UGT1A6

UDP glucuronosyltransferase family 1 member A6, the group of UDP glucuronosyltransferases

Basic information

Region (hg38): 2:233691606-233773300

Links

ENSG00000167165 ∙ NCBI:54578 ∙ OMIM:606431 ∙ HGNC:12538 ∙ Uniprot:P19224 ∙ 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 UGT1A6 gene.

• not provided (238 variants)
• Inborn genetic diseases (66 variants)
• Gilbert syndrome (60 variants)
• Crigler-Najjar syndrome (49 variants)
• Lucey-Driscoll syndrome (45 variants)
• UGT1A1-related condition (20 variants)
• Crigler-Najjar syndrome, type II (17 variants)
• Hyperbilirubinemia (16 variants)
• not specified (15 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 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			7	9	3	19
missense	3	8	79	1	3	94
nonsense	4		3			7
start loss						0
frameshift	4		1			5
inframe indel			2			2
splice donor/acceptor (+/-2bp)	1	3				4
splice region			2	1		3
non coding	15	10	114	26	18	183
Total	27	21	206	36	24

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)
2-233693150-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)
2-233693500-C-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

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: 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 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

• hipred: N
• hipred_score: 0.206

Essentials

• essential_gene_CRISPR: N
• 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

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