ILF3

interleukin enhancer binding factor 3

Basic information

Region (hg38): 19:10654304-10692400

Links

ENSG00000129351 ∙ NCBI:3609 ∙ OMIM:603182 ∙ HGNC:6038 ∙ Uniprot:Q12906 ∙ 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 ILF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ILF3 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	2
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	29	3	1

Variants in ILF3

This is a list of pathogenic ClinVar variants found in the ILF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-10671004-C-T		not specified	Uncertain significance (Apr 20, 2023)
19-10671014-T-C		not specified	Uncertain significance (May 09, 2023)
19-10671042-A-C			Likely benign (Apr 01, 2022)
19-10671194-A-G		not specified	Uncertain significance (Oct 06, 2022)
19-10671369-C-T		not specified	Uncertain significance (Sep 21, 2021)
19-10671457-G-T		not specified	Uncertain significance (Dec 21, 2023)
19-10671524-A-G		not specified	Uncertain significance (Apr 07, 2022)
19-10677169-A-G		not specified	Uncertain significance (Dec 19, 2023)
19-10677194-A-C		not specified	Uncertain significance (Sep 26, 2023)
19-10678628-A-C		not specified	Uncertain significance (Mar 30, 2024)
19-10678633-C-T		not specified	Uncertain significance (Mar 30, 2024)
19-10679175-G-C		not specified	Uncertain significance (Dec 22, 2023)
19-10681073-C-T		not specified	Uncertain significance (Sep 19, 2023)
19-10681204-G-A			Likely benign (Jun 28, 2020)
19-10681281-G-A		not specified	Uncertain significance (Sep 06, 2022)
19-10682001-G-T		not specified	Uncertain significance (Sep 26, 2023)
19-10682034-C-T		not specified	Uncertain significance (Oct 05, 2023)
19-10682187-G-A		not specified	Uncertain significance (Mar 29, 2022)
19-10682558-C-G		not specified	Uncertain significance (Jul 13, 2022)
19-10682586-G-A		not specified	Uncertain significance (Jan 10, 2023)
19-10682618-G-A		not specified	Uncertain significance (Feb 02, 2022)
19-10682637-C-T		not specified	Uncertain significance (Nov 19, 2022)
19-10682676-C-T		not specified	Uncertain significance (May 27, 2022)
19-10683254-G-A		not specified	Uncertain significance (Mar 25, 2024)
19-10683474-G-T		not specified	Uncertain significance (Jun 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ILF3	protein_coding	protein_coding	ENST00000449870	19	38157

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.27e-7	125676	0	2	125678	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.70	384	564	0.681	0.0000357	5793
Missense in Polyphen		77	216.48	0.35568		2344
Synonymous	-2.04	294	253	1.16	0.0000192	1813
Loss of Function	6.32	1	48.4	0.0207	0.00000261	539

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000549	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000926	0.00000880
Middle Eastern	0.0000549	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back- splicing circularization of pre-mRNAs. Within the nucleus, promotes circRNAs processing by stabilizing the regulatory elements residing in the flanking introns of the circularized exons. Plays thereby a role in the back-splicing of a subset of circRNAs (PubMed:28625552). As a consequence, participates in a wide range of transcriptional and post-transcriptional processes. Binds to poly-U elements and AU-rich elements (AREs) in the 3'-UTR of target mRNAs (PubMed:14731398). Upon viral infection, ILF3 accumulates in the cytoplasm and participates in the innate antiviral response (PubMed:21123651). Mechanistically, ILF3 becomes phosphorylated and activated by the double-stranded RNA- activated protein kinase/PKR which releases ILF3 from cellular mature circRNAs. In turn, unbound ILF3 molecules are able to interact with and thus inhibit viral mRNAs (PubMed:21123651, PubMed:28625552). {ECO:0000269|PubMed:14731398, ECO:0000269|PubMed:21123651, ECO:0000269|PubMed:28625552, ECO:0000269|PubMed:9442054}.

Recessive Scores

• pRec: 0.300

Intolerance Scores

• loftool: 0.192
• rvis_EVS: -1.15
• rvis_percentile_EVS: 6.27

Haploinsufficiency Scores

• pHI: 0.784
• hipred: Y
• hipred_score: 0.816
• ghis: 0.676

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.995

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ilf3
• Phenotype: respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); immune system phenotype; growth/size/body region phenotype; muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: protein phosphorylation;negative regulation of translation;negative regulation of viral genome replication;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;defense response to virus
• Cellular component: extracellular region;nucleus;nucleoplasm;nucleolus;cytoplasm;mitochondrion;membrane;ribonucleoprotein complex
• Molecular function: DNA binding;RNA binding;double-stranded RNA binding;single-stranded RNA binding;protein binding;AU-rich element binding