IKZF3
Basic information
Region (hg38): 17:39757715-39864312
Previous symbols: [ "ZNFN1A3" ]
Links
Phenotypes
GenCC
Source:
- immunodeficiency 84 (Limited), mode of inheritance: AD
- immunodeficiency 84 (Strong), mode of inheritance: AD
- immunodeficiency 84 (Moderate), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Immunodeficiency 84 | AD | Allergy/Immunology/Infectious; Oncologic | Individuals may be susceptible to infections, and early and aggressive treatment of infections may be beneficial; Lymphoma has been described, and awareness may allow early detection and management; BMT has been described | Allergy/Immunology/Infectious; Oncologic | 34155405 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (48 variants)
- not_provided (6 variants)
- Immunodeficiency_84 (6 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IKZF3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012481.5. 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 | 2 | |||||
| missense | 53 | 56 | ||||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 2 | 53 | 4 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IKZF3 | protein_coding | protein_coding | ENST00000346872 | 8 | 99244 |
| 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 | 125723 | 0 | 5 | 125728 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.14 | 203 | 309 | 0.657 | 0.0000185 | 3420 |
| Missense in Polyphen | 47 | 137.84 | 0.34097 | 1481 | ||
| Synonymous | 0.374 | 105 | 110 | 0.955 | 0.00000695 | 892 |
| Loss of Function | 3.89 | 2 | 21.4 | 0.0934 | 0.00000106 | 286 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor that plays an important role in the regulation of lymphocyte differentiation. Plays an essential role in regulation of B-cell differentiation, proliferation and maturation to an effector state. Involved in regulating BCL2 expression and controlling apoptosis in T-cells in an IL2- dependent manner. {ECO:0000269|PubMed:10369681}.;
- Pathway
- il-2 receptor beta chain in t cell activation;IL2-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.211
Intolerance Scores
- loftool
- 0.116
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.56
Haploinsufficiency Scores
- pHI
- 0.786
- hipred
- Y
- hipred_score
- 0.809
- ghis
- 0.624
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.853
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ikzf3
- Phenotype
- renal/urinary system phenotype; immune system phenotype; neoplasm; 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); hematopoietic system phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;mesoderm development;response to bacterium;regulation of B cell proliferation;B cell activation;regulation of apoptotic process;regulation of B cell differentiation;regulation of lymphocyte differentiation;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol;plasma membrane
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;identical protein binding;protein homodimerization activity;sequence-specific DNA binding;transcription regulatory region DNA binding;metal ion binding;protein heterodimerization activity