PGP

phosphoglycolate phosphatase

Basic information

Region (hg38): 16:2211593-2214840

Links

ENSG00000184207 ∙ NCBI:283871 ∙ OMIM:172280 ∙ HGNC:8909 ∙ Uniprot:A6NDG6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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						0
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in PGP

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

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

Position	Type	Phenotype	Significance	ClinVar
16-2213771-T-C		not specified	Uncertain significance (Jul 12, 2022)
16-2213792-T-G		not specified	Uncertain significance (Nov 24, 2024)
16-2213817-G-C		not specified	Uncertain significance (Dec 09, 2023)
16-2213826-T-G		not specified	Uncertain significance (Jun 06, 2023)
16-2213949-C-T		not specified	Uncertain significance (Jan 18, 2025)
16-2213976-T-C		not specified	Uncertain significance (Apr 07, 2022)
16-2214011-C-T		not specified	Uncertain significance (Jul 22, 2022)
16-2214203-C-T		not specified	Uncertain significance (Sep 16, 2021)
16-2214345-G-C		not specified	Uncertain significance (Nov 14, 2024)
16-2214407-A-G		not specified	Uncertain significance (Nov 14, 2024)
16-2214426-C-T		not specified	Uncertain significance (Dec 16, 2023)
16-2214572-T-C		not specified	Uncertain significance (Mar 16, 2022)
16-2214638-G-C		not specified	Uncertain significance (Apr 15, 2024)
16-2214713-T-G		not specified	Uncertain significance (Oct 12, 2024)
16-2214717-C-T		not specified	Uncertain significance (Aug 12, 2024)
16-2214723-C-G		not specified	Uncertain significance (Oct 24, 2024)
16-2214737-A-G		not specified	Uncertain significance (Mar 26, 2024)
16-2214744-G-A		not specified	Uncertain significance (Apr 09, 2024)
16-2214747-C-T		not specified	Uncertain significance (Jun 23, 2023)
16-2214752-T-C		not specified	Uncertain significance (Mar 29, 2022)
16-2214773-G-A		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

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: 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

	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