IGSF9B
protein-codingimmunoglobulin superfamily member 9B, the group of V-set domain containing|Fibronectin type III domain containing|I-set domain containing
Gene summary
Predicted to enable kinase binding activity. Predicted to be involved in synaptic membrane adhesion. Predicted to act upstream of or within homophilic cell-cell adhesion and positive regulation of inhibitory postsynaptic potential. Predicted to be located in dendrite; inhibitory synapse; and neuronal cell body. Predicted to be active in GABA-ergic synapse; neuron projection; and postsynaptic specialization of symmetric synapse. [provided by Alliance of Genome Resources, Jun 2026]
- MIR4697HG
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~60.5 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 IGSF9B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001277285.4. 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 | 4 | 6 | 1 | 11 | ||
| missense | 6 | 1 | 1 | 8 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 15 | 7 | 2 | 24 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001264214.1 | 20 | MANE Select | |
| Ensembl | ENSP00000436552.2 | 20 | MANE Select | |
| Ensembl | ENSP00000317980.8 | 19 | Standard | |
| Ensembl | ENSP00000435989.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vitamin D Receptor Pathway
Biological Process
- homophilic cell adhesion via plasma membrane adhesion molecules
- nervous system development
- positive regulation of inhibitory postsynaptic potential
- synaptic membrane adhesion
Molecular Function
- kinase binding
Cellular Component
- postsynaptic density
- integral component of membrane
- cell junction
- dendrite
- neuronal cell body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000533871
- Coding exons
- 20
- Length
- 48422
- Individuals with no LoFs
- 124630
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 21
- Defined
- 124651
- p
- 0.0000842
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.58 | 690 | 909 | 0.759 | 0.0000608 | 9111 |
| Missense (PolyPhen) | 235 | 361.47 | 0.65013 | 3614 | ||
| Synonymous | -0.171 | 405 | 401 | 1.01 | 0.0000293 | 3064 |
| Loss of Function | 5.90 | 13 | 63.9 | 0.204 | 0.00000365 | 660 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00027 | 0.00026 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0.000053 | 0.000046 | rare |
| European (Non-Finnish) | 0.000084 | 0.000080 | rare |
| South Asian | 0.000075 | 0.000065 | rare |
| Other | 0.00019 | 0.00017 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transmembrane protein which is abundantly expressed in interneurons, where it may regulate inhibitory synapse development. May mediate homophilic cell adhesion. {ECO:0000250|UniProtKB:D3ZB51, ECO:0000250|UniProtKB:E9PZ19}.;
Essentials
- Essential (CRISPR2)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.154
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |