UGT2A1

UDP glucuronosyltransferase family 2 member A1 complex locus, the group of UDP glucuronosyltransferases

Basic information

Region (hg38): 4:69588417-69653249

Links

ENSG00000173610 ∙ NCBI:10941 ∙ OMIM:604716 ∙ HGNC:12542 ∙ Uniprot:P0DTE4 ∙ 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 UGT2A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UGT2A1 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				2	1	3
missense			17	3	2	22
nonsense				2		2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			12			12
Total	0	0	29	7	3

Variants in UGT2A1

This is a list of pathogenic ClinVar variants found in the UGT2A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-69589493-G-T		not specified	Uncertain significance (Sep 14, 2021)
4-69589587-G-A			Likely benign (May 24, 2018)
4-69594602-C-T			Benign (Aug 17, 2018)
4-69594611-T-A			Benign (Jul 26, 2018)
4-69595205-G-A			Likely benign (May 29, 2018)
4-69595226-C-A			Likely benign (May 11, 2018)
4-69596275-G-A		not specified	Uncertain significance (Sep 26, 2023)
4-69599312-A-C			Likely benign (May 29, 2018)
4-69599313-C-T		not specified	Uncertain significance (Dec 01, 2022)
4-69635828-C-CAAAAAAAAAA			Likely benign (Jan 01, 2023)
4-69638932-C-T		not specified	Uncertain significance (Jun 16, 2024)
4-69638935-A-C		not specified	Uncertain significance (Oct 03, 2023)
4-69639004-T-C		not specified	Uncertain significance (Apr 26, 2023)
4-69639142-G-A		not specified	Uncertain significance (Oct 13, 2023)
4-69639190-C-G		not specified	Uncertain significance (Jun 24, 2022)
4-69639201-C-T		not specified	Uncertain significance (Dec 05, 2022)
4-69639288-T-C		not specified	Uncertain significance (Dec 08, 2021)
4-69639373-T-C		not specified	Uncertain significance (Apr 09, 2024)
4-69639436-A-G		not specified	Uncertain significance (Feb 23, 2023)
4-69639486-A-C		not specified	Uncertain significance (Nov 08, 2022)
4-69639501-A-G		not specified	Uncertain significance (Oct 04, 2022)
4-69639508-T-C		not specified	Uncertain significance (Aug 28, 2023)
4-69639615-A-C		not specified	Uncertain significance (Nov 18, 2022)
4-69639631-T-C		not specified	Uncertain significance (Aug 10, 2023)
4-69646959-G-A		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UGT2A1	protein_coding	protein_coding	ENST00000503640	6	64831

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.88e-17	0.00287	117512	193	8040	125745	0.0333

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.40	340	275	1.24	0.0000131	3453
Missense in Polyphen		115	93.338	1.2321		1258
Synonymous	-0.800	107	97.0	1.10	0.00000498	993
Loss of Function	-0.398	24	22.0	1.09	0.00000118	268

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0355	0.0355
Ashkenazi Jewish	0.0666	0.0672
East Asian	0.000984	0.000979
Finnish	0.0360	0.0357
European (Non-Finnish)	0.0464	0.0460
Middle Eastern	0.000984	0.000979
South Asian	0.0133	0.0132
Other	0.0463	0.0452

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. Active on odorants and seems to be involved in olfaction; it could help clear lipophilic odorant molecules from the sensory epithelium. {ECO:0000269|PubMed:19858781}.
• 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);Glucuronidation;Metapathway biotransformation Phase I and II;Glucuronidation;Phase II - Conjugation of compounds;Biological oxidations;Metabolism (Consensus)

Intolerance Scores

• loftool: 0.903
• rvis_EVS: 0.98
• rvis_percentile_EVS: 90.46

Haploinsufficiency Scores

• pHI: 0.0707
• hipred: N
• hipred_score: 0.112
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0490

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ugt2a1

Gene ontology

• Biological process: sensory perception of smell;detection of chemical stimulus;cellular glucuronidation
• Cellular component: integral component of membrane;intracellular membrane-bounded organelle
• Molecular function: UDP-glycosyltransferase activity;glucuronosyltransferase activity