STON1-GTF2A1L
protein-codingSTON1-GTF2A1L readthrough
Gene summary
STON1-GTF2A1L mRNAs are infrequent but naturally occurring read-through products of the neighboring STON1 and GTF2A1L genes. These transcripts encode fusion proteins composed of the vast majority of each of the individual elements, stonin 1 and general transcription factor IIA, 1-like. Alternative splicing results in multiple transcript variants. The significance of these read-through variants and the function of the resulting protein products have not yet been determined. [provided by RefSeq, Oct 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~246.6 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 STON1-GTF2A1L variants in ClinVar
No annotated ClinVar phenotypes.
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript . 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 | 36 | 1 | 1 | 38 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 36 | 1 | 1 | 38 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001185522.1 | 10 | Standard | |
| RefSeq | NP_001185523.1 | 8 | Standard | |
| RefSeq | NP_758515.1 | 10 | Standard | |
| Ensembl | ENSP00000378234.3 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vesicle-mediated transport
- Membrane Trafficking
- Clathrin-mediated endocytosis
- Cargo recognition for clathrin-mediated endocytosis
Biological Process
- transcription by RNA polymerase II
- transcription initiation from RNA polymerase II promoter
- endocytosis
- regulation of endocytosis
Cellular Component
- transcription factor TFIIA complex
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000394754
- Coding exons
- 10
- Length
- 246591
- Individuals with no LoFs
- 124654
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 228
- Defined
- 124882
- p
- 0.000913
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -2.79 | 779 | 589 | 1.32 | 0.0000282 | 7732 |
| Missense (PolyPhen) | 298 | 241.07 | 1.2361 | 3293 | ||
| Synonymous | -2.44 | 262 | 216 | 1.21 | 0.0000109 | 2255 |
| Loss of Function | 1.03 | 38 | 45.5 | 0.835 | 0.00000225 | 594 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0012 | 0.0012 | notable |
| Latino/Admixed American | 0.00088 | 0.00078 | rare |
| Ashkenazi Jewish | 0.0020 | 0.0018 | notable |
| East Asian | 0.0023 | 0.0023 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00082 | 0.00080 | rare |
| South Asian | 0.00077 | 0.00075 | rare |
| Other | 0.0012 | 0.0011 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in the endocytic machinery. {ECO:0000250}.;
Intolerance Scores
- RVIS EVS
- 1.24
- RVIS percentile EVS
- 93.31
Essentials
- Essential (CRISPR)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.106
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | Medium | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |