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
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.
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 | 12 | |||||
| missense | 22 | 24 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 22 | 9 | 5 |
Variants in SRPK2
This is a list of pathogenic ClinVar variants found in the SRPK2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-105110762-G-A | Likely benign (Oct 14, 2022) | |||
| 7-105110767-A-G | Likely benign (Dec 23, 2023) | |||
| 7-105110773-C-T | Inborn genetic diseases • KMT2E-related disorder | Likely benign (Jan 10, 2024) | ||
| 7-105110778-T-G | Inborn genetic diseases | Conflicting classifications of pathogenicity (Jun 04, 2024) | ||
| 7-105110795-C-A | Inborn genetic diseases | Uncertain significance (Mar 28, 2024) | ||
| 7-105110798-C-T | Inborn genetic diseases | Uncertain significance (Apr 27, 2022) | ||
| 7-105110804-C-T | Uncertain significance (May 16, 2023) | |||
| 7-105110805-G-A | Likely benign (Aug 17, 2023) | |||
| 7-105110809-G-C | Uncertain significance (Jan 18, 2024) | |||
| 7-105110840-C-G | not specified | Conflicting classifications of pathogenicity (Mar 29, 2024) | ||
| 7-105110840-C-T | Benign (Dec 31, 2023) | |||
| 7-105110844-TAAAAGTCCTCCAAAAATGAG-CTCATTTTTGGAGGACTTTTA | Uncertain significance (Nov 03, 2023) | |||
| 7-105110859-A-G | Likely benign (May 22, 2023) | |||
| 7-105110862-G-A | Uncertain significance (Apr 23, 2023) | |||
| 7-105110863-A-G | Benign (Mar 02, 2023) | |||
| 7-105110867-A-C | Inborn genetic diseases | Uncertain significance (May 01, 2022) | ||
| 7-105110868-G-C | O'Donnell-Luria-Rodan syndrome | Likely pathogenic (Sep 02, 2023) | ||
| 7-105110873-T-C | Uncertain significance (Sep 24, 2023) | |||
| 7-105110877-A-G | Likely benign (May 23, 2023) | |||
| 7-105110881-A-C | Likely benign (Apr 20, 2023) | |||
| 7-105110887-C-T | Likely benign (Nov 27, 2023) | |||
| 7-105110888-G-A | Benign (Jan 25, 2024) | |||
| 7-105111800-TATATA-T | Likely benign (Oct 06, 2023) | |||
| 7-105111820-C-T | Likely benign (Aug 28, 2023) | |||
| 7-105111832-C-T | Uncertain significance (Dec 10, 2020) |
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