LRRIQ4
protein-codingleucine rich repeats and IQ motif containing 4
Gene summary
Predicted to be active in cytoplasm. [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 ~24.9 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 LRRIQ4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001080460.3. 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 | 96 | 3 | 99 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 97 | 3 | 0 | 100 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001073929.1 | 5 | MANE Select | |
| Ensembl | ENSP00000342188.6 | 5 | MANE Select | |
| Ensembl | ENSP00000508855.1 | 4 | Standard | |
| RefSeq | XP_006713676.1 | 5 | Standard |
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000340806
- Coding exons
- 5
- Length
- 15854
- Individuals with no LoFs
- 124565
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 75
- Defined
- 124640
- p
- 0.000301
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.204 | 295 | 305 | 0.967 | 0.0000174 | 3641 |
| Missense (PolyPhen) | 99 | 95.337 | 1.0384 | 1259 | ||
| Synonymous | 1.17 | 120 | 137 | 0.873 | 0.00000855 | 1109 |
| Loss of Function | 1.17 | 13 | 18.4 | 0.707 | 8.60e-7 | 241 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00045 | 0.00045 | rare |
| Latino/Admixed American | 0.00021 | 0.00020 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00061 | 0.00061 | rare |
| Finnish | 0.00047 | 0.00046 | rare |
| European (Non-Finnish) | 0.00013 | 0.00013 | rare |
| South Asian | 0.00082 | 0.00082 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0988
Intolerance Scores
- LoFtool
- 0.887
- RVIS EVS
- 0.33
- RVIS percentile EVS
- 73.65
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.218
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |