SRPK2
SRSF protein kinase 2
Basic information
Region (hg38): 7:105110704-105399308
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (59 variants)
- not_provided (10 variants)
- SRPK2-related_disorder (7 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRPK2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000182692.3. 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 | 13 | |||||
| missense | 54 | 58 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 54 | 12 | 5 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SRPK2 | protein_coding | protein_coding | ENST00000393651 | 16 | 288605 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.997 | 0.00303 | 125738 | 0 | 5 | 125743 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.81 | 231 | 386 | 0.598 | 0.0000207 | 4601 |
| Missense in Polyphen | 74 | 174.34 | 0.42445 | 2171 | ||
| Synonymous | 0.107 | 146 | 148 | 0.989 | 0.00000877 | 1282 |
| Loss of Function | 5.05 | 5 | 39.1 | 0.128 | 0.00000206 | 479 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000463 | 0.0000462 |
| European (Non-Finnish) | 0.0000267 | 0.0000264 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Serine/arginine-rich protein-specific kinase which specifically phosphorylates its substrates at serine residues located in regions rich in arginine/serine dipeptides, known as RS domains and is involved in the phosphorylation of SR splicing factors and the regulation of splicing. Promotes neuronal apoptosis by up-regulating cyclin-D1 (CCND1) expression. This is done by the phosphorylation of SRSF2, leading to the suppression of p53/TP53 phosphorylation thereby relieving the repressive effect of p53/TP53 on cyclin-D1 (CCND1) expression. Phosphorylates ACIN1, and redistributes it from the nuclear speckles to the nucleoplasm, resulting in cyclin A1 but not cyclin A2 up- regulation. Plays an essential role in spliceosomal B complex formation via the phosphorylation of DDX23/PRP28. Can mediate hepatitis B virus (HBV) core protein phosphorylation. Plays a negative role in the regulation of HBV replication through a mechanism not involving the phosphorylation of the core protein but by reducing the packaging efficiency of the pregenomic RNA (pgRNA) without affecting the formation of the viral core particles. {ECO:0000269|PubMed:12134018, ECO:0000269|PubMed:16122776, ECO:0000269|PubMed:18425142, ECO:0000269|PubMed:18559500, ECO:0000269|PubMed:19592491, ECO:0000269|PubMed:21056976, ECO:0000269|PubMed:21157427, ECO:0000269|PubMed:9472028}.;
- Pathway
- mRNA Processing
(Consensus)
Recessive Scores
- pRec
- 0.124
Intolerance Scores
- loftool
- 0.475
- rvis_EVS
- -1.22
- rvis_percentile_EVS
- 5.57
Haploinsufficiency Scores
- pHI
- 0.763
- hipred
- Y
- hipred_score
- 0.701
- ghis
- 0.667
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.973
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Srpk2
- 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; hematopoietic system phenotype; immune system phenotype;
Gene ontology
- Biological process
- spliceosomal complex assembly;angiogenesis;protein phosphorylation;positive regulation of cell population proliferation;RNA splicing;regulation of gene expression;positive regulation of gene expression;cell differentiation;nuclear speck organization;intracellular signal transduction;positive regulation of neuron apoptotic process;positive regulation of viral genome replication;negative regulation of viral genome replication;innate immune response;positive regulation of cell cycle;regulation of mRNA splicing, via spliceosome;regulation of mRNA processing
- Cellular component
- nucleus;nucleoplasm;nucleolus;cytoplasm;cytosol
- Molecular function
- magnesium ion binding;RNA binding;protein serine/threonine kinase activity;protein binding;ATP binding;14-3-3 protein binding