SHISA7
protein-codingshisa family member 7, the group of Shisa family members
Gene summary
Predicted to enable GABA receptor binding activity and ionotropic glutamate receptor binding activity. Predicted to be involved in several processes, including gamma-aminobutyric acid receptor clustering; positive regulation of long-term synaptic potentiation; and regulation of GABA-A receptor activity. Predicted to be located in asymmetric, glutamatergic, excitatory synapse. Predicted to be active in glutamatergic synapse; postsynaptic density; and synaptic membrane. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~14.6 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 SHISA7 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001145176.2. 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 | 0 | |||||
| missense | 58 | 4 | 62 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 58 | 4 | 0 | 62 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001138648.1 | 4 | MANE Select | |
| Ensembl | ENSP00000365503.3 | 4 | MANE Select | |
| Ensembl | ENSP00000401307.2 | 5 | Standard | |
| Ensembl | ENSP00000401307.2 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- memory
- regulation of short-term neuronal synaptic plasticity
- regulation of postsynaptic neurotransmitter receptor activity
- positive regulation of long-term synaptic potentiation
- regulation of AMPA glutamate receptor clustering
Molecular Function
- ionotropic glutamate receptor binding
Cellular Component
- postsynaptic density
- cell junction
- AMPA glutamate receptor complex
- dendritic spine membrane
- synapse
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000376325
- Coding exons
- 4
- Length
- 14124
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.74 | 80 | 137 | 0.582 | 0.00000809 | 3316 |
| Missense (PolyPhen) | 21 | 36.671 | 0.57265 | 795 | ||
| Synonymous | 0.654 | 60 | 66.8 | 0.898 | 0.00000406 | 1286 |
| Loss of Function | 2.33 | 0 | 6.31 | 0.00 | 2.74e-7 | 135 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| 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 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Regulator of long-term synaptic potentiation specifically involved in the formation and retrieval of hippocampus-dependent contextual fear memory. Probably regulates induction and maintenance of long-term potentiation at Schaffer collaterals/CA3-CA1 excitatory synapses by affecting the recruitment of AMPA-type glutamate receptor (AMPAR) at postsynaptic density. {ECO:0000250|UniProtKB:Q8C3Q5}.;
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.283
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |