PPP1R16B
protein phosphatase 1 regulatory subunit 16B, the group of Protein phosphatase 1 regulatory subunits|Ankyrin repeat domain containing|Myosin phosphatase targeting family
Basic information
Region (hg38): 20:38805697-38923024
Links
Phenotypes
GenCC
Source:
No genCC data.
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 PPP1R16B 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 | 21 | 21 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 21 | 0 | 0 |
Variants in PPP1R16B
This is a list of pathogenic ClinVar variants found in the PPP1R16B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-38836111-G-C | not specified | Uncertain significance (Dec 21, 2023) | ||
| 20-38836136-G-A | not specified | Uncertain significance (Sep 22, 2021) | ||
| 20-38889618-G-A | not specified | Uncertain significance (Dec 27, 2022) | ||
| 20-38895676-G-A | not specified | Uncertain significance (May 24, 2023) | ||
| 20-38900585-G-A | not specified | Uncertain significance (Aug 21, 2023) | ||
| 20-38900588-G-A | not specified | Uncertain significance (Feb 02, 2022) | ||
| 20-38902694-A-G | not specified | Uncertain significance (Feb 05, 2024) | ||
| 20-38902770-T-C | not specified | Uncertain significance (Jan 02, 2024) | ||
| 20-38905987-A-G | not specified | Uncertain significance (May 30, 2023) | ||
| 20-38906032-C-T | not specified | Uncertain significance (Oct 16, 2023) | ||
| 20-38907051-A-G | not specified | Uncertain significance (Oct 05, 2023) | ||
| 20-38907833-T-C | not specified | Uncertain significance (Jan 22, 2024) | ||
| 20-38908098-A-C | not specified | Uncertain significance (Dec 17, 2023) | ||
| 20-38908171-C-T | not specified | Uncertain significance (Jul 14, 2021) | ||
| 20-38918225-C-G | not specified | Uncertain significance (Sep 16, 2021) | ||
| 20-38918326-T-C | not specified | Uncertain significance (Dec 04, 2023) | ||
| 20-38918422-G-A | not specified | Uncertain significance (Jan 18, 2022) | ||
| 20-38918488-C-T | not specified | Uncertain significance (Jan 10, 2023) | ||
| 20-38918572-A-G | not specified | Uncertain significance (Sep 23, 2023) | ||
| 20-38918575-C-T | not specified | Uncertain significance (Feb 27, 2024) | ||
| 20-38918629-T-C | not specified | Uncertain significance (Nov 17, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPP1R16B | protein_coding | protein_coding | ENST00000299824 | 10 | 117320 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000260 | 125475 | 0 | 1 | 125476 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.44 | 229 | 359 | 0.638 | 0.0000228 | 3698 |
| Missense in Polyphen | 66 | 142.42 | 0.46341 | 1495 | ||
| Synonymous | 1.93 | 123 | 153 | 0.802 | 0.0000105 | 1121 |
| Loss of Function | 4.73 | 1 | 28.0 | 0.0357 | 0.00000147 | 295 |
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 | 0.0000463 | 0.0000463 |
| 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: Regulator of protein phosphatase 1 (PP1) that acts as a positive regulator of pulmonary endothelial cell (EC) barrier function (PubMed:18586956). Involved in the regulation of the PI3K/AKT signaling pathway, angiogenesis and endothelial cell proliferation (PubMed:25007873). Regulates angiogenesis and endothelial cell proliferation through the control of ECE1 dephosphorylation, trafficking and activity (By similarity). Protects the endothelial barrier from lipopolysaccharide (LPS)- induced vascular leakage (By similarity). Involved in the regulation of endothelial cell filopodia extension (By similarity). May be a downstream target for TGF-beta1 signaling cascade in endothelial cells (PubMed:16263087, PubMed:18586956). Involved in PKA-mediated moesin dephosphorylation which is important in EC barrier protection against thrombin stimulation (PubMed:18586956). Promotes the interaction of PPP1CA with RPSA/LAMR1 and in turn facilitates the dephosphorylation of RPSA/LAMR1 (PubMed:16263087). Involved in the dephosphorylation of EEF1A1 (PubMed:26497934). {ECO:0000250|UniProtKB:Q8VHQ3, ECO:0000250|UniProtKB:Q95N27, ECO:0000269|PubMed:16263087, ECO:0000269|PubMed:18586956, ECO:0000269|PubMed:25007873, ECO:0000269|PubMed:26497934}.;
Intolerance Scores
- loftool
- rvis_EVS
- -0.38
- rvis_percentile_EVS
- 27.88
Haploinsufficiency Scores
- pHI
- 0.631
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.497
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.219
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppp1r16b
- Phenotype
- normal phenotype;
Gene ontology
- Biological process
- positive regulation of endothelial cell proliferation;regulation of phosphatidylinositol 3-kinase signaling;regulation of protein dephosphorylation;positive regulation of protein dephosphorylation;negative regulation of protein dephosphorylation;regulation of phosphoprotein phosphatase activity;regulation of filopodium assembly;establishment of endothelial barrier;negative regulation of peptidyl-serine dephosphorylation;positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis
- Cellular component
- nucleus;plasma membrane;nuclear speck;cell projection;perinuclear region of cytoplasm
- Molecular function
- protein binding;protein phosphatase regulator activity