ARPP19
Basic information
Region (hg38): 15:52547045-52569883
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 ARPP19 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 | 1 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 1 | 0 | 0 |
Variants in ARPP19
This is a list of pathogenic ClinVar variants found in the ARPP19 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 15-52568853-G-C | not specified | Uncertain significance (Jul 07, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ARPP19 | protein_coding | protein_coding | ENST00000566423 | 3 | 22839 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.774 | 0.219 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.20 | 35 | 61.5 | 0.569 | 0.00000332 | 723 |
| Missense in Polyphen | 9 | 20.007 | 0.44985 | 268 | ||
| Synonymous | -1.30 | 31 | 23.1 | 1.34 | 0.00000138 | 210 |
| Loss of Function | 2.06 | 0 | 4.92 | 0.00 | 2.05e-7 | 70 |
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) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Protein phosphatase inhibitor that specifically inhibits protein phosphatase 2A (PP2A) during mitosis. When phosphorylated at Ser-62 during mitosis, specifically interacts with PPP2R2D (PR55-delta) and inhibits its activity, leading to inactivation of PP2A, an essential condition to keep cyclin-B1-CDK1 activity high during M phase. May indirectly enhance GAP-43 expression. {ECO:0000269|PubMed:21164014}.;
- Pathway
- MASTL Facilitates Mitotic Progression;Mitotic Prophase;M Phase;Cell Cycle;Cell Cycle, Mitotic
(Consensus)
Intolerance Scores
- loftool
- 0.209
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 52.85
Haploinsufficiency Scores
- pHI
- hipred
- N
- hipred_score
- 0.350
- ghis
- 0.668
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.942
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Arpp19
- Phenotype
Gene ontology
- Biological process
- G2/M transition of mitotic cell cycle;mitotic cell cycle;negative regulation of phosphoprotein phosphatase activity;negative regulation of protein dephosphorylation;positive regulation of gluconeogenesis;positive regulation of glucose import;cell division
- Cellular component
- nucleoplasm;cytoplasm
- Molecular function
- protein phosphatase inhibitor activity;signaling receptor binding;potassium channel regulator activity;phosphatase inhibitor activity;protein phosphatase regulator activity;protein phosphatase 2A binding