STK39
serine/threonine kinase 39
Basic information
Region (hg38): 2:167954020-168247595
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (49 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the STK39 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000013233.3. 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 | 1 | |||||
| missense | 47 | 49 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 48 | 3 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| STK39 | protein_coding | protein_coding | ENST00000355999 | 18 | 294122 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000839 | 125123 | 0 | 10 | 125133 | 0.0000400 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.11 | 166 | 262 | 0.633 | 0.0000129 | 3542 |
| Missense in Polyphen | 25 | 86.989 | 0.28739 | 1104 | ||
| Synonymous | -0.0852 | 96 | 94.9 | 1.01 | 0.00000568 | 1022 |
| Loss of Function | 4.90 | 3 | 33.7 | 0.0890 | 0.00000178 | 416 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000646 | 0.0000644 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000557 | 0.0000546 |
| Finnish | 0.0000465 | 0.0000463 |
| European (Non-Finnish) | 0.0000532 | 0.0000529 |
| Middle Eastern | 0.0000557 | 0.0000546 |
| South Asian | 0.0000329 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May act as a mediator of stress-activated signals. Mediates the inhibition of SLC4A4, SLC26A6 as well as CFTR activities by the WNK scaffolds, probably through phosphorylation. Phosphorylates RELT. {ECO:0000250|UniProtKB:Q9Z1W9}.;
- Pathway
- Diuretics Pathway, Pharmacodynamics;TCR;TCR signaling in naïve CD4+ T cells
(Consensus)
Recessive Scores
- pRec
- 0.220
Intolerance Scores
- loftool
- 0.341
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.37
Haploinsufficiency Scores
- pHI
- 0.355
- hipred
- Y
- hipred_score
- 0.786
- ghis
- 0.533
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.832
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | High | Medium | High |
| Cancer | High | Medium | High |
Mouse Genome Informatics
- Gene name
- Stk39
- Phenotype
- reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); renal/urinary system phenotype; 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); muscle phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- activation of MAPK activity;protein phosphorylation;regulation of blood pressure;positive regulation of T cell chemotaxis;peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;signal transduction by protein phosphorylation;signal transduction by trans-phosphorylation;stress-activated protein kinase signaling cascade;activation of protein kinase activity;positive regulation of ion transmembrane transporter activity;intracellular signal transduction;maintenance of lens transparency;chemokine (C-X-C motif) ligand 12 signaling pathway;positive regulation of potassium ion transport;protein autophosphorylation;regulation of inflammatory response;ion homeostasis;cellular hypotonic response;negative regulation of pancreatic juice secretion;negative regulation of potassium ion transmembrane transporter activity;negative regulation of potassium ion transmembrane transport;negative regulation of creatine transmembrane transporter activity;cellular response to chemokine;negative regulation of sodium ion transmembrane transporter activity
- Cellular component
- nucleoplasm;cytoplasm;cytosol;cytoskeleton;basolateral plasma membrane;apical plasma membrane;extrinsic component of membrane;intracellular membrane-bounded organelle
- Molecular function
- protein serine/threonine kinase activity;protein binding;ATP binding;kinase activity;protein kinase binding