PCBP2
Basic information
Region (hg38): 12:53452101-53481162
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 PCBP2 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 | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 0 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PCBP2 | protein_coding | protein_coding | ENST00000359462 | 14 | 39422 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.996 | 0.00383 | 125730 | 0 | 1 | 125731 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 4.13 | 50 | 224 | 0.223 | 0.0000127 | 2399 |
| Missense in Polyphen | 8 | 48.243 | 0.16583 | 648 | ||
| Synonymous | -0.134 | 85 | 83.4 | 1.02 | 0.00000538 | 734 |
| Loss of Function | 4.03 | 1 | 20.8 | 0.0480 | 8.84e-7 | 251 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| 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: Single-stranded nucleic acid binding protein that binds preferentially to oligo dC. Major cellular poly(rC)-binding protein. Binds also poly(rU). Negatively regulates cellular antiviral responses mediated by MAVS signaling (PubMed:19881509). It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation (PubMed:19881509). {ECO:0000269|PubMed:12414943, ECO:0000269|PubMed:19881509}.;
- Pathway
- Ferroptosis - Homo sapiens (human);mRNA Processing;DDX58/IFIH1-mediated induction of interferon-alpha/beta;Metabolism of RNA;Innate Immune System;Immune System;mRNA Splicing - Major Pathway;Negative regulators of DDX58/IFIH1 signaling;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Intolerance Scores
- loftool
- 0.220
- rvis_EVS
- -0.19
- rvis_percentile_EVS
- 39.68
Haploinsufficiency Scores
- pHI
- 0.331
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.650
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.985
Mouse Genome Informatics
- Gene name
- Pcbp2
- Phenotype
- 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); hematopoietic system phenotype; 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); normal phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;RNA metabolic process;mRNA metabolic process;negative regulation of type I interferon production;viral RNA genome replication;proteasome-mediated ubiquitin-dependent protein catabolic process;innate immune response;negative regulation of defense response to virus;defense response to virus;IRES-dependent viral translational initiation
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol;focal adhesion;membrane;extracellular exosome
- Molecular function
- DNA binding;RNA binding;protein binding;enzyme binding;ubiquitin protein ligase binding