LRG1
protein-codingleucine rich alpha-2-glycoprotein 1
Gene summary
The leucine-rich repeat (LRR) family of proteins, including LRG1, have been shown to be involved in protein-protein interaction, signal transduction, and cell adhesion and development. LRG1 is expressed during granulocyte differentiation (O'Donnell et al., 2002 [PubMed 12223515]).[supplied by OMIM, Mar 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.6 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 LRG1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_052972.3. 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 | 0 | |||||
| missense | 61 | 7 | 68 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 64 | 7 | 0 | 71 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_443204.1 | 2 | MANE Select | |
| Ensembl | ENSP00000302621.4 | 2 | MANE Select | |
| Ensembl | ENSP00000555149.1 | 2 | Standard | |
| Ensembl | ENSP00000555149.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neutrophil degranulation
- Innate Immune System
- Immune System
Biological Process
- positive regulation of endothelial cell proliferation
- biological_process
- response to bacterium
- positive regulation of transforming growth factor beta receptor signaling pathway
- neutrophil degranulation
Molecular Function
- molecular_function
- transforming growth factor beta receptor binding
- protein binding
Cellular Component
- extracellular region
- extracellular space
- membrane
- specific granule lumen
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000306390
- Coding exons
- 2
- Length
- 4066
- Individuals with no LoFs
- 125747
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 125748
- p
- 0.00000398
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0461 | 203 | 201 | 1.01 | 0.0000129 | 2197 |
| Missense (PolyPhen) | 59 | 58.046 | 1.0164 | 768 | ||
| Synonymous | -0.648 | 110 | 102 | 1.08 | 0.00000683 | 787 |
| Loss of Function | 0.0691 | 1 | 1.08 | 0.928 | 4.58e-8 | 12 |
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) | 0.0000088 | 0.0000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.149
Intolerance Scores
- LoFtool
- 0.583
- RVIS EVS
- 0.4
- RVIS percentile EVS
- 76.41
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.285
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |