UGT2B15

UDP glucuronosyltransferase family 2 member B15, the group of UDP glucuronosyltransferases

Basic information

Region (hg38): 4:68646596-68670652

Links

ENSG00000196620 ∙ NCBI:7366 ∙ OMIM:600069 ∙ HGNC:12546 ∙ Uniprot:P54855 ∙ 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 UGT2B15 gene.

• Inborn genetic diseases (28 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UGT2B15 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
missense			27	2	1	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	27	2	3

Variants in UGT2B15

This is a list of pathogenic ClinVar variants found in the UGT2B15 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-68647117-T-C			Benign (Apr 05, 2018)
4-68647159-C-T		not specified	Uncertain significance (Oct 20, 2021)
4-68647190-C-T		not specified	Uncertain significance (Aug 19, 2023)
4-68647193-C-T		not specified	Uncertain significance (Jul 12, 2023)
4-68647211-C-T		not specified	Uncertain significance (Aug 31, 2023)
4-68647238-T-A		not specified	Uncertain significance (Dec 17, 2023)
4-68647289-G-A			Likely benign (Feb 01, 2023)
4-68647289-G-T		not specified	Uncertain significance (Oct 25, 2022)
4-68647337-G-A		not specified	Uncertain significance (Nov 08, 2022)
4-68647366-A-G		not specified	Uncertain significance (May 18, 2023)
4-68654071-G-A		not specified	Uncertain significance (Aug 30, 2022)
4-68654097-A-T		not specified	Uncertain significance (Jun 11, 2021)
4-68654105-A-T		not specified	Likely benign (Dec 06, 2022)
4-68654131-T-C		not specified	Uncertain significance (Jul 25, 2023)
4-68654163-A-G		not specified	Uncertain significance (Dec 06, 2022)
4-68654167-G-C		not specified	Uncertain significance (Jan 30, 2024)
4-68654197-T-C		not specified	Uncertain significance (Aug 03, 2022)
4-68654199-G-A		not specified	Uncertain significance (Dec 15, 2022)
4-68655101-G-A		not specified	Uncertain significance (Nov 07, 2022)
4-68655128-G-C		not specified	Uncertain significance (Aug 14, 2023)
4-68655137-T-G		not specified	Uncertain significance (Dec 19, 2023)
4-68655142-C-A		not specified	Uncertain significance (Dec 30, 2023)
4-68655149-T-A		not specified	Uncertain significance (Aug 22, 2022)
4-68663030-G-C		not specified	Uncertain significance (Jun 24, 2022)
4-68663039-A-G		not specified	Uncertain significance (Nov 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UGT2B15	protein_coding	protein_coding	ENST00000338206	6	23999

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.29e-21	0.000127	125682	0	58	125740	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.874	313	272	1.15	0.0000127	3486
Missense in Polyphen		83	82.635	1.0044		1155
Synonymous	-1.55	117	97.5	1.20	0.00000468	969
Loss of Function	-1.20	28	21.9	1.28	0.00000110	272

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000471	0.000470
Ashkenazi Jewish	0.000924	0.000893
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000252	0.000246
Middle Eastern	0.000109	0.000109
South Asian	0.0000659	0.0000653
Other	0.000333	0.000326

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 displays activity toward several classes of xenobiotic substrates, including simple phenolic compounds, 7-hydroxylated coumarins, flavonoids, anthraquinones, and certain drugs and their hydroxylated metabolites. It also catalyzes the glucuronidation of endogenous estrogens and androgens.
• Pathway: Benzodiazepine Pathway, Pharmacokinetics;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);Tamoxifen Pathway, Pharmacokinetics;Valproic Acid Pathway, Pharmacokinetics;Pathway_PA165986194 -need delete;Acetaminophen Pathway, Pharmacokinetics;Morphine Metabolism Pathway;Morphine Action Pathway;Acetaminophen Metabolism Pathway;Tamoxifen metabolism;Glucuronidation;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: 0.119

Intolerance Scores

• loftool: 0.887
• rvis_EVS: 1.38
• rvis_percentile_EVS: 94.57

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0787

Gene Damage Prediction

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

Gene ontology

• Biological process: xenobiotic metabolic process;steroid metabolic 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