RIMS3
protein-codingregulating synaptic membrane exocytosis 3, the group of Regulating synaptic membrane exocytosis family
Gene summary
Predicted to enable transmembrane transporter binding activity. Predicted to be a structural constituent of presynaptic active zone. Predicted to be involved in several processes, including regulated exocytosis; regulation of synapse organization; and regulation of synaptic vesicle exocytosis. Predicted to be located in presynaptic active zone. Predicted to be active in several cellular components, including postsynaptic cytosol; presynaptic active zone cytoplasmic component; and presynaptic 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 ~45.0 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 RIMS3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014747.3. 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 | 5 | 2 | 7 | |||
| missense | 57 | 3 | 2 | 62 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 60 | 8 | 4 | 72 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055562.2 | 6 | MANE Select | |
| Ensembl | ENSP00000361769.3 | 6 | MANE Select | |
| Ensembl | ENSP00000361768.1 | 6 | Standard | |
| Ensembl | ENSP00000361768.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- calcium ion regulated exocytosis
- regulation of membrane potential
- regulation of synaptic plasticity
- calcium ion-regulated exocytosis of neurotransmitter
- positive regulation of synaptic transmission
Molecular Function
- Rab GTPase binding
- ion channel binding
Cellular Component
- cell junction
- presynaptic membrane
- synapse
- presynaptic active zone
- cytoskeleton of presynaptic active zone
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000372684
- Coding exons
- 6
- Length
- 44979
- Individuals with no LoFs
- 125738
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 10
- Defined
- 125748
- p
- 0.0000398
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.974 | 162 | 201 | 0.807 | 0.0000134 | 1980 |
| Missense (PolyPhen) | 60 | 82.412 | 0.72805 | 826 | ||
| Synonymous | 1.20 | 68 | 81.9 | 0.831 | 0.00000544 | 650 |
| Loss of Function | 1.41 | 8 | 13.6 | 0.587 | 7.70e-7 | 138 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000053 | 0.000053 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Regulates synaptic membrane exocytosis. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- LoFtool
- 0.512
- RVIS EVS
- 0.06
- RVIS percentile EVS
- 58.74
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.812
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |