LRRC42
protein-codingleucine rich repeat containing 42
Gene summary
Located in nucleoplasm. [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 ~22.1 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 LRRC42 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001256409.2. 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 | 4 | 4 | ||||
| missense | 54 | 3 | 57 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 61 | 3 | 0 | 64 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001243338.1 | 7 | MANE Select | |
| Ensembl | ENSP00000360421.3 | 7 | MANE Select | |
| RefSeq | NP_443172.1 | 7 | Standard | |
| Ensembl | ENSP00000318185.4 | 7 | Standard |
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000371370
- Coding exons
- 7
- Length
- 22092
- Individuals with no LoFs
- 125602
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 146
- Defined
- 125748
- p
- 0.000581
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.219 | 244 | 235 | 1.04 | 0.0000125 | 2794 |
| Missense (PolyPhen) | 87 | 77.357 | 1.1247 | 1004 | ||
| Synonymous | 0.703 | 83 | 91.6 | 0.906 | 0.00000474 | 841 |
| Loss of Function | 1.15 | 15 | 20.6 | 0.727 | 0.00000126 | 238 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00068 | 0.00068 | rare |
| Latino/Admixed American | 0.00038 | 0.00038 | rare |
| Ashkenazi Jewish | 0.0051 | 0.0045 | notable |
| East Asian | 0.00054 | 0.00054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00049 | 0.00049 | rare |
| South Asian | 0.00023 | 0.00023 | rare |
| Other | 0.00066 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.329
- RVIS EVS
- -0.11
- RVIS percentile EVS
- 45.36
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.310
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |