PGD

phosphogluconate dehydrogenase

Basic information

Region (hg38): 1:10398592-10420511

Links

ENSG00000142657 ∙ NCBI:5226 ∙ OMIM:172200 ∙ HGNC:8891 ∙ Uniprot:P52209 ∙ 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 PGD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGD 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				1	2	3
missense			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	2	2

Variants in PGD

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

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

Position	Type	Phenotype	Significance	ClinVar
1-10400417-T-C		not specified	Uncertain significance (Dec 15, 2022)
1-10400522-A-T		not specified	Uncertain significance (Jun 04, 2024)
1-10400558-T-G		not specified	Uncertain significance (Sep 29, 2023)
1-10400569-A-T		not specified	Uncertain significance (Jun 22, 2021)
1-10404249-C-T		not specified	Uncertain significance (Dec 13, 2022)
1-10404276-C-G		not specified	Uncertain significance (Jun 07, 2024)
1-10408094-A-C		not specified	Uncertain significance (May 04, 2023)
1-10408108-A-G		not specified	Uncertain significance (Dec 22, 2023)
1-10411445-G-A			not provided (-)
1-10411540-C-G		not specified	Uncertain significance (May 20, 2024)
1-10413104-A-G		not specified	Uncertain significance (Dec 20, 2021)
1-10413142-C-T			Benign (Apr 23, 2018)
1-10413165-A-G		not specified	Uncertain significance (Aug 29, 2024)
1-10413212-A-G		not specified	Uncertain significance (May 24, 2023)
1-10413229-C-T		not specified	Likely benign (Feb 26, 2024)
1-10417043-A-G		not specified	Uncertain significance (Feb 16, 2023)
1-10417384-C-T			Benign (Jun 06, 2018)
1-10417442-G-A		not specified	Uncertain significance (Feb 28, 2024)
1-10417452-G-C		not specified	Uncertain significance (Jan 26, 2022)
1-10417461-A-G		not specified	Uncertain significance (Dec 27, 2023)
1-10417483-G-A		not specified	Uncertain significance (Jul 06, 2021)
1-10417494-G-A		not specified	Uncertain significance (Aug 04, 2023)
1-10417504-T-G		not specified	Uncertain significance (Jul 14, 2022)
1-10418827-G-C		not specified	Uncertain significance (Apr 19, 2023)
1-10418840-A-G		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGD	protein_coding	protein_coding	ENST00000270776	13	21553

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.988	0.0121	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	220	287	0.768	0.0000159	3166
Missense in Polyphen		71	128.65	0.55188		1416
Synonymous	-0.920	129	116	1.11	0.00000703	930
Loss of Function	4.23	3	26.5	0.113	0.00000127	308

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000231	0.000231
European (Non-Finnish)	0.0000533	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the oxidative decarboxylation of 6- phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH. {ECO:0000250}.
• Pathway: Glutathione metabolism - Homo sapiens (human);Pentose phosphate pathway - Homo sapiens (human);Pentose Phosphate Pathway (Erythrocyte);Warburg Effect;Pentose Phosphate Pathway;Nuclear Receptors Meta-Pathway;NRF2 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: 0.838

Intolerance Scores

• loftool: 0.408
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.76

Haploinsufficiency Scores

• pHI: 0.257
• hipred: Y
• hipred_score: 0.696
• ghis: 0.605

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pgd
• Phenotype: skeleton phenotype

Gene ontology

• Biological process: pentose-phosphate shunt;pentose-phosphate shunt, oxidative branch;pentose biosynthetic process;D-gluconate metabolic process;oxidation-reduction process
• Cellular component: nucleus;cytosol;extracellular exosome
• Molecular function: phosphogluconate dehydrogenase (decarboxylating) activity;NADP binding