IKZF2

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

Basic information

Region (hg38): 2:212999690-213152427

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

ClinVar

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

• Inborn genetic diseases (16 variants)
• not specified (5 variants)
• not provided (2 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.

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	1
missense			16		1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					5	5
Total	0	0	16	0	7

Variants in IKZF2

This is a list of pathogenic ClinVar variants found in the IKZF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-213007418-C-G		not specified	Uncertain significance (Jun 29, 2023)
2-213007566-T-C		not specified	Uncertain significance (May 17, 2023)
2-213007611-A-C		not specified	Uncertain significance (Aug 04, 2023)
2-213007690-G-C		not specified	Uncertain significance (Dec 20, 2023)
2-213007700-T-G		not specified	Uncertain significance (Aug 16, 2022)
2-213007778-C-T		not specified	Uncertain significance (Aug 08, 2022)
2-213007850-A-G		not specified	Uncertain significance (Oct 25, 2023)
2-213007940-T-C			Uncertain significance (Dec 01, 2023)
2-213007987-G-T		not specified	Uncertain significance (Jul 17, 2023)
2-213008036-T-C		not specified	Uncertain significance (Oct 26, 2022)
2-213008144-A-C		not specified	Benign (Jan 24, 2024)
2-213013851-T-C		not specified	Uncertain significance (Apr 22, 2022)
2-213013872-G-A			Uncertain significance (Dec 11, 2023)
2-213013886-T-C		not specified	Uncertain significance (Sep 14, 2022)
2-213013905-C-G		not specified	Uncertain significance (Feb 22, 2024)
2-213013916-C-A		not specified	Uncertain significance (May 09, 2023)
2-213013928-G-A		not specified	Uncertain significance (Jul 07, 2022)
2-213021923-A-ATTTTATCT		not specified	Benign (Jan 24, 2024)
2-213022044-A-G		not specified	Uncertain significance (Jan 09, 2024)
2-213022045-G-C		not specified	Uncertain significance (Oct 25, 2023)
2-213049619-C-T		not specified	Benign (Jan 24, 2024)
2-213049830-C-G		not specified	Uncertain significance (Jul 14, 2021)
2-213049854-A-G		not specified	Uncertain significance (Feb 26, 2024)
2-213056961-T-C			Benign (Jan 01, 2023)
2-213056979-C-T		not specified	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IKZF2	protein_coding	protein_coding	ENST00000457361	7	152723

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.987	0.0127	125612	2	132	125746	0.000533

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	229	297	0.771	0.0000155	3549
Missense in Polyphen		64	113.98	0.56152		1419
Synonymous	-1.37	120	102	1.17	0.00000544	931
Loss of Function	3.95	2	22.0	0.0909	0.00000126	272

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00583	0.00574
European (Non-Finnish)	0.0000536	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000326	0.000326

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

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

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