PPIE
peptidylprolyl isomerase E, the group of Spliceosomal B complex|Spliceosomal Bact complex|Spliceosomal P complex|RNA binding motif containing|Cyclophilin peptidylprolyl isomerases|Spliceosomal C complex
Basic information
Region (hg38): 1:39692182-39763914
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (26 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPIE gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006112.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 26 | 26 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 26 | 0 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPIE | protein_coding | protein_coding | ENST00000372830 | 10 | 71733 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.728 | 0.272 | 125744 | 0 | 4 | 125748 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.25 | 133 | 180 | 0.737 | 0.00000999 | 2088 |
| Missense in Polyphen | 56 | 100.34 | 0.55809 | 1155 | ||
| Synonymous | 0.234 | 62 | 64.4 | 0.963 | 0.00000360 | 568 |
| Loss of Function | 3.20 | 3 | 17.4 | 0.172 | 8.22e-7 | 216 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11991638, PubMed:28076346). Combines RNA- binding and PPIase activities (PubMed:8977107, PubMed:18258190, PubMed:20677832, PubMed:20460131). Binds mRNA and has a preference for single-stranded RNA molecules with poly-A and poly-U stretches, suggesting it binds to the poly(A)-region in the 3'-UTR of mRNA molecules (PubMed:8977107, PubMed:18258190, PubMed:20460131). Catalyzes the cis-trans isomerization of proline imidic peptide bonds in proteins (PubMed:8977107, PubMed:18258190, PubMed:20677832, PubMed:20541251). Inhibits KMT2A activity; this requires proline isomerase activity (PubMed:20677832, PubMed:20541251, PubMed:20460131). {ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:18258190, ECO:0000269|PubMed:20460131, ECO:0000269|PubMed:20541251, ECO:0000269|PubMed:20677832, ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:8977107}.;
- Pathway
- Spliceosome - Homo sapiens (human);DNA Repair;Neutrophil degranulation;Metabolism of RNA;Innate Immune System;Immune System;mRNA Splicing - Major Pathway;Formation of TC-NER Pre-Incision Complex;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA;Dual incision in TC-NER;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair
(Consensus)
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- loftool
- 0.284
- rvis_EVS
- -0.43
- rvis_percentile_EVS
- 25.15
Haploinsufficiency Scores
- pHI
- 0.235
- hipred
- Y
- hipred_score
- 0.665
- ghis
- 0.622
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.981
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppie
- Phenotype
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;protein peptidyl-prolyl isomerization;transcription-coupled nucleotide-excision repair;regulation of transcription, DNA-templated;protein folding;protein refolding;neutrophil degranulation;positive regulation of viral genome replication
- Cellular component
- extracellular region;nucleus;nucleoplasm;cytosol;nuclear speck;secretory granule lumen;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome;ficolin-1-rich granule lumen
- Molecular function
- RNA binding;mRNA binding;peptidyl-prolyl cis-trans isomerase activity;protein binding;poly(A) binding;cyclosporin A binding;unfolded protein binding