PPIA

peptidylprolyl isomerase A, the group of Cyclophilin peptidylprolyl isomerases

Basic information

Region (hg38): 7:44796679-44824564

Links

ENSG00000196262

∙ NCBI:5478 ∙ OMIM:123840 ∙ HGNC:9253 ∙ Uniprot:P62937 ∙ 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 PPIA gene.

Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPIA 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			1 clinvar			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region ? Intron variants in splice region, excluding donor/acceptor (+/-2bp)						0
non coding ? UTR, intron and other, non coding variants						0
Total	0	0	1	0	0

Variants in PPIA

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

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

Position	Type	Phenotype	Significance	ClinVar
7-44801307-T-G		not specified	Uncertain significance (Aug 15, 2023)	2619136

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPIA	protein_coding	protein_coding	ENST00000468812	5	27885

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.557	0.431	125737	0	3	125740	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	41	95.8	0.428	0.00000476	1103
Missense in Polyphen		0	7.8066	0		134
Synonymous	-0.00226	34	34.0	1.00	0.00000163	302
Loss of Function	2.03	1	6.65	0.150	2.78e-7	88

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000472	0.0000462
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides. {ECO:0000269|PubMed:20676357}.;
Pathway: Necroptosis - Homo sapiens (human);Tacrolimus/Cyclosporine Pathway, Pharmacodynamics;Prolactin Signaling Pathway;JAK-STAT;Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;Neutrophil degranulation;Disease;il-2 receptor beta chain in t cell activation;Prolactin;Minus-strand DNA synthesis;Assembly Of The HIV Virion;Budding and maturation of HIV virion;Late Phase of HIV Life Cycle;HIV Life Cycle;Host Interactions of HIV factors;HIV Infection;Plus-strand DNA synthesis;Infectious disease;Innate Immune System;Immune System;Binding and entry of HIV virion;APOBEC3G mediated resistance to HIV-1 infection;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Cell surface interactions at the vascular wall;Hemostasis;Basigin interactions;Uncoating of the HIV Virion;Reverse Transcription of HIV RNA;Integration of provirus;Early Phase of HIV Life Cycle (Consensus)

Recessive Scores

pRec: 0.413

Intolerance Scores

loftool: 0.296
rvis_EVS: 0.06
rvis_percentile_EVS: 58

Haploinsufficiency Scores

pHI: 0.164
hipred: Y
hipred_score: 0.556
ghis: 0.702

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.980

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ppia
Phenotype: homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; liver/biliary system phenotype; immune system phenotype; vision/eye phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Gene ontology

Biological process: protein peptidyl-prolyl isomerization;RNA-dependent DNA biosynthetic process;protein folding;viral life cycle;uncoating of virus;fusion of virus membrane with host plasma membrane;virion assembly;viral release from host cell;entry into host cell;lipid droplet organization;interleukin-12-mediated signaling pathway;protein refolding;neutrophil degranulation;regulation of viral genome replication;positive regulation of viral genome replication;positive regulation of protein secretion;leukocyte migration;establishment of integrated proviral latency
Cellular component: extracellular region;extracellular space;nucleus;cytosol;focal adhesion;membrane;vesicle;protein-containing complex;secretory granule lumen;extracellular exosome;ficolin-1-rich granule lumen
Molecular function: RNA binding;peptidyl-prolyl cis-trans isomerase activity;protein binding;cyclosporin A binding;virion binding;unfolded protein binding