IKZF5
Basic information
Region (hg38): 10:122990807-123008812
Previous symbols: [ "ZNFN1A5" ]
Links
Phenotypes
GenCC
Source:
- autosomal thrombocytopenia with normal platelets (Supportive), mode of inheritance: AD
- thrombocytopenia 7 (Strong), mode of inheritance: AD
- thrombocytopenia 7 (Moderate), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Thrombocytopenia 7 | AD | Hematologic | Some individuals have been described with severe bleeding episodes, and awareness may allow precautions and prompt management of bleeding episodes | Hematologic | 31217188; 32419556 |
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 IKZF5 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 | 1 | |||||
missense | 6 | |||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 1 | |||||
Total | 0 | 2 | 4 | 2 | 1 |
Variants in IKZF5
This is a list of pathogenic ClinVar variants found in the IKZF5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
10-122993890-C-T | Uncertain significance (Sep 22, 2022) | |||
10-122993928-A-G | Likely benign (Jun 01, 2022) | |||
10-122993968-G-T | Thrombocytopenia 7 | Uncertain significance (-) | ||
10-122994026-C-T | Likely benign (Jul 01, 2024) | |||
10-122994143-G-A | Likely benign (Oct 01, 2022) | |||
10-122994157-C-T | not specified | Uncertain significance (Apr 09, 2024) | ||
10-122994577-G-A | Thrombocytopenia 7 | Pathogenic (Dec 23, 2020) | ||
10-122994581-C-G | Thrombocytopenia 7 | Uncertain significance (Feb 23, 2023) | ||
10-122994622-A-G | Thrombocytopenia 7 | Pathogenic (Dec 23, 2020) | ||
10-122994639-C-T | Thrombocytopenia 7 | Pathogenic/Likely pathogenic (Dec 23, 2020) | ||
10-122994678-T-A | Thrombocytopenia 7 | Likely pathogenic (Jun 30, 2023) | ||
10-122994685-A-G | Thrombocytopenia 7 | Pathogenic/Likely pathogenic (Aug 10, 2021) | ||
10-122996010-GTGTT-AATCCACA | Thrombocytopenia 7 | Likely pathogenic (Nov 15, 2023) | ||
10-122996024-G-A | Thrombocytopenia 7 | Pathogenic/Likely pathogenic (Dec 23, 2020) | ||
10-122996056-C-T | IKZF5-related disorder | Uncertain significance (Aug 09, 2023) | ||
10-123008776-G-A | Deficiency of 2-methylbutyryl-CoA dehydrogenase | Benign (Jan 15, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
IKZF5 | protein_coding | protein_coding | ENST00000368886 | 3 | 18012 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.780 | 0.220 | 124792 | 0 | 2 | 124794 | 0.00000801 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.89 | 155 | 237 | 0.654 | 0.0000125 | 2804 |
Missense in Polyphen | 37 | 85.245 | 0.43404 | 1021 | ||
Synonymous | 0.869 | 73 | 83.1 | 0.879 | 0.00000452 | 789 |
Loss of Function | 2.94 | 2 | 13.8 | 0.145 | 7.88e-7 | 172 |
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) | 0.0000177 | 0.0000177 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: DNA-binding protein that binds to the 5'GNNTGTNG-3' core sequence. Transcriptional repressor. {ECO:0000269|PubMed:10978333}.;
Recessive Scores
- pRec
- 0.119
Intolerance Scores
- loftool
- 0.229
- rvis_EVS
- -0.3
- rvis_percentile_EVS
- 32.62
Haploinsufficiency Scores
- pHI
- 0.474
- hipred
- Y
- hipred_score
- 0.673
- ghis
- 0.670
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.896
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ikzf5
- Phenotype
- immune system phenotype; hearing/vestibular/ear phenotype; hematopoietic system phenotype;
Zebrafish Information Network
- Gene name
- ikzf5
- Affected structure
- pancreas
- Phenotype tag
- abnormal
- Phenotype quality
- mislocalised
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II;protein heterooligomerization
- Cellular component
- nucleoplasm;protein-containing complex
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;zinc ion binding;protein domain specific binding;transcription regulatory region DNA binding