ILF2

interleukin enhancer binding factor 2

Basic information

Region (hg38): 1:153661788-153671028

Links

ENSG00000143621

∙ NCBI:3608 ∙ OMIM:603181 ∙ HGNC:6037 ∙ Uniprot:Q12905 ∙ 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 ILF2 gene.

not_specified (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ILF2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004515.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			14 clinvar			14
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	14	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ILF2	protein_coding	protein_coding	ENST00000361891	14	9013

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00350	125742	0	4	125746	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.40	76	217	0.350	0.0000109	2533
Missense in Polyphen		11	45.171	0.24352		545
Synonymous	0.190	72	74.1	0.972	0.00000358	784
Loss of Function	4.31	2	25.5	0.0785	0.00000148	272

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000621	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Appears to function predominantly as a heterodimeric complex with ILF3. This complex may regulate transcription of the IL2 gene during T-cell activation. It can also promote the formation of stable DNA-dependent protein kinase holoenzyme complexes on DNA. Essential for the efficient reshuttling of ILF3 (isoform 1 and isoform 2) into the nucleus. {ECO:0000269|PubMed:10574923, ECO:0000269|PubMed:11739746, ECO:0000269|PubMed:21123651, ECO:0000269|PubMed:9442054}.;
Pathway: B Cell Receptor Signaling Pathway;Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

pRec: 0.156

Intolerance Scores

loftool: 0.405
rvis_EVS: -0.03
rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

pHI: 0.774
hipred: Y
hipred_score: 0.802
ghis: 0.719

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.977

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ilf2
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);

Gene ontology

Biological process: transcription, DNA-templated;neutrophil degranulation;positive regulation of transcription, DNA-templated
Cellular component: extracellular region;nucleus;nucleolus;membrane;specific granule lumen;tertiary granule lumen;ficolin-1-rich granule lumen;ribonucleoprotein complex
Molecular function: DNA binding;RNA binding;double-stranded RNA binding;protein binding;ATP binding;transferase activity