STK16
protein-codingserine/threonine kinase 16
Gene summary
Predicted to enable protein serine/threonine kinase activity. Involved in protein autophosphorylation. Located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~4.9 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 STK16 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001330213.2. 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 | 0 | |||||
| missense | 49 | 1 | 50 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 53 | 1 | 0 | 54 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001317142.1 | 7 | MANE Select | |
| Ensembl | ENSP00000379964.2 | 7 | MANE Select | |
| RefSeq | NP_001008910.1 | 7 | Standard | |
| RefSeq | NP_001317143.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- peptidyl-tyrosine phosphorylation
- positive regulation of transcription by RNA polymerase II
- protein autophosphorylation
- cellular response to transforming growth factor beta stimulus
Molecular Function
- protein serine/threonine kinase activity
- non-membrane spanning protein tyrosine kinase activity
- protein binding
- ATP binding
Cellular Component
- Golgi-associated vesicle
- cytosol
- membrane
- perinuclear region of cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000409638
- Coding exons
- 7
- Length
- 4883
- Individuals with no LoFs
- 124752
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 52
- Defined
- 124804
- p
- 0.000208
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.02 | 147 | 186 | 0.789 | 0.0000108 | 1990 |
| Missense (PolyPhen) | 44 | 66.541 | 0.66125 | 715 | ||
| Synonymous | 2.02 | 53 | 75.3 | 0.704 | 0.00000437 | 603 |
| Loss of Function | 1.83 | 9 | 17.2 | 0.524 | 9.83e-7 | 169 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00032 | 0.00032 | rare |
| Latino/Admixed American | 0.00032 | 0.00032 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00019 | 0.00019 | rare |
| South Asian | 0.00023 | 0.00023 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Membrane-associated protein kinase that phosphorylates on serine and threonine residues. In vitro substrates include DRG1, ENO1 and EIF4EBP1. Also autophosphorylates. May be involved in secretory vesicle trafficking or intracellular signaling. May have a role in regulating stromal-epithelial interactions that occur during ductal morphogenesis in the mammary gland. May be involved in TGF-beta signaling. Able to autophosphorylate on Tyr residue; it is however unclear whether it has tyrosine-protein kinase toward other proteins. {ECO:0000269|PubMed:10364453}.;
Recessive Scores
- pRec
- 0.133
Intolerance Scores
- LoFtool
- 0.714
- RVIS EVS
- -0.29
- RVIS percentile EVS
- 33.2
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.992
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |