STK33
protein-codingserine/threonine kinase 33
Gene summary
Enables protein serine/threonine kinase activity. Involved in negative regulation of protein metabolic process; peptidyl-threonine phosphorylation; and spermatogenesis. Predicted to be located in manchette. Predicted to be active in cytoplasm and nucleus. Implicated in colorectal cancer; depressive disorder; and spermatogenic failure 93. [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 ~202.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0971000
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Genitourinary
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to STK33 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001352389.2. 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 | 1 | 1 | ||||
| missense | 78 | 10 | 88 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 1 | 0 | 80 | 11 | 0 | 92 |
Highest pathogenic variant AF is 0.00000557625
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001339318.1 | 12 | MANE Select | |
| Ensembl | ENSP00000509322.1 | 12 | MANE Select | |
| RefSeq | NP_001275987.1 | 12 | Standard | |
| RefSeq | NP_001275988.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- signal transduction in response to DNA damage
- mitotic DNA damage checkpoint
- protein autophosphorylation
Molecular Function
- protein serine/threonine kinase activity
- ATP binding
Cellular Component
- nucleus
- cytoplasm
- perinuclear region of cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000447869
- Coding exons
- 12
- Length
- 202419
- Individuals with no LoFs
- 125708
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 39
- Defined
- 125747
- p
- 0.000155
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.490 | 233 | 255 | 0.914 | 0.0000123 | 3393 |
| Missense (PolyPhen) | 45 | 65.922 | 0.68262 | 897 | ||
| Synonymous | -1.18 | 104 | 89.8 | 1.16 | 0.00000484 | 900 |
| Loss of Function | 2.09 | 13 | 24.1 | 0.540 | 0.00000111 | 332 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00022 | 0.00020 | rare |
| Ashkenazi Jewish | 0.00011 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000095 | 0.000092 | rare |
| European (Non-Finnish) | 0.00018 | 0.00018 | rare |
| South Asian | 0.00036 | 0.00029 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Serine/threonine protein kinase which phosphorylates VIME. May play a specific role in the dynamic behavior of the intermediate filament cytoskeleton by phosphorylation of VIME (By similarity). Not essential for the survival of KRAS-dependent AML cell lines. {ECO:0000250, ECO:0000269|PubMed:21742770}.;
Recessive Scores
- pRec
- 0.0835
Intolerance Scores
- LoFtool
- 0.878
- RVIS EVS
- -0.07
- RVIS percentile EVS
- 48.69
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.616
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |