INSYN2A
protein-codinginhibitory synaptic factor 2A
Gene summary
Predicted to be involved in inhibitory postsynaptic potential. Predicted to be active in GABA-ergic synapse and postsynaptic density. [provided by Alliance of Genome Resources, Jun 2026]
- C10orf141
- FAM196A
- INSYN2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~61.2 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 INSYN2A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001039762.3. 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 | 0 | |||||
| missense | 94 | 7 | 101 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 95 | 7 | 0 | 102 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001034851.1 | 3 | MANE Select | |
| Ensembl | ENSP00000429763.1 | 3 | MANE Select | |
| Ensembl | ENSP00000428730.1 | 2 | Standard | |
| Ensembl | ENSP00000428730.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- inhibitory postsynaptic potential
Cellular Component
- postsynaptic density
- cell junction
- postsynaptic membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000522781
- Coding exons
- 3
- Length
- 60729
- Individuals with no LoFs
- 125740
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 8
- Defined
- 125748
- p
- 0.0000318
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.121 | 308 | 302 | 1.02 | 0.0000196 | 3107 |
| Missense (PolyPhen) | 96 | 121.83 | 0.78796 | 1306 | ||
| Synonymous | 0.259 | 130 | 134 | 0.971 | 0.00000999 | 977 |
| Loss of Function | 3.34 | 2 | 16.7 | 0.120 | 8.15e-7 | 197 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000045 | 0.000044 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the protein machinery at the inhibitory synapses, probably acting as a scaffold. Inhibitory synapses dampen neuronal activity through postsynaptic hyperpolarization. This synaptic inhibition is fundamental for the functioning of the central nervous system, shaping and orchestrating the flow of information through neuronal networks to generate a precise neural code. {ECO:0000250|UniProtKB:Q3USH1}.;
Intolerance Scores
- RVIS EVS
- -0.22
- RVIS percentile EVS
- 37.6
Essentials
- Essential (gene trap)
- N