PGP

phosphoglycolate phosphatase

Basic information

Region (hg38): 16:2211593-2214840

Links

ENSG00000184207NCBI:283871OMIM:172280HGNC:8909Uniprot:A6NDG6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • 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.

EffectPLPVUSLBBSum
synonymous
0
missense
31
clinvar
1
clinvar
32
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 31 1 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PGPprotein_codingprotein_codingENST00000333503 22811
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.1630.780124719041247230.0000160
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.30981420.6920.000006572003
Missense in Polyphen3065.3970.45873884
Synonymous-1.157361.51.190.00000300703
Loss of Function1.5626.180.3242.69e-777

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00003560.0000353
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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