PAN3
Basic information
Region (hg38): 13:28138506-28295335
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (78 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAN3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000175854.8. 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 | 0 | |||||
| missense | 76 | 77 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 77 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PAN3 | protein_coding | protein_coding | ENST00000380958 | 19 | 156833 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.00000741 | 125507 | 0 | 3 | 125510 | 0.0000120 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.52 | 285 | 432 | 0.659 | 0.0000214 | 5734 |
| Missense in Polyphen | 73 | 171.13 | 0.42657 | 2176 | ||
| Synonymous | 0.310 | 145 | 150 | 0.968 | 0.00000740 | 1783 |
| Loss of Function | 5.72 | 2 | 42.0 | 0.0477 | 0.00000243 | 507 |
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 | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000268 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Regulatory subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in general and miRNA-mediated mRNA turnover. PAN specifically shortens poly(A) tails of RNA and the activity is stimulated by poly(A)-binding protein (PABP). PAN deadenylation is followed by rapid degradation of the shortened mRNA tails by the CCR4-NOT complex. Deadenylated mRNAs are then degraded by two alternative mechanisms, namely exosome-mediated 3'-5' exonucleolytic degradation, or deadenlyation-dependent mRNA decaping and subsequent 5'-3' exonucleolytic degradation by XRN1. PAN3 acts as a positive regulator for PAN activity, recruiting the catalytic subunit PAN2 to mRNA via its interaction with RNA and PABP, and to miRNA targets via its interaction with GW182 family proteins. {ECO:0000255|HAMAP-Rule:MF_03181, ECO:0000269|PubMed:14583602, ECO:0000269|PubMed:23932717}.;
- Pathway
- RNA degradation - Homo sapiens (human);Metabolism of RNA;Deadenylation of mRNA;Deadenylation-dependent mRNA decay
(Consensus)
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- loftool
- rvis_EVS
- -0.49
- rvis_percentile_EVS
- 22.65
Haploinsufficiency Scores
- pHI
- 0.608
- hipred
- Y
- hipred_score
- 0.728
- ghis
- 0.581
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.831
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pan3
- Phenotype
Gene ontology
- Biological process
- nuclear-transcribed mRNA poly(A) tail shortening;deadenylation-dependent decapping of nuclear-transcribed mRNA;mRNA processing;protein phosphorylation;protein targeting;positive regulation of cytoplasmic mRNA processing body assembly;RNA phosphodiester bond hydrolysis, exonucleolytic
- Cellular component
- P-body;cytosol;PAN complex
- Molecular function
- RNA binding;poly(A)-specific ribonuclease activity;protein kinase activity;protein binding;ATP binding;metal ion binding