GeneBe

IKZF2

IKAROS family zinc finger 2, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 2:212999691-213152427

Previous symbols: [ "ZNFN1A2" ]

Links

ENSG00000030419 ∙ NCBI:22807 ∙ OMIM:606234 ∙ HGNC:13177 ∙ Uniprot:Q9UKS7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • HELIOS deficiency (Moderate), mode of inheritance: Semidominant
  • hearing loss disorder (Limited), mode of inheritance: AD
  • HELIOS deficiency (Limited), mode of inheritance: AR
  • immunodeficiency disease (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IKZF2 gene.

  • not_specified (54 variants)
  • not_provided (7 variants)
  • ICHAD_SYNDROME (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IKZF2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001387220.1. 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
2
clinvar
 2
missense
55
clinvar
2
clinvar
 57
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 55 2 2
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
IKZF2protein_codingprotein_codingENST00000457361 7152723
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.9870.012712561221321257460.000533
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.402292970.7710.00001553549
Missense in Polyphen64113.980.561521419
Synonymous-1.371201021.170.00000544931
Loss of Function3.95222.00.09090.00000126272

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002900.0000290
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.005830.00574
European (Non-Finnish)0.00005360.0000527
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.0003260.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Associates with Ikaros at centromeric heterochromatin.;

Recessive Scores

pRec
0.171

Intolerance Scores

loftool
0.515
rvis_EVS
0.02
rvis_percentile_EVS
55.61

Haploinsufficiency Scores

pHI
0.912
hipred
Y
hipred_score
0.595
ghis
0.541

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
N
essential_gene_gene_trap
K
gene_indispensability_pred
E
gene_indispensability_score
0.922

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ikzf2
Phenotype
growth/size/body region phenotype; immune system phenotype; hematopoietic system phenotype; 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); vision/eye phenotype; hearing/vestibular/ear phenotype;

Gene ontology

Biological process
biological_process;positive regulation of transcription by RNA polymerase II
Cellular component
nucleoplasm
Molecular function
DNA-binding transcription factor activity, RNA polymerase II-specific;molecular_function;DNA-binding transcription factor activity;protein binding;protein homodimerization activity;transcription regulatory region DNA binding;metal ion binding