PDP2

pyruvate dehydrogenase phosphatase catalytic subunit 2, the group of Protein phosphatases, Mg2+/Mn2+ dependent

Basic information

Region (hg38): 16:66878589-66895754

Links

ENSG00000172840 ∙ NCBI:57546 ∙ OMIM:615499 ∙ HGNC:30263 ∙ Uniprot:Q9P2J9 ∙ 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 PDP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDP2 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			45	6		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	6	0

Variants in PDP2

This is a list of pathogenic ClinVar variants found in the PDP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-66884321-A-G		not specified	Likely benign (Jun 01, 2023)
16-66884357-C-T		not specified	Uncertain significance (Sep 02, 2024)
16-66884375-G-A		not specified	Uncertain significance (Jan 22, 2024)
16-66884415-G-A		not specified	Likely benign (Aug 02, 2021)
16-66884423-C-A		not specified	Uncertain significance (Jan 23, 2025)
16-66884457-C-T		not specified	Uncertain significance (Jun 06, 2023)
16-66884505-A-G		not specified	Uncertain significance (Sep 08, 2024)
16-66884549-G-A		not specified	Uncertain significance (Sep 25, 2024)
16-66884597-T-C		not specified	Uncertain significance (May 21, 2024)
16-66884606-C-T		not specified	Uncertain significance (Mar 07, 2024)
16-66884607-G-A		not specified	Likely benign (May 11, 2022)
16-66884634-A-G		not specified	Uncertain significance (Jul 02, 2024)
16-66884652-G-A		not specified	Uncertain significance (Oct 06, 2022)
16-66884655-G-A		not specified	Uncertain significance (Jan 26, 2022)
16-66884657-G-C		not specified	Uncertain significance (Jan 08, 2025)
16-66884697-G-A		not specified	Uncertain significance (Dec 12, 2023)
16-66884744-G-A		not specified	Uncertain significance (Aug 19, 2023)
16-66884765-G-A		not specified	Uncertain significance (May 26, 2024)
16-66884790-C-T		not specified	Uncertain significance (Dec 21, 2023)
16-66884810-G-A		not specified	Uncertain significance (Apr 23, 2024)
16-66884810-G-C		not specified	Uncertain significance (Aug 01, 2024)
16-66884820-G-A		not specified	Likely benign (Jun 21, 2022)
16-66884829-C-T		not specified	Uncertain significance (Jan 12, 2024)
16-66884855-A-C		not specified	Uncertain significance (Mar 13, 2023)
16-66884864-G-C		not specified	Uncertain significance (Sep 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDP2	protein_coding	protein_coding	ENST00000311765	1	17166

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000818	0.932	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	236	299	0.789	0.0000163	3456
Missense in Polyphen		59	94.626	0.62351		1115
Synonymous	-0.575	137	129	1.06	0.00000721	1085
Loss of Function	1.67	9	16.3	0.554	9.35e-7	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000408	0.000408
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.0000473	0.0000462
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex. {ECO:0000250}.
• Pathway: Regulation of pyruvate dehydrogenase (PDH) complex;Pyruvate metabolism;Pyruvate metabolism and Citric Acid (TCA) cycle;The citric acid (TCA) cycle and respiratory electron transport;Metabolism (Consensus)

Intolerance Scores

• loftool: 0.743
• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.55

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.350
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.913

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdp2

Gene ontology

• Biological process: protein dephosphorylation;regulation of acetyl-CoA biosynthetic process from pyruvate;positive regulation of pyruvate dehydrogenase activity
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: protein serine/threonine phosphatase activity;magnesium-dependent protein serine/threonine phosphatase activity;[pyruvate dehydrogenase (lipoamide)] phosphatase activity;metal ion binding