PPA1

inorganic pyrophosphatase 1

Basic information

Region (hg38): 10:70202835-70233911

Previous symbols: [ "PP" ]

Links

ENSG00000180817 ∙ NCBI:5464 ∙ OMIM:179030 ∙ HGNC:9226 ∙ Uniprot:Q15181 ∙ 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 PPA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPA1 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	7	0	1

Variants in PPA1

This is a list of pathogenic ClinVar variants found in the PPA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-70206310-C-T		not specified	Uncertain significance (Oct 06, 2022)
10-70209226-G-A		not specified	Uncertain significance (Aug 22, 2023)
10-70209572-C-T		not specified	Uncertain significance (Sep 23, 2023)
10-70209658-G-C		not specified	Uncertain significance (Oct 16, 2023)
10-70213553-G-T		not specified	Uncertain significance (Jul 05, 2023)
10-70214565-T-C		not specified	Uncertain significance (Jun 29, 2023)
10-70214585-G-A		not specified	Uncertain significance (May 14, 2024)
10-70217870-T-C		not specified	Uncertain significance (Aug 12, 2021)
10-70233338-T-G		not specified	Benign (Mar 29, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPA1	protein_coding	protein_coding	ENST00000373232	11	31082

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000192	0.899	125683	0	60	125743	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.837	129	159	0.813	0.00000794	1940
Missense in Polyphen		42	58.209	0.72154		748
Synonymous	0.541	48	53.0	0.905	0.00000281	491
Loss of Function	1.55	10	16.9	0.592	7.16e-7	225

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000909	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000601	0.000448
Middle Eastern	0.00	0.00
South Asian	0.000167	0.000163
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Oxidative phosphorylation - Homo sapiens (human);tRNA Aminoacylation;Translation;Metabolism of proteins;Pyrophosphate hydrolysis;Metabolism;Cytosolic tRNA aminoacylation (Consensus)

Recessive Scores

• pRec: 0.693

Intolerance Scores

• loftool: 0.771
• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.600
• hipred: Y
• hipred_score: 0.672
• ghis: 0.652

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.674

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppa1

Gene ontology

• Biological process: tRNA aminoacylation for protein translation;phosphate-containing compound metabolic process;diphosphate metabolic process
• Cellular component: cytoplasm;cytosol;extracellular exosome
• Molecular function: magnesium ion binding;inorganic diphosphatase activity