PDPR

pyruvate dehydrogenase phosphatase regulatory subunit

Basic information

Region (hg38): 16:70114332-70162537

Links

ENSG00000090857 ∙ NCBI:55066 ∙ OMIM:617835 ∙ HGNC:30264 ∙ Uniprot:Q8NCN5 ∙ 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 PDPR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDPR 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		1
missense			50	3	2	55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	50	4	2

Variants in PDPR

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

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

Position	Type	Phenotype	Significance	ClinVar
16-70120498-G-A		not specified	Uncertain significance (May 29, 2024)
16-70120574-A-G		not specified	Uncertain significance (Nov 14, 2023)
16-70120577-A-G			not provided (-)
16-70120616-C-G			Likely benign (Aug 01, 2022)
16-70120668-A-C		not specified	Uncertain significance (Nov 14, 2023)
16-70127276-A-G		not specified	Uncertain significance (Mar 07, 2024)
16-70127282-T-C		not specified	Uncertain significance (May 23, 2023)
16-70127333-A-G		not specified	Uncertain significance (Apr 06, 2024)
16-70127360-T-C			Benign (May 25, 2017)
16-70128847-G-A		not specified	Uncertain significance (Mar 07, 2023)
16-70128964-T-C		not specified	Uncertain significance (Nov 10, 2022)
16-70129008-C-T		not specified	Uncertain significance (Feb 14, 2023)
16-70129026-G-A		not specified	Uncertain significance (Jun 04, 2024)
16-70129032-G-T		not specified	Uncertain significance (Jan 24, 2024)
16-70129038-G-C		not specified	Uncertain significance (Dec 31, 2023)
16-70129059-G-C		not specified	Uncertain significance (Oct 27, 2022)
16-70129108-C-G		not specified	Uncertain significance (Sep 13, 2022)
16-70130440-C-T		not specified	Uncertain significance (Dec 21, 2022)
16-70130486-G-C		not specified	Uncertain significance (Nov 16, 2021)
16-70131311-G-A		not specified	Uncertain significance (Nov 01, 2022)
16-70131317-G-C		not specified	Uncertain significance (Mar 18, 2024)
16-70131354-A-G		not specified	Uncertain significance (Apr 20, 2023)
16-70132155-T-C			Likely benign (Jun 01, 2024)
16-70132184-G-A		not specified	Uncertain significance (May 31, 2022)
16-70132187-A-C		not specified	Uncertain significance (Nov 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDPR	protein_coding	protein_coding	ENST00000288050	17	47675

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.35e-9	1.00	124396	0	265	124661	0.00106

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.494	499	469	1.06	0.0000263	5547
Missense in Polyphen		176	172.45	1.0206		1968
Synonymous	-1.14	196	177	1.11	0.0000105	1599
Loss of Function	3.29	21	44.7	0.470	0.00000243	498

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00324	0.00321
Ashkenazi Jewish	0.00643	0.00638
East Asian	0.00129	0.00128
Finnish	0.0000933	0.0000928
European (Non-Finnish)	0.000794	0.000779
Middle Eastern	0.00129	0.00128
South Asian	0.000305	0.000294
Other	0.00117	0.00116

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Decreases the sensitivity of PDP1 to magnesium ions, and this inhibition is reversed by the polyamine spermine. {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;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.450
• rvis_EVS: 0.87
• rvis_percentile_EVS: 88.89

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.554
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.174

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdpr

Gene ontology

• Biological process: protein dephosphorylation;regulation of acetyl-CoA biosynthetic process from pyruvate;oxidation-reduction process
• Cellular component: cytoplasm;mitochondrion;mitochondrial matrix
• Molecular function: [pyruvate dehydrogenase (lipoamide)] phosphatase activity;oxidoreductase activity