UGT3A1

UDP glycosyltransferase family 3 member A1, the group of UDP glucuronosyltransferases

Basic information

Region (hg38): 5:35951006-36001028

Links

ENSG00000145626 ∙ NCBI:133688 ∙ OMIM:616383 ∙ HGNC:26625 ∙ Uniprot:Q6NUS8 ∙ 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 UGT3A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UGT3A1 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						0
missense			33	2		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	2	0

Variants in UGT3A1

This is a list of pathogenic ClinVar variants found in the UGT3A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-35954225-C-G		not specified	Uncertain significance (Jul 13, 2021)
5-35954231-G-A		not specified	Likely benign (May 24, 2024)
5-35954273-A-C		not specified	Uncertain significance (Jan 23, 2023)
5-35954368-G-A		not specified	Uncertain significance (Jan 23, 2024)
5-35954371-G-A		not specified	Uncertain significance (Jun 12, 2023)
5-35954390-T-C		not specified	Uncertain significance (Mar 29, 2022)
5-35954397-G-C		not specified	Uncertain significance (May 18, 2023)
5-35954420-C-T		not specified	Uncertain significance (Jul 15, 2021)
5-35954428-A-G		not specified	Uncertain significance (May 24, 2023)
5-35955668-C-T		not specified	Uncertain significance (Jan 04, 2022)
5-35955746-C-T		not specified	Uncertain significance (Nov 30, 2022)
5-35955748-T-C		not specified	Uncertain significance (Feb 15, 2023)
5-35955749-G-C		not specified	Uncertain significance (Oct 04, 2022)
5-35955796-C-T		not specified	Uncertain significance (Dec 05, 2022)
5-35955811-C-T		not specified	Uncertain significance (Oct 10, 2023)
5-35957229-T-C		not specified	Uncertain significance (Aug 19, 2023)
5-35957245-C-A		not specified	Uncertain significance (Jan 07, 2022)
5-35957321-C-G		not specified	Uncertain significance (Oct 03, 2022)
5-35957354-C-T		not specified	Uncertain significance (Oct 10, 2023)
5-35965472-A-G		not specified	Uncertain significance (Jun 12, 2023)
5-35965528-C-T		not specified	Uncertain significance (Nov 13, 2023)
5-35965543-A-T		not specified	Uncertain significance (Oct 04, 2022)
5-35965570-G-A		not specified	Uncertain significance (Jan 09, 2024)
5-35965580-T-G		not specified	Likely benign (Dec 17, 2023)
5-35965645-A-C		not specified	Uncertain significance (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UGT3A1	protein_coding	protein_coding	ENST00000274278	7	50019

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.54e-13	0.0231	125539	0	209	125748	0.000831

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.147	290	283	1.02	0.0000141	3453
Missense in Polyphen		97	98.461	0.98517		1328
Synonymous	-1.02	120	107	1.13	0.00000525	1036
Loss of Function	-0.0555	19	18.7	1.01	9.67e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00743	0.00744
Ashkenazi Jewish	0.00	0.00
East Asian	0.000707	0.000707
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000414	0.000413
Middle Eastern	0.000707	0.000707
South Asian	0.000261	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: UDP-glucuronosyltransferases catalyze phase II biotransformation reactions in which lipophilic substrates are conjugated with glucuronic acid to increase water solubility and enhance excretion. They are of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds (By similarity). {ECO:0000250}.
• Pathway: Glucuronidation;Phase II - Conjugation of compounds;Biological oxidations;Metabolism (Consensus)

Recessive Scores

• pRec: 0.0701

Intolerance Scores

• loftool: 0.934
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.6

Haploinsufficiency Scores

• pHI: 0.0530
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0798

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ugt3a2

Gene ontology

• Cellular component: integral component of membrane;intracellular membrane-bounded organelle;UDP-N-acetylglucosamine transferase complex
• Molecular function: UDP-glycosyltransferase activity;glucuronosyltransferase activity