IKZF4

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

Basic information

Region (hg38): 12:56007659-56038435

Previous symbols: [ "ZNFN1A4" ]

Links

ENSG00000123411 ∙ NCBI:64375 ∙ OMIM:606239 ∙ HGNC:13179 ∙ Uniprot:Q9H2S9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	0

Variants in IKZF4

This is a list of pathogenic ClinVar variants found in the IKZF4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-56021521-C-T		not specified	Uncertain significance (Feb 28, 2024)
12-56021536-G-A		not specified	Uncertain significance (Apr 15, 2024)
12-56021546-G-A		not specified	Uncertain significance (Mar 20, 2023)
12-56021552-C-T		not specified	Uncertain significance (Jan 31, 2024)
12-56021560-C-T		not specified	Uncertain significance (Dec 19, 2022)
12-56021563-C-T		not specified	Uncertain significance (Jan 31, 2022)
12-56023702-C-T		not specified	Uncertain significance (Apr 07, 2022)
12-56023732-A-G		not specified	Uncertain significance (Dec 19, 2023)
12-56025122-A-G		not specified	Uncertain significance (Nov 13, 2024)
12-56025137-T-G		not specified	Uncertain significance (Nov 10, 2024)
12-56026952-G-A		not specified	Uncertain significance (Dec 19, 2023)
12-56026992-G-T		not specified	Uncertain significance (Oct 03, 2022)
12-56027917-G-A		not specified	Uncertain significance (Oct 19, 2024)
12-56032609-G-A		not specified	Uncertain significance (Oct 06, 2021)
12-56032707-C-A		not specified	Uncertain significance (May 28, 2024)
12-56034573-G-A		not specified	Uncertain significance (Dec 03, 2021)
12-56034579-C-A		not specified	Uncertain significance (Oct 27, 2023)
12-56034584-G-A		not specified	Uncertain significance (Dec 31, 2023)
12-56034681-G-C		not specified	Uncertain significance (Jan 23, 2024)
12-56034720-C-A		not specified	Uncertain significance (Feb 16, 2023)
12-56034808-G-A		not specified	Uncertain significance (May 04, 2023)
12-56034808-G-T		not specified	Uncertain significance (Jan 19, 2024)
12-56034844-G-C		not specified	Uncertain significance (Jan 23, 2024)
12-56034888-C-G		not specified	Uncertain significance (Aug 12, 2021)
12-56034922-G-A		not specified	Uncertain significance (Jun 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IKZF4	protein_coding	protein_coding	ENST00000262032	8	30777

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.898	0.102	124629	0	8	124637	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.41	228	356	0.641	0.0000214	3800
Missense in Polyphen		39	123.37	0.31613		1255
Synonymous	0.575	128	137	0.937	0.00000764	1197
Loss of Function	3.59	3	20.6	0.146	0.00000110	253

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000126	0.000126
Ashkenazi Jewish	0.0000995	0.0000994
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000183	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.0000347	0.0000327
Other	0.000166	0.000165

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ikzf4

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