UGT2B4

UDP glucuronosyltransferase family 2 member B4, the group of UDP glucuronosyltransferases

Basic information

Region (hg38): 4:69480165-69526014

Links

ENSG00000156096 ∙ NCBI:7363 ∙ OMIM:600067 ∙ HGNC:12553 ∙ Uniprot:P06133 ∙ 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 UGT2B4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UGT2B4 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				1	1	2
missense			47	2	2	51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	47	3	3

Variants in UGT2B4

This is a list of pathogenic ClinVar variants found in the UGT2B4 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-69480649-C-G		not specified	Uncertain significance (Oct 26, 2021)
4-69480711-C-T		not specified	Uncertain significance (Aug 04, 2023)
4-69480722-C-A		not specified	Uncertain significance (May 02, 2024)
4-69480725-G-A		not specified	Uncertain significance (Jan 07, 2022)
4-69480792-G-A		not specified	Uncertain significance (Aug 15, 2023)
4-69480835-G-T		not specified	Uncertain significance (Aug 04, 2023)
4-69480836-A-T		not specified	Uncertain significance (Aug 04, 2023)
4-69480863-G-A		not specified	Uncertain significance (Feb 26, 2024)
4-69480870-C-G		not specified	Uncertain significance (Aug 12, 2021)
4-69480903-C-T		not specified	Uncertain significance (May 18, 2023)
4-69485232-A-G		not specified	Uncertain significance (Feb 16, 2023)
4-69485256-G-C		not specified	Uncertain significance (Nov 21, 2023)
4-69485260-T-C		not specified	Uncertain significance (May 16, 2024)
4-69485284-C-T		not specified	Uncertain significance (Dec 27, 2023)
4-69485306-T-A			Benign (Jun 13, 2018)
4-69485380-T-C		not specified	Uncertain significance (Dec 16, 2021)
4-69486638-T-C		not specified	Uncertain significance (Aug 15, 2023)
4-69489451-C-A		not specified	Uncertain significance (Aug 31, 2022)
4-69489455-G-C		not specified	Uncertain significance (Jul 17, 2023)
4-69489482-C-A		not specified	Uncertain significance (Dec 08, 2023)
4-69489558-A-G		not specified	Uncertain significance (May 02, 2024)
4-69489565-C-T		not specified	Uncertain significance (Jul 14, 2023)
4-69489575-GA-G			Benign (Apr 26, 2018)
4-69493719-A-G		not specified	Uncertain significance (Aug 08, 2022)
4-69493721-T-A		not specified	Uncertain significance (Jan 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UGT2B4	protein_coding	protein_coding	ENST00000305107	6	45850

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.38e-9	0.364	125651	0	96	125747	0.000382

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.15	331	277	1.19	0.0000134	3481
Missense in Polyphen		101	81.82	1.2344		1112
Synonymous	-1.93	123	98.6	1.25	0.00000509	993
Loss of Function	0.838	15	18.9	0.792	8.68e-7	233

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000899	0.000892
Ashkenazi Jewish	0.00	0.00
East Asian	0.00101	0.000979
Finnish	0.00	0.00
European (Non-Finnish)	0.000347	0.000334
Middle Eastern	0.00101	0.000979
South Asian	0.000408	0.000392
Other	0.000173	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: UDPGTs are of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isozyme is active on polyhydroxylated estrogens (such as estriol, 4-hydroxyestrone and 2-hydroxyestriol) and xenobiotics (such as 4-methylumbelliferone, 1-naphthol, 4- nitrophenol, 2-aminophenol, 4-hydroxybiphenyl and menthol). It is capable of 6 alpha-hydroxyglucuronidation of hyodeoxycholic acid.
• Pathway: Benzodiazepine Pathway, Pharmacokinetics;Retinol metabolism - Homo sapiens (human);Steroid hormone biosynthesis - Homo sapiens (human);Bile secretion - 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);Ibuprofen Action Pathway;Ibuprofen Metabolism Pathway;Morphine Metabolism Pathway;Morphine Action Pathway;Codeine and Morphine Metabolism;Farnesoid X Receptor Pathway;Nuclear Receptors Meta-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: 0.203

Intolerance Scores

• loftool: 0.944
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.43

Haploinsufficiency Scores

• pHI: 0.0522
• hipred: N
• hipred_score: 0.112
• ghis: 0.438

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0572

Gene Damage Prediction

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

Gene ontology

• Biological process: cellular glucuronidation
• Cellular component: endoplasmic reticulum membrane;integral component of membrane;organelle membrane;intracellular membrane-bounded organelle
• Molecular function: retinoic acid binding;UDP-glycosyltransferase activity;glucuronosyltransferase activity