UGP2

UDP-glucose pyrophosphorylase 2

Basic information

Region (hg38): 2:63840952-63891562

Previous symbols: [ "UGP1" ]

Links

ENSG00000169764 ∙ NCBI:7360 ∙ OMIM:191760 ∙ HGNC:12527 ∙ Uniprot:Q16851 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• developmental and epileptic encephalopathy, 83 (Moderate), mode of inheritance: AR
• developmental and epileptic encephalopathy, 83 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 83	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	31820119

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UGP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UGP2 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				4	1	5
missense			15	1		16
nonsense			1			1
start loss		1				1
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			2	1		3
non coding					1	1
Total	0	1	17	5	2

Variants in UGP2

This is a list of pathogenic ClinVar variants found in the UGP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-63841233-G-A		Developmental and epileptic encephalopathy, 83	Uncertain significance (Dec 20, 2023)
2-63842192-A-G		Inborn genetic diseases	Uncertain significance (Jul 26, 2024)
2-63842200-A-G			Likely benign (Oct 01, 2023)
2-63842208-A-G			Uncertain significance (Apr 19, 2023)
2-63856320-A-G		Developmental and epileptic encephalopathy, 83 • D-6618	Pathogenic/Likely pathogenic (Oct 04, 2024)
2-63856360-G-A		Inborn genetic diseases	Uncertain significance (Jul 05, 2023)
2-63856418-A-G			Likely benign (Sep 01, 2024)
2-63856421-A-C			Likely benign (Mar 01, 2023)
2-63857835-A-C		Inborn genetic diseases	Uncertain significance (Dec 07, 2023)
2-63857857-G-A		Inborn genetic diseases	Uncertain significance (Apr 20, 2024)
2-63857869-A-G		Inborn genetic diseases	Uncertain significance (Jun 16, 2024)
2-63857980-G-A		Developmental and epileptic encephalopathy, 83	Benign (Dec 05, 2021)
2-63882551-A-G		Inborn genetic diseases	Uncertain significance (Aug 17, 2022)
2-63882620-C-G		Inborn genetic diseases	Uncertain significance (May 02, 2024)
2-63882631-C-G		Inborn genetic diseases	Uncertain significance (Dec 20, 2023)
2-63882637-G-C		Inborn genetic diseases	Uncertain significance (Aug 22, 2022)
2-63884054-A-G		Inborn genetic diseases	Uncertain significance (Aug 02, 2021)
2-63884063-G-T		Inborn genetic diseases	Uncertain significance (Nov 06, 2023)
2-63885572-C-CT		UGP2-related disorder	Likely benign (Dec 14, 2020)
2-63885636-T-C		Inborn genetic diseases	Uncertain significance (Oct 03, 2024)
2-63885798-A-G		UGP2-related disorder	Likely benign (Feb 22, 2023)
2-63885819-A-G		Inborn genetic diseases	Uncertain significance (Nov 23, 2022)
2-63885863-A-G		Inborn genetic diseases	Uncertain significance (Jul 06, 2021)
2-63885873-G-A		Inborn genetic diseases	Uncertain significance (Jan 24, 2023)
2-63886482-G-A		Inborn genetic diseases	Uncertain significance (May 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UGP2	protein_coding	protein_coding	ENST00000337130	10	50623

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.35e-8	0.590	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.93	180	269	0.668	0.0000136	3344
Missense in Polyphen		37	87.699	0.4219		1125
Synonymous	-0.595	105	97.5	1.08	0.00000487	983
Loss of Function	1.15	15	20.7	0.726	8.66e-7	295

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000764	0.000764
Ashkenazi Jewish	0.000596	0.000595
East Asian	0.000219	0.000217
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000285	0.000281
Middle Eastern	0.000219	0.000217
South Asian	0.000166	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a central role as a glucosyl donor in cellular metabolic pathways.
• Pathway: Starch and sucrose metabolism - Homo sapiens (human);Galactose metabolism - Homo sapiens (human);Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Pentose and glucuronate interconversions - Homo sapiens (human);Galactosemia III;Galactosemia II (GALK);Glycogen synthetase deficiency;Glycogenosis, Type III. Cori disease, Debrancher glycogenosis;Mucopolysaccharidosis VI. Sly syndrome;Sucrase-isomaltase deficiency;Glycogenosis, Type IV. Amylopectinosis, Anderson disease;Glycogenosis, Type VI. Hers disease;Galactose Metabolism;Starch and Sucrose Metabolism;GLUT-1 deficiency syndrome;Congenital disorder of glycosylation CDG-IId;Nucleotide Sugars Metabolism;Lactose Synthesis;Galactosemia;Exercise-induced Circadian Regulation;Glycogen Metabolism;Glucuronidation;Formation of the active cofactor, UDP-glucuronate;Glucuronidation;Metabolism of carbohydrates;Phase II - Conjugation of compounds;Glycolysis Gluconeogenesis;Biological oxidations;Metabolism;glycogen biosynthesis;Galactose metabolism;Glycogen synthesis;Glycogen metabolism (Consensus)

Recessive Scores

• pRec: 0.399

Intolerance Scores

• loftool: 0.891
• rvis_EVS: -0.98
• rvis_percentile_EVS: 8.75

Haploinsufficiency Scores

• pHI: 0.971
• hipred: Y
• hipred_score: 0.543
• ghis: 0.629

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ugp2

Gene ontology

• Biological process: glycogen metabolic process;glycogen biosynthetic process;UDP-glucose metabolic process;UDP-glucuronate biosynthetic process;glucose 1-phosphate metabolic process
• Cellular component: nucleus;cytoplasm;cytosol;extracellular exosome
• Molecular function: UTP:glucose-1-phosphate uridylyltransferase activity;protein binding;glucose binding;pyrimidine ribonucleotide binding;identical protein binding;metal ion binding