STYXL1
protein-codingserine/threonine/tyrosine interacting like 1, the group of MAP kinase phosphatases
Gene summary
Enables protein phosphatase binding activity and pseudophosphatase activity. Involved in negative regulation of stress granule assembly; positive regulation of intrinsic apoptotic signaling pathway; and positive regulation of neuron projection development. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]
- DUSP24
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~51.7 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 STYXL1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001317785.2. 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 | 3 | 3 | ||||
| missense | 52 | 6 | 1 | 59 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 61 | 6 | 1 | 68 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001304714.1 | 8 | MANE Select | |
| Ensembl | ENSP00000352726.3 | 8 | MANE Select | |
| RefSeq | NP_001304715.1 | 8 | Standard | |
| RefSeq | NP_001304716.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- protein dephosphorylation
- positive regulation of neuron projection development
- negative regulation of phosphoprotein phosphatase activity
- intracellular signal transduction
- negative regulation of stress granule assembly
Molecular Function
- pseudophosphatase activity
- protein phosphatase inhibitor activity
- protein binding
- protein tyrosine/serine/threonine phosphatase activity
- protein phosphatase binding
Cellular Component
- mitochondrion
- mitochondrial matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000248600
- Coding exons
- 8
- Length
- 51667
- Individuals with no LoFs
- 125703
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 45
- Defined
- 125748
- p
- 0.000179
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.604 | 162 | 185 | 0.875 | 0.0000104 | 2080 |
| Missense (PolyPhen) | 50 | 48.437 | 1.0323 | 574 | ||
| Synonymous | 0.588 | 64 | 70.3 | 0.911 | 0.00000400 | 580 |
| Loss of Function | 0.387 | 13 | 14.6 | 0.891 | 6.81e-7 | 180 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.00023 | 0.00023 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.00015 | 0.00015 | rare |
| South Asian | 0.00041 | 0.00039 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalytically inactive phosphatase (PubMed:20180778, PubMed:23163895). By binding to G3BP1, inhibits the formation of G3BP1-induced stress granules (PubMed:20180778, PubMed:23163895). Does not act by protecting the dephosphorylation of G3BP1 at 'Ser- 149' (PubMed:23163895). Inhibits PTPMT1 phosphatase activity (PubMed:24709986). By inhibiting PTPMT1, positively regulates intrinsic apoptosis (PubMed:21262771). May play a role in the formation of neurites during neuronal development (PubMed:29250526). {ECO:0000269|PubMed:20180778, ECO:0000269|PubMed:21262771, ECO:0000269|PubMed:23163895, ECO:0000269|PubMed:24709986, ECO:0000269|PubMed:29250526}.;
Recessive Scores
- pRec
- 0.0884
Intolerance Scores
- LoFtool
- 0.558
- RVIS EVS
- 0.04
- RVIS percentile EVS
- 57.15
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.638
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |