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10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
KIRREL3
kirre like nephrin family adhesion molecule 3
Chromosome 11 Β· 11q24.2
NCBI Gene: 84623Ensembl: ENSG00000149571.12HGNC: HGNC:23204UniProt: E9PRX9
25PubMed Papers
20Diseases
0Drugs
3Pathogenic Variants
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingsynaptic vesiclehomophilic cell-cell adhesionsynapse assemblyintellectual disability, autosomal dominant 4alcohol drinkingautosomal dominant non-syndromic intellectual disabilitymajor depressive disorder
✦AI Summary

KIRREL3 is a synaptic cell adhesion molecule of the immunoglobulin superfamily that plays critical roles in synapse formation and axonal targeting during neurodevelopment. The protein functions as a homophilic adhesion molecule, with crystal structure studies demonstrating that KIRREL3 forms homodimers through its N-terminal immunoglobulin domains, which is essential for proper axonal coalescence 1. In the hippocampus, KIRREL3 is required for formation of target-specific mossy fiber synapses and mossy fiber filopodia connecting dentate granule and GABA neurons 2. The protein is also crucial for coalescence of vomeronasal sensory neuron axons into glomeruli, with dimerization being necessary for proper glomerular formation 1. KIRREL3 shows extensive expression throughout the adult mouse brain, including hippocampus, cerebral cortex, olfactory bulb, amygdala, thalamus, and cerebellum, exclusively in neurons 2. The gene undergoes complex alternative splicing, generating multiple isoforms including both transmembrane and secreted forms, with splicing patterns varying between mouse and human 3. KIRREL3 interacts with key neuronal proteins including MAP1B and MYO16, which are involved in synaptogenesis and actin cytoskeleton development 4. Clinically, KIRREL3 variants have been implicated in autism spectrum disorder, intellectual disability, and Jacobsen syndrome, though its status as a definitive disease gene requires further validation 5.

Sources cited
1
KIRREL3 forms homodimers through N-terminal immunoglobulin domains essential for axonal coalescence and glomerular formation
PMID: 34731636
2
KIRREL3 is required for hippocampal mossy fiber synapse formation and is expressed exclusively in neurons throughout adult mouse brain
PMID: 34062388
3
KIRREL3 undergoes alternative splicing generating transmembrane and secreted isoforms
PMID: 37977826
4
KIRREL3 interacts with neuronal proteins MAP1B and MYO16 involved in synaptogenesis and actin cytoskeleton
PMID: 25902260
5
KIRREL3 variants are implicated in autism spectrum disorder, intellectual disability, and Jacobsen syndrome
PMID: 41059509
Disease Associationsβ“˜20
intellectual disability, autosomal dominant 4Open Targets
0.54Moderate
alcohol drinkingOpen Targets
0.41Moderate
autosomal dominant non-syndromic intellectual disabilityOpen Targets
0.37Weak
major depressive disorderOpen Targets
0.37Weak
autism spectrum disorderOpen Targets
0.36Weak
mathematical abilityOpen Targets
0.33Weak
KeloidOpen Targets
0.32Weak
adolescent idiopathic scoliosisOpen Targets
0.31Weak
neurotic disorderOpen Targets
0.31Weak
response to paracetamolOpen Targets
0.30Weak
risk-taking behaviourOpen Targets
0.27Weak
mood disorderOpen Targets
0.27Weak
pericarditisOpen Targets
0.27Weak
sialadenitisOpen Targets
0.27Weak
substance-related disorderOpen Targets
0.26Weak
cardiac arrestOpen Targets
0.25Weak
smoking initiationOpen Targets
0.25Weak
ProteinuriaOpen Targets
0.25Weak
male infertilityOpen Targets
0.23Weak
spermatoceleOpen Targets
0.23Weak
Pathogenic Variants3
NM_032531.4(KIRREL3):c.997+1G>ALikely pathogenic
not provided
β˜…β˜†β˜†β˜†2016
NM_032531.4(KIRREL3):c.2019G>A (p.Met673Ile)Likely pathogenic
Intellectual disability, autosomal dominant 4
β˜…β˜†β˜†β˜†2015β†’ Residue 673
NM_032531.4(KIRREL3):c.941G>T (p.Cys314Phe)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†β†’ Residue 314
View on ClinVar β†—
Related Genes
NPHS1Protein interaction84%CD2APProtein interaction84%CDH15Protein interaction77%PDZK1Protein interaction77%NPHS2Protein interaction77%KIRREL1Protein interaction77%
Tissue Expression6 tissues
Brain
100%
Heart
5%
Bone Marrow
5%
Ovary
4%
Liver
1%
Lung
1%
Gene Interaction Network
Click a node to explore
KIRREL3NPHS1CD2APCDH15PDZK1NPHS2KIRREL1
PROTEIN STRUCTURE
Preparing viewer…
PDB2CRY Β· NMR
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.68LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.51 [0.39–0.68]
RankingsWhere KIRREL3 stands among ~20K protein-coding genes
  • #13,005of 20,598
    Most Researched25
  • #4,138of 5,498
    Most Pathogenic Variants3
  • #5,009of 17,882
    Most Constrained (LOEUF)0.68
Genes detectedKIRREL3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Comprehensive expression pattern of kin of irregular chiasm-like 3 in the adult mouse brain.
PMID: 34062388
Biochem Biophys Res Commun Β· 2021
1.00
2
Identification of novel Kirrel3 gene splice variants in adult human skeletal muscle.
PMID: 25488023
BMC Physiol Β· 2014
0.90
3
Evaluation of the synapse adhesion molecule Kirrel3 in neurological disease.
PMID: 41059509
Front Neurol Β· 2025
0.80
4
Autism and Intellectual Disability-Associated KIRREL3 Interacts with Neuronal Proteins MAP1B and MYO16 with Potential Roles in Neurodevelopment.
PMID: 25902260
PLoS One Β· 2015
0.70
5
Modular Splicing Is Linked to Evolution in the Synapse-Specificity Molecule Kirrel3.
PMID: 37977826
eNeuro Β· 2023
0.60