UGT2A2

UDP glucuronosyltransferase family 2 member A2, the group of UDP glucuronosyltransferases

Basic information

Region (hg38): 4:69588416-69639642

Links

ENSG00000271271 ∙ NCBI:574537 ∙ OMIM:619809 ∙ HGNC:28183 ∙ Uniprot:P0DTE5 ∙ 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 UGT2A2 gene.

• Inborn genetic diseases (11 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UGT2A2 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			11	1	1	13
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	11	5	2

Variants in UGT2A2

This is a list of pathogenic ClinVar variants found in the UGT2A2 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)
4-69638935-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)
4-69639436-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)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UGT2A2	protein_coding	protein_coding	ENST00000457664	6	51226

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.75e-14	0.0263	125427	0	319	125746	0.00127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.70	358	278	1.29	0.0000130	3513
Missense in Polyphen		120	95.002	1.2631		1263
Synonymous	-1.69	118	96.8	1.22	0.00000482	1014
Loss of Function	0.169	21	21.9	0.961	0.00000118	269

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00772	0.00756
Ashkenazi Jewish	0.00169	0.00169
East Asian	0.00227	0.00223
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000904	0.000897
Middle Eastern	0.00227	0.00223
South Asian	0.000692	0.000686
Other	0.000660	0.000652

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

• rvis_EVS: 1.69
• rvis_percentile_EVS: 96.41

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ugt2a2