LRRC4B
protein-codingleucine rich repeat containing 4B, the group of I-set domain containing|Ig-like cell adhesion molecule family|Receptor ligands
Gene summary
Predicted to enable cell-cell adhesion mediator activity. Predicted to be involved in regulation of synapse assembly and synaptic membrane adhesion. Predicted to be located in cerebellar mossy fiber and presynaptic membrane. Predicted to be active in glutamatergic synapse and postsynaptic density membrane. [provided by Alliance of Genome Resources, Jun 2026]
- LRIG4
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~51.5 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 LRRC4B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001080457.2. 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 | 2 | 2 | ||||
| missense | 71 | 1 | 72 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 71 | 3 | 0 | 74 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001073926.1 | 2 | MANE Select | |
| Ensembl | ENSP00000498662.1 | 2 | MANE Select | |
| RefSeq | NP_001335497.1 | 2 | Standard | |
| Ensembl | ENSP00000373853.3 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cell adhesion molecules (CAMs) - Homo sapiens (human)
- Neuronal System
- Receptor-type tyrosine-protein phosphatases
- Protein-protein interactions at synapses
Biological Process
- positive regulation of synapse assembly
- regulation of postsynaptic density assembly
- synaptic membrane adhesion
- regulation of presynapse assembly
Molecular Function
- signaling receptor binding
Cellular Component
- plasma membrane
- cell junction
- presynaptic membrane
- cerebellar mossy fiber
- glutamatergic synapse
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000599957
- Coding exons
- 2
- Length
- 51154
- Individuals with no LoFs
- 117707
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 117709
- p
- 0.00000850
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 4.36 | 222 | 495 | 0.448 | 0.0000374 | 4517 |
| Missense (PolyPhen) | 20 | 137.81 | 0.14512 | 1337 | ||
| Synonymous | 1.50 | 221 | 251 | 0.880 | 0.0000220 | 1578 |
| Loss of Function | 3.22 | 2 | 15.8 | 0.127 | 7.45e-7 | 167 |
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) | 0.000021 | 0.000019 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Synaptic adhesion protein. Regulates the formation of excitatory synapses. The trans-synaptic adhesion between LRRC4B and PTPRF regulates the formation of excitatory synapses in a bidirectional manner (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- LoFtool
- 0.0528
- RVIS EVS
- -0.38
- RVIS percentile EVS
- 27.69
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.210
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |