GAS2L3
protein-codinggrowth arrest specific 2 like 3
Gene summary
Enables actin binding activity and microtubule binding activity. Involved in actin cytoskeleton organization and microtubule cytoskeleton organization. Located in actin cytoskeleton and microtubule cytoskeleton. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~54.6 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 GAS2L3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_174942.3. 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 | 2 | 3 | |||
| missense | 84 | 8 | 3 | 95 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 86 | 9 | 5 | 100 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_777602.1 | 8 | MANE Select | |
| Ensembl | ENSP00000448955.1 | 8 | MANE Select | |
| RefSeq | NP_001290059.1 | 8 | Standard | |
| RefSeq | NP_001290060.1 | 5 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| gas2l3 | Danio rerio | Structure: ventricular system Quality: closed abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- microtubule cytoskeleton organization
- actin cytoskeleton organization
Molecular Function
- actin binding
- protein binding
- microtubule binding
Cellular Component
- cytoplasm
- microtubule
- actin cytoskeleton
- microtubule cytoskeleton
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000539410
- Coding exons
- 8
- Length
- 54604
- Individuals with no LoFs
- 125663
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 83
- Defined
- 125746
- p
- 0.000330
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.131 | 369 | 362 | 1.02 | 0.0000186 | 4438 |
| Missense (PolyPhen) | 85 | 86.696 | 0.98043 | 954 | ||
| Synonymous | -1.23 | 153 | 135 | 1.13 | 0.00000718 | 1416 |
| Loss of Function | 1.04 | 23 | 29.0 | 0.792 | 0.00000152 | 395 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00056 | 0.00055 | rare |
| Latino/Admixed American | 0.00024 | 0.00023 | rare |
| Ashkenazi Jewish | 0.00062 | 0.00060 | rare |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0.00019 | 0.00018 | rare |
| European (Non-Finnish) | 0.00039 | 0.00039 | rare |
| South Asian | 0.00016 | 0.00016 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Cytoskeletal linker protein. May promote and stabilize the formation of the actin and microtubule network. {ECO:0000269|PubMed:21561867}.;
Recessive Scores
- pRec
- 0.0897
Intolerance Scores
- RVIS EVS
- 0.89
- RVIS percentile EVS
- 89.27
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.338
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |