IKZF5

IKAROS family zinc finger 5, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 10:122990807-123008812

Previous symbols: [ "ZNFN1A5" ]

Links

ENSG00000095574NCBI:64376OMIM:606238HGNC:14283Uniprot:Q9H5V7AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Thrombocytopenia 7ADHematologicSome individuals have been described with severe bleeding episodes, and awareness may allow precautions and prompt management of bleeding episodesHematologic31217188; 32419556

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IKZF5 gene.

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
clinvar
1
missense
1
clinvar
4
clinvar
1
clinvar
6
nonsense
1
clinvar
1
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
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)2446258
10-122993928-A-G Likely benign (Jun 01, 2022)1694573
10-122993968-G-T Thrombocytopenia 7 Uncertain significance (-)2572151
10-122994026-C-T Likely benign (Jul 01, 2024)3257231
10-122994143-G-A Likely benign (Oct 01, 2022)1879148
10-122994157-C-T not specified Uncertain significance (Apr 09, 2024)3251397
10-122994577-G-A Thrombocytopenia 7 Pathogenic (Dec 23, 2020)1684455
10-122994581-C-G Thrombocytopenia 7 Uncertain significance (Feb 23, 2023)2444044
10-122994622-A-G Thrombocytopenia 7 Pathogenic (Dec 23, 2020)1684456
10-122994639-C-T Thrombocytopenia 7 Pathogenic/Likely pathogenic (Dec 23, 2020)1684457
10-122994678-T-A Thrombocytopenia 7 Likely pathogenic (Jun 30, 2023)1703863
10-122994685-A-G Thrombocytopenia 7 Pathogenic/Likely pathogenic (Aug 10, 2021)989447
10-122996010-GTGTT-AATCCACA Thrombocytopenia 7 Likely pathogenic (Nov 15, 2023)2671954
10-122996024-G-A Thrombocytopenia 7 Pathogenic/Likely pathogenic (Dec 23, 2020)1684458
10-122996056-C-T IKZF5-related disorder Uncertain significance (Aug 09, 2023)2634601
10-123008776-G-A Deficiency of 2-methylbutyryl-CoA dehydrogenase Benign (Jan 15, 2024)1166420

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
IKZF5protein_codingprotein_codingENST00000368886 318012
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.7800.220124792021247940.00000801
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.891552370.6540.00001252804
Missense in Polyphen3785.2450.434041021
Synonymous0.8697383.10.8790.00000452789
Loss of Function2.94213.80.1457.88e-7172

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001770.0000177
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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