PGLS

6-phosphogluconolactonase

Basic information

Region (hg38): 19:17511636-17521288

Links

ENSG00000130313 ∙ NCBI:25796 ∙ OMIM:604951 ∙ HGNC:8903 ∙ Uniprot:O95336 ∙ 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 PGLS gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGLS 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			40	1		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	1	0

Variants in PGLS

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

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

Position	Type	Phenotype	Significance	ClinVar
19-17511679-G-A		not specified	Uncertain significance (Dec 17, 2023)
19-17511685-G-A		not specified	Uncertain significance (Dec 22, 2023)
19-17511692-G-A		not specified	Uncertain significance (Mar 26, 2024)
19-17511694-C-T			Uncertain significance (Nov 09, 2023)
19-17511703-G-A		not specified	Uncertain significance (Mar 04, 2025)
19-17511713-G-C		not specified	Uncertain significance (Mar 14, 2025)
19-17511714-T-G		not specified	Uncertain significance (Nov 22, 2023)
19-17511784-C-G		not specified	Uncertain significance (Aug 08, 2023)
19-17511791-G-A		not specified	Uncertain significance (Feb 06, 2023)
19-17511791-G-C		not specified	Uncertain significance (Jan 01, 2025)
19-17511799-C-G		not specified	Uncertain significance (Sep 01, 2021)
19-17511819-C-A		not specified	Uncertain significance (May 03, 2023)
19-17511841-G-A		not specified	Uncertain significance (Sep 06, 2022)
19-17511863-C-T		not specified	Uncertain significance (Jul 01, 2024)
19-17511865-G-A		not specified	Uncertain significance (Jul 06, 2021)
19-17511877-A-C		not specified	Uncertain significance (Nov 09, 2024)
19-17511908-A-C		not specified	Uncertain significance (Oct 20, 2023)
19-17511913-C-G		not specified	Uncertain significance (Mar 28, 2024)
19-17511923-C-T		not specified	Uncertain significance (Mar 06, 2023)
19-17511927-C-G		not specified	Uncertain significance (Mar 07, 2023)
19-17511943-A-T		not specified	Uncertain significance (Mar 15, 2024)
19-17516185-T-C		not specified	Uncertain significance (Feb 25, 2025)
19-17516189-G-A		not specified	Likely benign (Jan 17, 2024)
19-17516195-C-T		not specified	Uncertain significance (Apr 26, 2023)
19-17516200-C-G		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGLS	protein_coding	protein_coding	ENST00000252603	5	9660

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000753	0.781	125724	0	19	125743	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.207	126	133	0.949	0.00000764	1565
Missense in Polyphen		38	47.119	0.80647		563
Synonymous	-0.0383	65	64.6	1.01	0.00000429	568
Loss of Function	1.04	6	9.44	0.636	5.02e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000223	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000990	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolysis of 6-phosphogluconolactone to 6- phosphogluconate.
• Pathway: Pentose phosphate pathway - Homo sapiens (human);Pentose Phosphate Pathway (Erythrocyte);Warburg Effect;Pentose Phosphate Pathway;Glucose-6-phosphate dehydrogenase deficiency;Ribose-5-phosphate isomerase deficiency;Transaldolase deficiency;Pentose Phosphate Pathway;Pentose phosphate pathway (hexose monophosphate shunt);Metabolism of carbohydrates;pentose phosphate pathway (oxidative branch);Metabolism;Pentose phosphate cycle;pentose phosphate pathway (Consensus)

Recessive Scores

• pRec: 0.220

Haploinsufficiency Scores

• pHI: 0.456
• hipred: N
• hipred_score: 0.231
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pgls

Gene ontology

• Biological process: carbohydrate metabolic process;pentose-phosphate shunt;pentose-phosphate shunt, oxidative branch
• Cellular component: cytosol;extracellular exosome
• Molecular function: protein binding;6-phosphogluconolactonase activity