SYPL2
protein-codingsynaptophysin like 2, the group of Synaptophysins|MARVEL domain containing
Gene summary
Involved in substantia nigra development. Predicted to be located in membrane and synaptic vesicle. Predicted to be active in synaptic vesicle membrane. [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 ~15.6 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 SYPL2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001040709.2. 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 | 35 | 35 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 35 | 1 | 0 | 36 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001035799.1 | 6 | MANE Select | |
| Ensembl | ENSP00000358888.3 | 6 | MANE Select | |
| Ensembl | ENSP00000550216.1 | 5 | Standard | |
| Ensembl | ENSP00000550216.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cellular calcium ion homeostasis
- substantia nigra development
Cellular Component
- synaptic vesicle
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000369872
- Coding exons
- 6
- Length
- 15580
- Individuals with no LoFs
- 124772
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 29
- Defined
- 124801
- p
- 0.000116
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.398 | 148 | 162 | 0.912 | 0.00000908 | 1779 |
| Missense (PolyPhen) | 67 | 69.156 | 0.96882 | 729 | ||
| Synonymous | -0.164 | 69 | 67.3 | 1.03 | 0.00000419 | 532 |
| Loss of Function | 1.04 | 9 | 13.1 | 0.689 | 6.32e-7 | 136 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00013 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00061 | 0.00061 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000080 | 0.000079 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in communication between the T-tubular and junctional sarcoplasmic reticulum (SR) membranes. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- LoFtool
- 0.546
- RVIS EVS
- 0.93
- RVIS percentile EVS
- 89.7
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.141
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |