VRK3
VRK serine/threonine kinase 3
Basic information
Region (hg38): 19:49976468-50025946
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 VRK3 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 | 19 | 20 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 19 | 1 | 0 |
Variants in VRK3
This is a list of pathogenic ClinVar variants found in the VRK3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-49979116-A-G | not specified | Uncertain significance (May 14, 2024) | ||
| 19-49980985-C-T | not specified | Uncertain significance (Dec 27, 2023) | ||
| 19-49988411-C-T | not specified | Uncertain significance (Nov 02, 2023) | ||
| 19-49988444-T-C | not specified | Uncertain significance (Nov 09, 2023) | ||
| 19-49989714-C-A | not specified | Uncertain significance (Jan 10, 2023) | ||
| 19-49989726-C-T | not specified | Uncertain significance (Nov 17, 2022) | ||
| 19-49989740-C-T | not specified | Uncertain significance (Dec 18, 2023) | ||
| 19-49989753-C-A | not specified | Uncertain significance (Dec 19, 2023) | ||
| 19-49992888-A-G | not specified | Uncertain significance (Oct 03, 2022) | ||
| 19-49994870-C-T | not specified | Uncertain significance (May 09, 2023) | ||
| 19-49997524-C-T | not specified | Uncertain significance (Nov 06, 2023) | ||
| 19-49997545-T-C | not specified | Uncertain significance (Aug 31, 2022) | ||
| 19-50007694-T-C | not specified | Uncertain significance (Nov 10, 2022) | ||
| 19-50007706-G-A | not specified | Uncertain significance (Jun 16, 2024) | ||
| 19-50007718-G-A | not specified | Uncertain significance (Dec 17, 2023) | ||
| 19-50007729-G-T | not specified | Uncertain significance (Jun 11, 2024) | ||
| 19-50007754-C-A | not specified | Uncertain significance (Oct 26, 2021) | ||
| 19-50009254-A-G | not specified | Likely benign (Feb 21, 2024) | ||
| 19-50009361-C-T | not specified | Uncertain significance (Dec 19, 2023) | ||
| 19-50016039-C-T | not specified | Uncertain significance (Aug 01, 2022) | ||
| 19-50016048-T-C | not specified | Uncertain significance (Jun 06, 2023) | ||
| 19-50016098-C-T | not specified | Uncertain significance (Feb 22, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| VRK3 | protein_coding | protein_coding | ENST00000599538 | 12 | 49480 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 3.24e-11 | 0.489 | 125645 | 0 | 102 | 125747 | 0.000406 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.572 | 242 | 268 | 0.902 | 0.0000149 | 3082 |
| Missense in Polyphen | 92 | 107.42 | 0.85642 | 1211 | ||
| Synonymous | -0.243 | 112 | 109 | 1.03 | 0.00000630 | 915 |
| Loss of Function | 1.26 | 20 | 27.1 | 0.739 | 0.00000141 | 297 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000590 | 0.000589 |
| Ashkenazi Jewish | 0.00248 | 0.00248 |
| East Asian | 0.000217 | 0.000217 |
| Finnish | 0.0000926 | 0.0000924 |
| European (Non-Finnish) | 0.000423 | 0.000422 |
| Middle Eastern | 0.000217 | 0.000217 |
| South Asian | 0.000198 | 0.000196 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Inactive kinase that suppresses ERK activity by promoting phosphatase activity of DUSP3 which specifically dephosphorylates and inactivates ERK in the nucleus. {ECO:0000250, ECO:0000269|PubMed:14645249, ECO:0000269|PubMed:19141289}.;
- Pathway
- Toll Like Receptor 7/8 (TLR7/8) Cascade;Interleukin-17 signaling;Signal Transduction;Signaling by Interleukins;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;Toll-Like Receptors Cascades;Innate Immune System;Immune System;Nuclear Events (kinase and transcription factor activation);ERKs are inactivated;Signaling by NTRK1 (TRKA);Signaling by NTRKs;ERK/MAPK targets;MAPK targets/ Nuclear events mediated by MAP kinases;MAP kinase activation;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;MyD88 dependent cascade initiated on endosome;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;Signaling by Receptor Tyrosine Kinases;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade
(Consensus)
Recessive Scores
- pRec
- 0.0818
Intolerance Scores
- loftool
- 0.926
- rvis_EVS
- 0.89
- rvis_percentile_EVS
- 89.24
Haploinsufficiency Scores
- pHI
- 0.0731
- hipred
- N
- hipred_score
- 0.173
- ghis
- 0.396
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Vrk3
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Gene ontology
- Biological process
- peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;positive regulation of phosphoprotein phosphatase activity;negative regulation of ERK1 and ERK2 cascade
- Cellular component
- nucleus;nucleolus;cytoplasm;intracellular membrane-bounded organelle
- Molecular function
- protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding;protein phosphatase binding