PPIG
Basic information
Region (hg38): 2:169584342-169641406
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 PPIG 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 | 4 | |||||
missense | 29 | 30 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 1 | |||||
Total | 0 | 0 | 29 | 1 | 5 |
Variants in PPIG
This is a list of pathogenic ClinVar variants found in the PPIG region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
2-169604247-G-A | not specified | Uncertain significance (Dec 28, 2023) | ||
2-169606064-T-A | Benign (Jul 17, 2018) | |||
2-169606081-A-G | not specified | Uncertain significance (Jan 23, 2024) | ||
2-169606088-T-A | not specified | Uncertain significance (Jan 09, 2024) | ||
2-169614707-T-C | not specified | Uncertain significance (Sep 06, 2022) | ||
2-169630791-A-C | not specified | Uncertain significance (Mar 21, 2023) | ||
2-169630819-C-G | not specified | Uncertain significance (Jun 06, 2023) | ||
2-169630919-A-G | Likely benign (Nov 01, 2022) | |||
2-169631806-C-T | not specified | Uncertain significance (Apr 24, 2023) | ||
2-169631944-A-G | Benign (Sep 14, 2018) | |||
2-169636123-G-A | not specified | Uncertain significance (Jul 27, 2022) | ||
2-169636198-C-T | not specified | Uncertain significance (Sep 12, 2023) | ||
2-169636421-T-G | not specified | Uncertain significance (May 01, 2024) | ||
2-169636543-C-G | not specified | Uncertain significance (May 03, 2023) | ||
2-169636565-G-A | not specified | Uncertain significance (Mar 21, 2023) | ||
2-169636743-A-G | Benign (May 17, 2018) | |||
2-169636879-C-T | not specified | Uncertain significance (Dec 11, 2023) | ||
2-169636882-G-A | not specified | Uncertain significance (May 07, 2024) | ||
2-169636927-A-G | not specified | Uncertain significance (Oct 04, 2022) | ||
2-169636928-G-A | not specified | Uncertain significance (Aug 08, 2022) | ||
2-169636996-C-T | not specified | Uncertain significance (Aug 02, 2021) | ||
2-169636997-A-G | not specified | Uncertain significance (Oct 20, 2023) | ||
2-169637008-C-T | not specified | Uncertain significance (Jul 19, 2023) | ||
2-169637030-A-G | not specified | Uncertain significance (Jun 27, 2022) | ||
2-169637036-A-C | not specified | Uncertain significance (Feb 28, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PPIG | protein_coding | protein_coding | ENST00000260970 | 12 | 57067 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.963 | 0.0371 | 125694 | 0 | 51 | 125745 | 0.000203 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.72 | 289 | 384 | 0.753 | 0.0000200 | 5026 |
Missense in Polyphen | 17 | 63.884 | 0.26611 | 776 | ||
Synonymous | -1.20 | 141 | 124 | 1.14 | 0.00000610 | 1252 |
Loss of Function | 4.93 | 7 | 41.1 | 0.170 | 0.00000259 | 533 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000751 | 0.000744 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000276 | 0.000272 |
Finnish | 0.0000939 | 0.0000924 |
European (Non-Finnish) | 0.000144 | 0.000141 |
Middle Eastern | 0.000276 | 0.000272 |
South Asian | 0.000207 | 0.000196 |
Other | 0.000171 | 0.000163 |
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). May be implicated in the folding, transport, and assembly of proteins. May play an important role in the regulation of pre-mRNA splicing. {ECO:0000269|PubMed:20676357}.;
- Pathway
- Methionine and cysteine metabolism
(Consensus)
Recessive Scores
- pRec
- 0.518
Intolerance Scores
- loftool
- 0.847
- rvis_EVS
- 0.02
- rvis_percentile_EVS
- 55.69
Haploinsufficiency Scores
- pHI
- 0.641
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.584
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.818
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | High | Medium | High |
Mouse Genome Informatics
- Gene name
- Ppig
- Phenotype
Gene ontology
- Biological process
- protein peptidyl-prolyl isomerization;RNA splicing;protein refolding
- Cellular component
- cytosol;nuclear matrix;nuclear speck
- Molecular function
- RNA binding;peptidyl-prolyl cis-trans isomerase activity;protein binding;cyclosporin A binding;unfolded protein binding