UGT1A7

UDP glucuronosyltransferase family 1 member A7, the group of UDP glucuronosyltransferases

Basic information

Region (hg38): 2:233681900-233773300

Links

ENSG00000244122 ∙ NCBI:54577 ∙ OMIM:606432 ∙ HGNC:12539 ∙ Uniprot:Q9HAW7 ∙ 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 UGT1A7 gene.

• not provided (264 variants)
• Inborn genetic diseases (78 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 UGT1A7 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	3	20
missense	3	8	73	5	4	93
nonsense	4		5			9
start loss						0
frameshift	4		2			6
inframe indel			2			2
splice donor/acceptor (+/-2bp)	1	3				4
splice region			2	1		3
non coding	15	10	142	28	24	219
Total	27	21	231	43	31

Highest pathogenic variant AF is 0.0000919

Variants in UGT1A7

This is a list of pathogenic ClinVar variants found in the UGT1A7 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-233681970-C-A			Benign (Nov 30, 2023)
2-233682005-C-A		not specified	Uncertain significance (May 09, 2022)
2-233682041-G-A		not specified	Uncertain significance (Dec 08, 2023)
2-233682060-G-A		not specified	Uncertain significance (Nov 30, 2018)
2-233682109-G-T		not specified	Uncertain significance (Jun 22, 2021)
2-233682129-G-A			Uncertain significance (Mar 27, 2023)
2-233682180-C-A			Uncertain significance (Dec 20, 2023)
2-233682199-C-T			Uncertain significance (Feb 22, 2020)
2-233682205-T-C		not specified	Uncertain significance (May 01, 2019)
2-233682211-G-A		not specified	Uncertain significance (Oct 05, 2023)
2-233682220-G-A		not specified	Likely benign (Sep 17, 2021)
2-233682278-A-G			Uncertain significance (Dec 23, 2022)
2-233682280-G-A			Likely benign (Jul 26, 2023)
2-233682289-G-T			Uncertain significance (Jun 27, 2018)
2-233682301-T-C		not specified	Uncertain significance (Aug 09, 2021)
2-233682323-A-G			Likely benign (Nov 30, 2023)
2-233682323-AT-GG			Likely benign (Nov 30, 2023)
2-233682324-T-G			Benign (Nov 30, 2023)
2-233682328-C-A			Benign (Nov 30, 2023)
2-233682328-CG-AA			Benign (Nov 30, 2023)
2-233682329-G-A			Benign (Nov 30, 2023)
2-233682354-G-C			Likely benign (Sep 14, 2023)
2-233682359-G-C			Uncertain significance (Jul 02, 2021)
2-233682404-T-C		not specified	Uncertain significance (Feb 28, 2023)
2-233682412-A-G		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UGT1A7	protein_coding	protein_coding	ENST00000373426	5	91362

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.66e-14	0.0195	125537	0	211	125748	0.000839

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.411	314	294	1.07	0.0000173	3463
Missense in Polyphen		142	135.35	1.0492		1605
Synonymous	-2.56	150	115	1.30	0.00000726	1049
Loss of Function	-0.0316	20	19.8	1.01	0.00000118	237

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00585	0.00586
Ashkenazi Jewish	0.00	0.00
East Asian	0.000544	0.000544
Finnish	0.000647	0.000647
European (Non-Finnish)	0.000550	0.000545
Middle Eastern	0.000544	0.000544
South Asian	0.000621	0.000621
Other	0.000326	0.000326

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:23360619}.
• 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);Mycophenolic acid Pathway, Pharmacokinetics;Mycophenolic acid Pathway, Pharmacokinetics/Pharmacodynamics;Mycophenolic Acid Metabolism Pathway;Aryl Hydrocarbon Receptor Pathway;Nuclear Receptors Meta-Pathway;NRF2 pathway;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: 0.989
• rvis_EVS: -0.15
• rvis_percentile_EVS: 42.23

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: 0.0472

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: excretion;coumarin metabolic process;drug metabolic process;retinoic acid metabolic process;negative regulation of catalytic activity;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;enzyme inhibitor activity;protein kinase C binding;UDP-glycosyltransferase activity;glucuronosyltransferase activity;protein homodimerization activity;protein heterodimerization activity