STK39
protein-codingserine/threonine kinase 39
Gene summary
This gene encodes a serine/threonine kinase that is thought to function in the cellular stress response pathway. The kinase is activated in response to hypotonic stress, leading to phosphorylation of several cation-chloride-coupled cotransporters. The catalytically active kinase specifically activates the p38 MAP kinase pathway, and its interaction with p38 decreases upon cellular stress, suggesting that this kinase may serve as an intermediate in the response to cellular stress. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~293.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to STK39 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_013233.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 53 | 2 | 55 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 58 | 3 | 0 | 61 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_037365.2 | 18 | MANE Select | |
| Ensembl | ENSP00000348278.4 | 18 | MANE Select | |
| RefSeq | NP_001397890.1 | 17 | Standard | |
| Ensembl | ENSP00000513185.1 | 17 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Diuretics Pathway, Pharmacodynamics
- TCR
- TCR signaling in naï
- ve CD4+ T cells
Biological Process
- activation of MAPK activity
- protein phosphorylation
- regulation of blood pressure
- positive regulation of T cell chemotaxis
- peptidyl-serine phosphorylation
Molecular Function
- protein serine/threonine kinase activity
- protein binding
- ATP binding
- kinase activity
- protein kinase binding
Cellular Component
- nucleoplasm
- cytoplasm
- cytosol
- cytoskeleton
- basolateral plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000355999
- Coding exons
- 18
- Length
- 294122
- Individuals with no LoFs
- 125123
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 10
- Defined
- 125133
- p
- 0.0000400
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.11 | 166 | 262 | 0.633 | 0.0000129 | 3542 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000064 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000055 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000053 | 0.000053 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
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}.;
Recessive Scores
- pRec
- 0.220
Intolerance Scores
- LoFtool
- 0.341
- RVIS EVS
- -0.34
- RVIS percentile EVS
- 30.37
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.832
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | High | Medium | High |
| Cancer | High | Medium | High |