SYNPO2L
protein-codingsynaptopodin 2 like, the group of PDZ domain containing
Gene summary
Predicted to enable actin binding activity. Predicted to be involved in several processes, including positive regulation of Rho protein signal transduction; positive regulation of stress fiber assembly; and sarcomere organization. Predicted to be located in cytoplasm and cytoskeleton. Predicted to be active in Z disc; actin cytoskeleton; and nucleus. [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 ~18.9 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 SYNPO2L variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001114133.3. 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 | 1 | ||||
| missense | 136 | 1 | 137 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 138 | 1 | 0 | 139 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001107605.1 | 4 | MANE Select | |
| Ensembl | ENSP00000378289.2 | 4 | MANE Select | |
| RefSeq | NP_079151.2 | 2 | Standard | |
| Ensembl | ENSP00000361964.4 | 2 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| synpo2lb | Danio rerio | Structure: post-vent region Quality: curved ventral abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- heart morphogenesis
- positive regulation of actin filament bundle assembly
- positive regulation of Rho protein signal transduction
- sarcomere organization
- positive regulation of stress fiber assembly
Molecular Function
- actin binding
Cellular Component
- nucleus
- nucleoplasm
- cytosol
- actin cytoskeleton
- nuclear speck
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000394810
- Coding exons
- 4
- Length
- 18923
- Individuals with no LoFs
- 125368
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 377
- Defined
- 125745
- p
- 0.00150
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.32 | 474 | 562 | 0.843 | 0.0000312 | 6097 |
| Missense (PolyPhen) | 201 | 255.63 | 0.78628 | 2738 | ||
| Synonymous | -0.0333 | 233 | 232 | 1.00 | 0.0000127 | 2303 |
| Loss of Function | 1.85 | 20 | 31.2 | 0.642 | 0.00000221 | 286 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00057 | 0.00055 | rare |
| Latino/Admixed American | 0.0024 | 0.0022 | notable |
| Ashkenazi Jewish | 0.0033 | 0.0029 | notable |
| East Asian | 0.0029 | 0.0029 | notable |
| Finnish | 0.00038 | 0.00032 | rare |
| European (Non-Finnish) | 0.0013 | 0.0012 | notable |
| South Asian | 0.0020 | 0.0018 | notable |
| Other | 0.0016 | 0.0015 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Actin-associated protein that may play a role in modulating actin-based shape. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0910
Intolerance Scores
- LoFtool
- 0.794
- RVIS EVS
- -0.49
- RVIS percentile EVS
- 22.7
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.218
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | Medium | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |