IL1RAPL1
interleukin 1 receptor accessory protein like 1, the group of TIR domain containing|MicroRNA protein coding host genes|I-set domain containing|Interleukin receptors
Basic information
Region (hg38): X:28587446-29956718
Previous symbols: [ "IL1RAPL", "MRX34", "MRX21", "MRX10" ]
Links
Phenotypes
GenCC
Source:
- intellectual disability, X-linked 21 (Strong), mode of inheritance: XL
- intellectual disability, X-linked 21 (Moderate), mode of inheritance: XL
- non-syndromic X-linked intellectual disability (Supportive), mode of inheritance: XL
- intellectual disability, X-linked 21 (Definitive), mode of inheritance: XL
- non-syndromic X-linked intellectual disability (Definitive), mode of inheritance: XL
- intellectual disability, X-linked 21 (Definitive), mode of inheritance: XL
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Intellectual developmental disorder, X-linked 21 | XL | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 8230164; 10471494; 16470793; 18005360; 19012350; 18801879; 21484992 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (210 variants)
- Intellectual_disability,_X-linked_21 (48 variants)
- Inborn_genetic_diseases (40 variants)
- not_specified (13 variants)
- IL1RAPL1-related_disorder (8 variants)
- Intellectual_disability (2 variants)
- See_cases (2 variants)
- History_of_neurodevelopmental_disorder (1 variants)
- Schizophrenia (1 variants)
- Non-syndromic_X-linked_intellectual_disability (1 variants)
- Developmental_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL1RAPL1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014271.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 45 | 13 | 62 | |||
| missense | 110 | 19 | 132 | |||
| nonsense | 10 | |||||
| start loss | 0 | |||||
| frameshift | 10 | 13 | ||||
| splice donor/acceptor (+/-2bp) | 4 | |||||
| Total | 8 | 19 | 115 | 64 | 15 |
Highest pathogenic variant AF is 9.12101e-7
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IL1RAPL1 | protein_coding | protein_coding | ENST00000378993 | 10 | 1369325 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.00114 | 125709 | 0 | 2 | 125711 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.77 | 140 | 267 | 0.524 | 0.0000202 | 4572 |
| Missense in Polyphen | 36 | 120.02 | 0.29995 | 2089 | ||
| Synonymous | -0.00657 | 97 | 96.9 | 1.00 | 0.00000761 | 1300 |
| Loss of Function | 4.36 | 1 | 24.1 | 0.0415 | 0.00000182 | 424 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000245 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May regulate secretion and presynaptic differentiation through inhibition of the activity of N-type voltage-gated calcium channel (PubMed:12783849). May activate the MAP kinase JNK (PubMed:15123616). Plays a role in neurite outgrowth (By similarity). During dendritic spine formation can bidirectionally induce pre- and post-synaptic differentiation of neurons by trans- synaptically binding to PTPRD (By similarity). {ECO:0000250|UniProtKB:P59823, ECO:0000250|UniProtKB:P59824, ECO:0000269|PubMed:12783849, ECO:0000269|PubMed:15123616}.;
- Pathway
- Signaling by Interleukins;Cytokine Signaling in Immune system;Immune System;Neuronal System;Receptor-type tyrosine-protein phosphatases;Protein-protein interactions at synapses;Interleukin-38 signaling;Interleukin-1 family signaling
(Consensus)
Recessive Scores
- pRec
- 0.227
Intolerance Scores
- loftool
- rvis_EVS
- -0.6
- rvis_percentile_EVS
- 17.75
Haploinsufficiency Scores
- pHI
- 0.788
- hipred
- Y
- hipred_score
- 0.717
- ghis
- 0.482
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Il1rapl1
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- il1rapl1b
- Affected structure
- olfactory receptor cell
- Phenotype tag
- abnormal
- Phenotype quality
- increased size
Gene ontology
- Biological process
- heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;signal transduction;regulation of neuron projection development;neuron differentiation;negative regulation of exocytosis;positive regulation of dendrite morphogenesis;positive regulation of synapse assembly;calcium ion transmembrane transport;cellular response to cytokine stimulus;presynaptic membrane assembly;regulation of postsynapse organization;trans-synaptic signaling by trans-synaptic complex;regulation of presynapse assembly
- Cellular component
- cytoplasm;plasma membrane;cell surface;integral component of membrane;axon;dendrite;postsynaptic membrane;glutamatergic synapse
- Molecular function
- signaling receptor binding;voltage-gated calcium channel activity;protein binding;interleukin-1 binding