PGP
Basic information
Region (hg38): 16:2211593-2214840
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (32 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGP gene is commonly pathogenic or not. These statistics are base on transcript: NM_001042371.3. 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 | 0 | |||||
missense | 31 | 32 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 31 | 1 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PGP | protein_coding | protein_coding | ENST00000333503 | 2 | 2811 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.163 | 0.780 | 124719 | 0 | 4 | 124723 | 0.0000160 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.30 | 98 | 142 | 0.692 | 0.00000657 | 2003 |
Missense in Polyphen | 30 | 65.397 | 0.45873 | 884 | ||
Synonymous | -1.15 | 73 | 61.5 | 1.19 | 0.00000300 | 703 |
Loss of Function | 1.56 | 2 | 6.18 | 0.324 | 2.69e-7 | 77 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000356 | 0.0000353 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Glycerol-3-phosphate phosphatase hydrolyzing glycerol-3- phosphate into glycerol. Thereby, regulates the cellular levels of glycerol-3-phosphate a metabolic intermediate of glucose, lipid and energy metabolism. Was also shown to have a 2-phosphoglycolate phosphatase activity and a tyrosine-protein phosphatase activity. However, their physiological relevance is unclear (PubMed:26755581). In vitro, has also a phosphatase activity toward ADP, ATP, GDP and GTP (By similarity). {ECO:0000250|UniProtKB:Q8CHP8, ECO:0000269|PubMed:26755581}.;
- Pathway
- Glyoxylate and dicarboxylate metabolism - Homo sapiens (human);Metabolism of carbohydrates;Metabolism;Glycolysis;Glucose metabolism
(Consensus)
Recessive Scores
- pRec
- 0.190
Haploinsufficiency Scores
- pHI
- 0.195
- hipred
- Y
- hipred_score
- 0.516
- ghis
- 0.411
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.773
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pgp
- Phenotype
- embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); cellular phenotype;
Gene ontology
- Biological process
- glycerol biosynthetic process;glycerophospholipid metabolic process;dephosphorylation;peptidyl-tyrosine dephosphorylation;negative regulation of gluconeogenesis
- Cellular component
- cytoplasm
- Molecular function
- glycerol-1-phosphatase activity;magnesium ion binding;protein tyrosine phosphatase activity;phosphoglycolate phosphatase activity;phosphatase activity;glycerol-3-phosphatase activity;nucleotide phosphatase activity, acting on free nucleotides