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
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.

Inborn_genetic_diseases (39 variants)
not_provided (11 variants)
Developmental_and_epileptic_encephalopathy,_83 (5 variants)
UGP2-related_disorder (2 variants)
D-6618 (1 variants)

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. These statistics are base on transcript: NM_000006759.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	7 clinvar		9
missense		1 clinvar	41 clinvar	1 clinvar		43
nonsense			1 clinvar			1
start loss						0
frameshift			3 clinvar			3
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	1	54	8	0

Highest pathogenic variant AF is 0.000038441696

Loading clinvar variants...

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
Phenotype

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