UGP2
protein-codingUDP-glucose pyrophosphorylase 2
Gene summary
The enzyme encoded by this gene is an important intermediary in mammalian carbohydrate interconversions. It transfers a glucose moiety from glucose-1-phosphate to MgUTP and forms UDP-glucose and MgPPi. In liver and muscle tissue, UDP-glucose is a direct precursor of glycogen; in lactating mammary gland it is converted to UDP-galactose which is then converted to lactose. The eukaryotic enzyme has no significant sequence similarity to the prokaryotic enzyme. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
- UGP1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~50.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0032895
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0032895
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0032895
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0032895
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Musculoskeletal; Neurologic
Intervention: General
Rationale: 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to UGP2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006759.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 12 | 13 | |||
| missense | 1 | 46 | 2 | 49 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 3 | 3 | ||||
| splice donor/acceptor (+/-2bp) | 7 | 7 | ||||
| Total | 0 | 1 | 58 | 14 | 0 | 73 |
Highest pathogenic variant AF is 0.000038441696
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006750.3 | 10 | MANE Select | |
| Ensembl | ENSP00000338703.5 | 10 | MANE Select | |
| RefSeq | NP_001001521.1 | 9 | Standard | |
| RefSeq | NP_001364453.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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
Biological Process
- glycogen metabolic process
- glycogen biosynthetic process
- UDP-glucose metabolic process
- UDP-glucuronate biosynthetic process
- glucose 1-phosphate metabolic process
Molecular Function
- UTP:glucose-1-phosphate uridylyltransferase activity
- protein binding
- glucose binding
- pyrimidine ribonucleotide binding
- identical protein binding
Cellular Component
- nucleus
- cytoplasm
- cytosol
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000337130
- Coding exons
- 10
- Length
- 50623
- Individuals with no LoFs
- 125678
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 70
- Defined
- 125748
- p
- 0.000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.93 | 180 | 269 | 0.668 | 0.0000136 | 3344 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.00046 | 0.00043 | rare |
| Ashkenazi Jewish | 0.00060 | 0.00060 | rare |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00028 | 0.00028 | rare |
| South Asian | 0.00017 | 0.00016 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a central role as a glucosyl donor in cellular metabolic pathways.;
Recessive Scores
- pRec
- 0.399
Intolerance Scores
- LoFtool
- 0.891
- RVIS EVS
- -0.98
- RVIS percentile EVS
- 8.75
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- K
- Indispensability pred.
- E
- Indispensability score
- 0.993
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |