PAIP2
Basic information
Region (hg38): 5:139341587-139369720
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 PAIP2 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in PAIP2
This is a list of pathogenic ClinVar variants found in the PAIP2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-139363810-C-T | not specified | Uncertain significance (Sep 28, 2022) | ||
| 5-139363828-A-G | not specified | Uncertain significance (Nov 03, 2023) | ||
| 5-139363853-T-G | not specified | Uncertain significance (Mar 01, 2023) | ||
| 5-139363864-A-T | not specified | Uncertain significance (Apr 07, 2022) | ||
| 5-139364564-A-G | not specified | Uncertain significance (May 09, 2024) | ||
| 5-139364603-T-C | not specified | Uncertain significance (Aug 09, 2021) | ||
| 5-139368787-G-A | not specified | Uncertain significance (Dec 03, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PAIP2 | protein_coding | protein_coding | ENST00000394795 | 3 | 28131 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.554 | 0.434 | 125444 | 0 | 1 | 125445 | 0.00000399 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.40 | 37 | 69.9 | 0.529 | 0.00000354 | 882 |
| Missense in Polyphen | 4 | 9.4401 | 0.42372 | 119 | ||
| Synonymous | 0.219 | 20 | 21.3 | 0.940 | 0.00000112 | 193 |
| Loss of Function | 2.02 | 1 | 6.61 | 0.151 | 3.48e-7 | 69 |
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 | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as a repressor in the regulation of translation initiation of poly(A)-containing mRNAs. Its inhibitory activity on translation is mediated via its action on PABPC1. Displaces the interaction of PABPC1 with poly(A) RNA and competes with PAIP1 for binding to PABPC1. Its association with PABPC1 results in disruption of the cytoplasmic poly(A) RNP structure organization. {ECO:0000269|PubMed:11172725}.;
Intolerance Scores
- loftool
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.25
Haploinsufficiency Scores
- pHI
- 0.545
- hipred
- Y
- hipred_score
- 0.802
- ghis
- 0.598
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.731
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Paip2
- Phenotype
- growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; reproductive system phenotype;
Gene ontology
- Biological process
- spermatogenesis;memory;negative regulation of translational initiation;regulation of long-term synaptic potentiation
- Cellular component
- cytoplasm
- Molecular function
- mRNA binding;protein binding;translation repressor activity