain significance (Mar 17, 2023)
2-233636680-A-T		not specified	Uncertain significance (Jan 23, 2024)
2-233636872-T-C		not specified	Uncertain significance (Dec 01, 2022)
2-233636892-T-C		not specified	Uncertain significance (Feb 16, 2023)
2-233637108-G-C		not specified	Uncertain significance (Apr 12, 2022)
2-233637119-T-C			Benign (Jul 19, 2018)
2-233637156-G-C		not specified	Uncertain significance (Nov 22, 2021)
2-233637171-C-A		not specified	Uncertain significance (Aug 16, 2022)
2-233637213-G-A		not specified	Uncertain significance (Dec 01, 2022)
2-233637235-C-T		not specified	Uncertain significance (Oct 05, 2023)
2-233637304-A-G		not specified	Uncertain significance (Nov 09, 2021)
2-233637315-G-A		not specified	Uncertain significance (Nov 17, 2023)
2-233637351-T-C		not specified	Uncertain significance (Oct 20, 2023)
2-233669782-C-T			Benign (Jan 11, 2019)
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)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UGT1A10	protein_coding	protein_coding	ENST00000344644	5	136852

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.59e-19	0.000405	125415	2	331	125748	0.00133

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.40	366	298	1.23	0.0000173	3490
Missense in Polyphen		165	140.13	1.1775		1679
Synonymous	-3.56	166	117	1.42	0.00000748	1037
Loss of Function	-1.09	25	19.8	1.26	0.00000112	232

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00664	0.00665
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000326	0.000326
Finnish	0.000554	0.000554
European (Non-Finnish)	0.000981	0.000967
Middle Eastern	0.000326	0.000326
South Asian	0.00140	0.00134
Other	0.00147	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. Isoform 2 lacks transferase activity but acts as a negative regulator of isoform 1. {ECO:0000269|PubMed:19545173}.
• Pathway: 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);Tamoxifen Pathway, Pharmacokinetics;Valproic Acid Pathway, Pharmacokinetics;Mycophenolic acid Pathway, Pharmacokinetics;Mycophenolic acid Pathway, Pharmacokinetics/Pharmacodynamics;Ibuprofen Pathway, Pharmacokinetics;Irinotecan Pathway, Pharmacokinetics;Irinotecan Pathway, Pharmacodynamics;Ibuprofen Action Pathway;Ibuprofen Metabolism Pathway;Celecoxib Action Pathway;Irinotecan Action Pathway;Tamoxifen Action Pathway;Celecoxib Metabolism Pathway;Nevirapine Metabolism Pathway;Irinotecan Metabolism Pathway;Tamoxifen Metabolism Pathway;Codeine and Morphine Metabolism;Irinotecan Pathway;Tamoxifen metabolism;Glucuronidation;Metapathway biotransformation Phase I and II;Glucuronidation;Phase II - Conjugation of compounds;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

• loftool: 0.969
• rvis_EVS: -0.48
• rvis_percentile_EVS: 22.75

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0640

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: 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;protein kinase C binding;UDP-glycosyltransferase activity;glucuronosyltransferase activity;protein homodimerization activity;protein heterodimerization activity