LRRIQ3
Geneleucine rich repeats and IQ motif containing 3
Gene summary
No gene description available in the current model. Review primary literature for detailed gene function and characteristics.
- LRRC44
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~172.2 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 LRRIQ3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001105659.2. 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 | 3 | 3 | ||||
| missense | 82 | 8 | 3 | 93 | ||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | 2 | |||
| Total | 0 | 0 | 86 | 12 | 3 | 101 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001099129.1 | 7 | MANE Select | |
| Ensembl | ENSP00000346414.4 | 7 | MANE Select | |
| RefSeq | NP_001309244.1 | 7 | Standard | |
| Ensembl | ENSP00000359946.2 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- protein binding
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000354431
- Coding exons
- 7
- Length
- 172173
- Individuals with no LoFs
- 125520
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 182
- Defined
- 125704
- p
- 0.000732
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.824 | 327 | 288 | 1.14 | 0.0000133 | 4116 |
| Missense (PolyPhen) | 58 | 48.619 | 1.1929 | 730 | ||
| Synonymous | -0.555 | 103 | 96.1 | 1.07 | 0.00000423 | 1082 |
| Loss of Function | 0.685 | 22 | 25.7 | 0.854 | 0.00000149 | 354 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0073 | 0.0064 | notable |
| Latino/Admixed American | 0.00068 | 0.00061 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00034 | 0.00033 | rare |
| Finnish | 0.00024 | 0.00023 | rare |
| European (Non-Finnish) | 0.00031 | 0.00029 | rare |
| South Asian | 0.00047 | 0.00039 | rare |
| Other | 0.00060 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.966
- RVIS EVS
- 1.38
- RVIS percentile EVS
- 94.6
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0000400
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |