LRRC39
protein-codingleucine rich repeat containing 39
Gene summary
Predicted to be involved in intracellular signal transduction. Predicted to be located in M band. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~29.8 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 LRRC39 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_144620.4. 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 | 2 | 1 | 3 | |||
| missense | 51 | 3 | 54 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 55 | 3 | 1 | 59 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_653221.1 | 8 | MANE Select | |
| Ensembl | ENSP00000359156.1 | 8 | MANE Select | |
| RefSeq | NP_001243314.1 | 8 | Standard | |
| RefSeq | NP_001243315.1 | 8 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| lrrc39 | Danio rerio | Structure: skeletal muscle cell Quality: morphology abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- protein binding
Cellular Component
- M band
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000370138
- Coding exons
- 8
- Length
- 29363
- Individuals with no LoFs
- 125116
- Homozygous LoFs
- 5
- Heterozygous LoFs
- 621
- Defined
- 125742
- p
- 0.00249
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.256 | 160 | 169 | 0.945 | 0.00000813 | 2225 |
| Missense (PolyPhen) | 59 | 63.157 | 0.93417 | 843 | ||
| Synonymous | 0.0982 | 58 | 59.0 | 0.984 | 0.00000273 | 631 |
| Loss of Function | 2.12 | 9 | 18.9 | 0.475 | 0.00000105 | 225 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0033 | 0.0032 | notable |
| Latino/Admixed American | 0.00039 | 0.00038 | rare |
| Ashkenazi Jewish | 0.0029 | 0.0029 | notable |
| East Asian | 0.024 | 0.023 | notable |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00049 | 0.00048 | rare |
| South Asian | 0.0015 | 0.0014 | notable |
| Other | 0.0015 | 0.0015 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the sarcomeric M-band which plays a role in myocyte response to biomechanical stress. May regulate expression of other M-band proteins via an SRF-dependent pathway. Important for normal contractile function in heart. {ECO:0000250|UniProtKB:D3ZXS4}.;
Recessive Scores
- pRec
- 0.0916
Intolerance Scores
- LoFtool
- 0.902
- RVIS EVS
- -0.56
- RVIS percentile EVS
- 19.54
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.102
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |