LRRC25
protein-codingleucine rich repeat containing 25
Gene summary
Predicted to act upstream of or within several processes, including canonical NF-kappaB signal transduction; connective tissue replacement involved in inflammatory response wound healing; and response to hydrostatic pressure. Located in cytosol. [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 ~6.5 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 LRRC25 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_145256.3. 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 | ||||
| missense | 41 | 4 | 1 | 46 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 42 | 4 | 1 | 47 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_660299.2 | 2 | MANE Select | |
| Ensembl | ENSP00000340983.2 | 2 | MANE Select | |
| Ensembl | ENSP00000472290.1 | 2 | Standard | |
| Ensembl | ENSP00000472290.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vitamin D Receptor Pathway
Molecular Function
- protein binding
Cellular Component
- cytoplasm
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000339007
- Coding exons
- 2
- Length
- 6474
- Individuals with no LoFs
- 125703
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 125705
- p
- 0.00000796
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.807 | 154 | 185 | 0.833 | 0.0000122 | 1944 |
| Missense (PolyPhen) | 9 | 24.686 | 0.36457 | 307 | ||
| Synonymous | 1.43 | 75 | 92.5 | 0.811 | 0.00000661 | 670 |
| Loss of Function | 2.81 | 0 | 9.16 | 0.00 | 6.63e-7 | 75 |
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) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in the inhibition of RLR-mediated type I interferon signaling pathway by targeting DDX58/RIG-I for autophagic degradation. Interacts specifically with ISG15- associated DDX58 to promote interaction between DDX58 and the autophagic cargo receptor p62/SQSTM1 to mediate DDX58 degradation via selective autophagy (PubMed:29288164). Plays also a role in the inhibition of NF-kappa-B signaling pathway and inflammatory response by promoting the degradation of p65/RELA. {ECO:0000269|PubMed:12384430, ECO:0000269|PubMed:29044191, ECO:0000269|PubMed:29288164}.;
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- LoFtool
- 0.243
- RVIS EVS
- 0.73
- RVIS percentile EVS
- 86.08
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.467
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |