IL1RAPL2
Basic information
Region (hg38): X:104566199-105767829
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (83 variants)
- not_provided (10 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL1RAPL2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017416.2. 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 | 1 | |||||
missense | 47 | 50 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
Total | 0 | 0 | 49 | 4 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
IL1RAPL2 | protein_coding | protein_coding | ENST00000372582 | 10 | 1200827 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.984 | 0.0158 | 125685 | 2 | 2 | 125689 | 0.0000159 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.00 | 157 | 245 | 0.641 | 0.0000175 | 4516 |
Missense in Polyphen | 50 | 104.96 | 0.47636 | 1976 | ||
Synonymous | 0.0796 | 88 | 89.0 | 0.989 | 0.00000633 | 1270 |
Loss of Function | 3.89 | 2 | 21.4 | 0.0934 | 0.00000157 | 426 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000780 | 0.0000615 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000247 | 0.0000176 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000642 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Pathway
- Neuronal System;Receptor-type tyrosine-protein phosphatases;Protein-protein interactions at synapses
(Consensus)
Recessive Scores
- pRec
- 0.123
Intolerance Scores
- loftool
- 0.280
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.37
Haploinsufficiency Scores
- pHI
- 0.301
- hipred
- Y
- hipred_score
- 0.809
- ghis
- 0.397
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Il1rapl2
- Phenotype
Gene ontology
- Biological process
- central nervous system development;cytokine-mediated signaling pathway;regulation of presynapse assembly
- Cellular component
- plasma membrane;integral component of membrane;glutamatergic synapse
- Molecular function
- interleukin-1 receptor activity;interleukin-1, type II, blocking receptor activity