LRRC15
protein-codingleucine rich repeat containing 15
Gene summary
Enables several functions, including fibronectin binding activity; laminin binding activity; and protein sequestering activity. Involved in several processes, including host-mediated suppression of symbiont invasion; negative regulation of protein localization to plasma membrane; and receptor-mediated virion attachment to host cell. Located in plasma membrane. Is active in apical plasma 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 ~14.5 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 LRRC15 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_130830.5. 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 | 1 | 1 | 2 | |||
| missense | 122 | 2 | 1 | 125 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 122 | 3 | 2 | 127 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_570843.2 | 1 | MANE Select | |
| Ensembl | ENSP00000306276.4 | 1 | MANE Select | |
| RefSeq | NP_001128529.2 | 2 | Standard | |
| Ensembl | ENSP00000413707.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- positive regulation of cell migration
- receptor-mediated virion attachment to host cell
- negative regulation of protein localization to plasma membrane
Molecular Function
- fibronectin binding
- collagen binding
- laminin binding
Cellular Component
- extracellular space
- integral component of membrane
- extracellular matrix
- collagen-containing extracellular matrix
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000439944
- Coding exons
- 2
- Length
- 14497
- Individuals with no LoFs
- 125672
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 76
- Defined
- 125748
- p
- 0.000302
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.462 | 375 | 351 | 1.07 | 0.0000212 | 3827 |
| Missense (PolyPhen) | 96 | 93.596 | 1.0257 | 1221 | ||
| Synonymous | -1.51 | 182 | 158 | 1.15 | 0.0000101 | 1245 |
| Loss of Function | 0.344 | 14 | 15.5 | 0.906 | 8.39e-7 | 152 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00055 | 0.00055 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0011 | 0.0011 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00023 | 0.00023 | rare |
| South Asian | 0.00023 | 0.00023 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.157
Intolerance Scores
- LoFtool
- 0.939
- RVIS EVS
- -0.9
- RVIS percentile EVS
- 10.14
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.545
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |