UGT2B28

UDP glucuronosyltransferase family 2 member B28, the group of UDP glucuronosyltransferases

Basic information

Region (hg38): 4:69280475-69295050

Links

ENSG00000135226 ∙ NCBI:54490 ∙ OMIM:606497 ∙ HGNC:13479 ∙ Uniprot:Q9BY64 ∙ 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 UGT2B28 gene.

• not_specified (88 variants)
• not_provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UGT2B28 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000053039.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	1	5
missense			78	12	2	92
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	78	16	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UGT2B28	protein_coding	protein_coding	ENST00000335568	6	14552

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.24e-18	0.000883	122995	17	107	123119	0.000504

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.18	373	272	1.37	0.0000125	3481
Missense in Polyphen		116	88.112	1.3165		1199
Synonymous	-2.55	125	93.6	1.34	0.00000449	967
Loss of Function	-0.877	24	19.8	1.21	0.00000102	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00216	0.00163
Ashkenazi Jewish	0.00	0.00
East Asian	0.000733	0.000606
Finnish	0.000151	0.000142
European (Non-Finnish)	0.000628	0.000541
Middle Eastern	0.000733	0.000606
South Asian	0.000690	0.000547
Other	0.000352	0.000166

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 has glucuronidating capacity with steroid substrates such as 5-beta-androstane 3-alpha,17-beta- diol, estradiol, ADT, eugenol and bile acids. Only isoform 1 seems to be active. {ECO:0000269|PubMed:11300766}.
• 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;Tyrosine metabolism;Androgen and estrogen biosynthesis and metabolism;Biological oxidations;Metabolism;Linoleate metabolism;Vitamin A (retinol) metabolism;Xenobiotics metabolism;Porphyrin metabolism (Consensus)

Intolerance Scores

• loftool: 0.884
• rvis_EVS: 1.53
• rvis_percentile_EVS: 95.56

Haploinsufficiency Scores

• pHI: 0.0801
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0676

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Ugt2b5

Gene ontology

• Biological process: steroid metabolic process;xenobiotic glucuronidation
• Cellular component: nuclear outer membrane;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;intracellular membrane-bounded organelle
• Molecular function: UDP-glycosyltransferase activity;glucuronosyltransferase activity