IGFLR1
protein-codingIGF like family receptor 1
Gene summary
Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]
- U2AF1L4
- TMEM149
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.7 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 IGFLR1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024660.4. 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 | 66 | 3 | 69 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 70 | 3 | 0 | 73 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_078936.1 | 4 | MANE Select | |
| Ensembl | ENSP00000246532.1 | 4 | MANE Select | |
| RefSeq | NP_001332932.1 | 3 | Standard | |
| RefSeq | NP_001332933.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- protein binding
Cellular Component
- plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000592537
- Coding exons
- 4
- Length
- 3297
- Individuals with no LoFs
- 125364
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 372
- Defined
- 125736
- p
- 0.00148
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.805 | 239 | 206 | 1.16 | 0.0000111 | 2188 |
| Missense (PolyPhen) | 91 | 62.452 | 1.4571 | 696 | ||
| Synonymous | -1.22 | 115 | 99.5 | 1.16 | 0.00000568 | 820 |
| Loss of Function | 0.766 | 10 | 13.0 | 0.770 | 6.34e-7 | 135 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0030 | 0.0030 | notable |
| Latino/Admixed American | 0.00093 | 0.00093 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.0027 | 0.0027 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0019 | 0.0019 | notable |
| South Asian | 0.00082 | 0.00082 | rare |
| Other | 0.00066 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Probable cell membrane receptor for the IGF-like family proteins. Binds IGFL1 and IGFL3 with a higher affinity. May also bind IGFL2. {ECO:0000269|PubMed:21454693}.;
Recessive Scores
- pRec
- 0.0911
Intolerance Scores
- RVIS EVS
- 0.44
- RVIS percentile EVS
- 77.85
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |