PUM2
pumilio RNA binding family member 2, the group of Pumilio homology domain containing
Basic information
Region (hg38): 2:20248691-20352234
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (97 variants)
- not_provided (1 variants)
- Autism_spectrum_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PUM2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015317.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 95 | 97 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 0 | 96 | 2 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PUM2 | protein_coding | protein_coding | ENST00000338086 | 20 | 103544 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.995 | 0.00508 | 125736 | 0 | 12 | 125748 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.59 | 408 | 584 | 0.699 | 0.0000301 | 6896 |
| Missense in Polyphen | 156 | 245.8 | 0.63467 | 2907 | ||
| Synonymous | -1.06 | 221 | 202 | 1.10 | 0.0000102 | 2142 |
| Loss of Function | 5.77 | 9 | 55.3 | 0.163 | 0.00000290 | 635 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000120 | 0.000120 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000631 | 0.0000615 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Sequence-specific RNA-binding protein that acts as a post-transcriptional repressor by binding the 3'-UTR of mRNA targets. Binds to an RNA consensus sequence, the Pumilio Response Element (PRE), 5'-UGUANAUA-3', that is related to the Nanos Response Element (NRE) (, PubMed:21397187). Mediates post- transcriptional repression of transcripts via different mechanisms: acts via direct recruitment of the CCR4-POP2-NOT deadenylase leading to translational inhibition and mRNA degradation (PubMed:22955276). Also mediates deadenylation- independent repression by promoting accessibility of miRNAs (PubMed:18776931, PubMed:22345517). Acts as a post-transcriptional repressor of E2F3 mRNAs by binding to its 3'-UTR and facilitating miRNA regulation (PubMed:22345517). Plays a role in cytoplasmic sensing of viral infection (PubMed:25340845). Represses a program of genes necessary to maintain genomic stability such as key mitotic, DNA repair and DNA replication factors. Its ability to repress those target mRNAs is regulated by the lncRNA NORAD (non- coding RNA activated by DNA damage) which, due to its high abundance and multitude of PUMILIO binding sites, is able to sequester a significant fraction of PUM1 and PUM2 in the cytoplasm (PubMed:26724866). May regulate DCUN1D3 mRNA levels (PubMed:25349211). May support proliferation and self-renewal of stem cells. Binds specifically to miRNA MIR199A precursor, with PUM1, regulates miRNA MIR199A expression at a postranscriptional level (PubMed:28431233). {ECO:0000269|PubMed:18776931, ECO:0000269|PubMed:21397187, ECO:0000269|PubMed:22345517, ECO:0000269|PubMed:22955276, ECO:0000269|PubMed:25340845, ECO:0000269|PubMed:25349211, ECO:0000269|PubMed:26724866, ECO:0000269|PubMed:28431233}.;
Recessive Scores
- pRec
- 0.0946
Intolerance Scores
- loftool
- 0.375
- rvis_EVS
- -0.84
- rvis_percentile_EVS
- 11.18
Haploinsufficiency Scores
- pHI
- 0.769
- hipred
- Y
- hipred_score
- 0.768
- ghis
- 0.683
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.800
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pum2
- Phenotype
- endocrine/exocrine gland phenotype; reproductive system phenotype;
Gene ontology
- Biological process
- regulation of translation;posttranscriptional regulation of gene expression;stress granule assembly;production of miRNAs involved in gene silencing by miRNA;regulation of mRNA stability;regulation of chromosome segregation;regulation of gene silencing by miRNA;positive regulation of RIG-I signaling pathway;positive regulation of gene silencing by miRNA
- Cellular component
- cytosol;cytoplasmic stress granule;nuclear membrane;perinuclear region of cytoplasm
- Molecular function
- RNA binding;mRNA 3'-UTR binding;protein binding;miRNA binding