PPIF
peptidylprolyl isomerase F, the group of Cyclophilin peptidylprolyl isomerases
Basic information
Region (hg38): 10:79347469-79355334
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPIF 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 | 2 | |||||
| missense | 14 | 14 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 0 | 2 |
Variants in PPIF
This is a list of pathogenic ClinVar variants found in the PPIF region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 10-79347601-G-C | not specified | Uncertain significance (Nov 30, 2022) | ||
| 10-79347730-G-T | not specified | Uncertain significance (Jan 08, 2024) | ||
| 10-79347742-A-T | not specified | Uncertain significance (May 24, 2024) | ||
| 10-79349091-G-A | not specified | Uncertain significance (May 25, 2022) | ||
| 10-79349703-G-A | not specified | Uncertain significance (Nov 09, 2023) | ||
| 10-79349716-C-T | not specified | Uncertain significance (Apr 13, 2023) | ||
| 10-79351493-G-A | not specified | Uncertain significance (Mar 01, 2024) | ||
| 10-79351499-A-G | not specified | Uncertain significance (May 27, 2022) | ||
| 10-79351541-C-T | not specified | Uncertain significance (Jan 23, 2024) | ||
| 10-79351574-G-A | not specified | Uncertain significance (Mar 29, 2022) | ||
| 10-79352358-T-G | not specified | Uncertain significance (Mar 24, 2023) | ||
| 10-79352382-A-G | not specified | Uncertain significance (Oct 26, 2022) | ||
| 10-79352385-A-C | not specified | Uncertain significance (Feb 27, 2024) | ||
| 10-79353738-G-A | not specified | Uncertain significance (Jun 06, 2023) | ||
| 10-79353756-G-T | not specified | Uncertain significance (Feb 14, 2023) | ||
| 10-79353779-C-T | Benign (Jun 18, 2018) | |||
| 10-79353830-C-G | Benign (Dec 31, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPIF | protein_coding | protein_coding | ENST00000225174 | 6 | 7869 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00199 | 0.753 | 125681 | 0 | 67 | 125748 | 0.000266 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.676 | 88 | 108 | 0.817 | 0.00000610 | 1335 |
| Missense in Polyphen | 47 | 53.915 | 0.87174 | 599 | ||
| Synonymous | 0.916 | 38 | 45.9 | 0.828 | 0.00000305 | 420 |
| Loss of Function | 0.909 | 5 | 7.73 | 0.647 | 3.27e-7 | 98 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000490 | 0.000489 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000168 | 0.000167 |
| Middle Eastern | 0.000490 | 0.000489 |
| South Asian | 0.00121 | 0.00121 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: PPIase that catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides and may therefore assist protein folding (PubMed:20676357). Involved in regulation of the mitochondrial permeability transition pore (mPTP). It is proposed that its association with the mPTP is masking a binding site for inhibiting inorganic phosphate (Pi) and promotes the open probability of the mPTP leading to apoptosis or necrosis; the requirement of the PPIase activity for this function is debated. In cooperation with mitochondrial TP53 is involved in activating oxidative stress-induced necrosis. Involved in modulation of mitochondrial membrane F(1)F(0) ATP synthase activity and regulation of mitochondrial matrix adenine nucleotide levels. Has anti-apoptotic activity independently of mPTP and in cooperation with BCL2 inhibits cytochrome c-dependent apoptosis. {ECO:0000269|PubMed:19228691, ECO:0000269|PubMed:20676357, ECO:0000269|PubMed:22726440, ECO:0000269|PubMed:26387735}.;
- Pathway
- Huntington,s disease - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Toxoplasmosis - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase
(Consensus)
Recessive Scores
- pRec
- 0.199
Haploinsufficiency Scores
- pHI
- 0.245
- hipred
- N
- hipred_score
- 0.394
- ghis
- 0.536
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.938
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppif
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- protein peptidyl-prolyl isomerization;response to ischemia;protein folding;regulation of proton-transporting ATPase activity, rotational mechanism;negative regulation of ATPase activity;protein refolding;negative regulation of apoptotic process;regulation of mitochondrial membrane permeability;cellular response to hydrogen peroxide;cellular response to arsenic-containing substance;cellular response to calcium ion;positive regulation of release of cytochrome c from mitochondria;negative regulation of release of cytochrome c from mitochondria;negative regulation of oxidative phosphorylation;regulation of mitochondrial membrane permeability involved in programmed necrotic cell death;mitochondrial outer membrane permeabilization involved in programmed cell death;negative regulation of oxidative phosphorylation uncoupler activity;negative regulation of intrinsic apoptotic signaling pathway
- Cellular component
- mitochondrion;mitochondrial proton-transporting ATP synthase complex;mitochondrial permeability transition pore complex;membrane
- Molecular function
- peptidyl-prolyl cis-trans isomerase activity;protein binding;cyclosporin A binding;unfolded protein binding