IKZF4

IKAROS family zinc finger 4, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 12:56007659-56038435

Previous symbols: [ "ZNFN1A4" ]

Links

ENSG00000123411NCBI:64375OMIM:606239HGNC:13179Uniprot:Q9H2S9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IKZF4 gene.

  • not_specified (55 variants)
  • not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IKZF4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000022465.4. 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.

EffectPLPVUSLBBSum
synonymous
0
missense
55
clinvar
55
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 55 0 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
IKZF4protein_codingprotein_codingENST00000262032 830777
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8980.102124629081246370.0000321
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.412283560.6410.00002143800
Missense in Polyphen39123.370.316131255
Synonymous0.5751281370.9370.000007641197
Loss of Function3.59320.60.1460.00000110253

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001260.000126
Ashkenazi Jewish0.00009950.0000994
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001830.0000177
Middle Eastern0.000.00
South Asian0.00003470.0000327
Other0.0001660.000165

dbNSFP

Source: dbNSFP

Function
FUNCTION: DNA-binding protein that binds to the 5'GGGAATRCC-3' Ikaros-binding sequence. Transcriptional repressor. Interacts with SPI1 and MITF to repress transcription of the CTSK and ACP5 promoters via recruitment of corepressors SIN3A and CTBP2. May be involved in the development of central and peripheral nervous systems. Essential for the inhibitory function of regulatory T- cells (Treg). Mediates FOXP3-mediated gene silencing in regulatory T-cells (Treg) via recruitment of corepressor CTBP1 (By similarity). {ECO:0000250|UniProtKB:Q8C208, ECO:0000269|PubMed:10978333, ECO:0000269|PubMed:12015313, ECO:0000269|PubMed:12444977}.;

Recessive Scores

pRec
0.267

Intolerance Scores

loftool
0.218
rvis_EVS
-0.49
rvis_percentile_EVS
22.51

Haploinsufficiency Scores

pHI
0.855
hipred
Y
hipred_score
0.675
ghis
0.650

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.801

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ikzf4
Phenotype

Gene ontology

Biological process
negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;protein homooligomerization;protein heterooligomerization
Cellular component
nucleus;nucleoplasm;nuclear body;protein-containing complex
Molecular function
DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;zinc ion binding;protein domain specific binding;bHLH transcription factor binding;sequence-specific DNA binding;transcription regulatory region DNA binding