PPIH
Basic information
Region (hg38): 1:42658335-42676758
Links
Phenotypes
GenCC
Source:
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 PPIH 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 | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 3 | 0 | 0 |
Variants in PPIH
This is a list of pathogenic ClinVar variants found in the PPIH region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-42658451-C-A | not specified | Uncertain significance (Nov 25, 2024) | ||
| 1-42658847-G-A | not specified | Uncertain significance (Feb 06, 2025) | ||
| 1-42666023-C-T | not specified | Uncertain significance (Sep 15, 2021) | ||
| 1-42667400-C-T | not specified | Uncertain significance (Sep 07, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPIH | protein_coding | protein_coding | ENST00000304979 | 9 | 18334 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000746 | 0.765 | 125722 | 0 | 25 | 125747 | 0.0000994 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.67 | 55 | 103 | 0.536 | 0.00000498 | 1179 |
| Missense in Polyphen | 8 | 31.818 | 0.25143 | 417 | ||
| Synonymous | 0.244 | 35 | 36.9 | 0.949 | 0.00000196 | 327 |
| Loss of Function | 1.10 | 8 | 12.1 | 0.659 | 5.13e-7 | 145 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000505 | 0.000503 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000218 | 0.000217 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.000218 | 0.000217 |
| South Asian | 0.000131 | 0.000131 |
| 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). Participates in pre-mRNA splicing. May play a role in the assembly of the U4/U5/U6 tri- snRNP complex, one of the building blocks of the spliceosome. May act as a chaperone. {ECO:0000269|PubMed:11823439, ECO:0000269|PubMed:12875835, ECO:0000269|PubMed:20676357, ECO:0000269|PubMed:9570313}.;
- Pathway
- Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.124
Intolerance Scores
- loftool
- 0.696
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.185
- hipred
- Y
- hipred_score
- 0.769
- ghis
- 0.686
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppih
- Phenotype
Zebrafish Information Network
- Gene name
- ppih
- Affected structure
- intersegmental vessel
- Phenotype tag
- abnormal
- Phenotype quality
- decreased functionality
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;protein peptidyl-prolyl isomerization;angiogenesis;protein folding;protein refolding;positive regulation of viral genome replication;protein-containing complex assembly
- Cellular component
- nucleoplasm;spliceosomal complex;cytoplasm;nuclear speck;U4/U6 x U5 tri-snRNP complex;U4/U6 snRNP
- Molecular function
- peptidyl-prolyl cis-trans isomerase activity;protein binding;cyclosporin A binding;ribonucleoprotein complex binding;unfolded protein binding