ILF2
Basic information
Region (hg38): 1:153661787-153671028
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ILF2 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 6 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 0 | 0 |
Variants in ILF2
This is a list of pathogenic ClinVar variants found in the ILF2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-153662420-T-G | not specified | Uncertain significance (Jan 09, 2024) | ||
| 1-153662440-G-C | not specified | Uncertain significance (Jun 06, 2023) | ||
| 1-153662761-C-T | not specified | Uncertain significance (Apr 17, 2023) | ||
| 1-153663270-A-C | not specified | Uncertain significance (Nov 09, 2023) | ||
| 1-153664429-G-C | not specified | Uncertain significance (Oct 27, 2022) | ||
| 1-153665262-T-C | not specified | Uncertain significance (Jun 13, 2024) | ||
| 1-153665696-C-A | not specified | Uncertain significance (Nov 06, 2023) | ||
| 1-153668466-T-C | not specified | Uncertain significance (Jun 07, 2024) | ||
| 1-153668514-G-C | not specified | Uncertain significance (Jun 03, 2024) | ||
| 1-153668542-G-A | not specified | Uncertain significance (May 23, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ILF2 | protein_coding | protein_coding | ENST00000361891 | 14 | 9013 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.997 | 0.00350 | 125742 | 0 | 4 | 125746 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.40 | 76 | 217 | 0.350 | 0.0000109 | 2533 |
| Missense in Polyphen | 11 | 45.171 | 0.24352 | 545 | ||
| Synonymous | 0.190 | 72 | 74.1 | 0.972 | 0.00000358 | 784 |
| Loss of Function | 4.31 | 2 | 25.5 | 0.0785 | 0.00000148 | 272 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000621 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000266 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Appears to function predominantly as a heterodimeric complex with ILF3. This complex may regulate transcription of the IL2 gene during T-cell activation. It can also promote the formation of stable DNA-dependent protein kinase holoenzyme complexes on DNA. Essential for the efficient reshuttling of ILF3 (isoform 1 and isoform 2) into the nucleus. {ECO:0000269|PubMed:10574923, ECO:0000269|PubMed:11739746, ECO:0000269|PubMed:21123651, ECO:0000269|PubMed:9442054}.;
- Pathway
- B Cell Receptor Signaling Pathway;Neutrophil degranulation;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- loftool
- 0.405
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.04
Haploinsufficiency Scores
- pHI
- 0.774
- hipred
- Y
- hipred_score
- 0.802
- ghis
- 0.719
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.977
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ilf2
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- transcription, DNA-templated;neutrophil degranulation;positive regulation of transcription, DNA-templated
- Cellular component
- extracellular region;nucleus;nucleolus;membrane;specific granule lumen;tertiary granule lumen;ficolin-1-rich granule lumen;ribonucleoprotein complex
- Molecular function
- DNA binding;RNA binding;double-stranded RNA binding;protein binding;ATP binding;transferase activity