NFIL3

nuclear factor, interleukin 3 regulated, the group of Basic leucine zipper proteins

Basic information

Region (hg38): 9:91408748-91424626

Previous symbols: [ "IL3BP1" ]

Links

ENSG00000165030 ∙ NCBI:4783 ∙ OMIM:605327 ∙ HGNC:7787 ∙ Uniprot:Q16649 ∙ 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 NFIL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFIL3 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					4	4
missense			13	2	1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	2	5

Variants in NFIL3

This is a list of pathogenic ClinVar variants found in the NFIL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-91409346-T-C			Benign (Aug 20, 2018)
9-91409405-C-T		not specified	Uncertain significance (Aug 10, 2023)
9-91409443-A-G		not specified	Uncertain significance (Oct 13, 2023)
9-91409482-A-G		not specified	Uncertain significance (Nov 09, 2024)
9-91409905-G-A		not specified	Uncertain significance (Mar 30, 2024)
9-91409913-C-T			Benign (Jun 18, 2018)
9-91409914-G-A		not specified	Uncertain significance (Nov 14, 2023)
9-91409965-T-G		not specified	Uncertain significance (Jul 26, 2021)
9-91410031-T-G		not specified	Uncertain significance (Nov 02, 2023)
9-91410201-G-C			Benign (Jun 18, 2018)
9-91410225-C-T		NFIL3-related disorder	Likely benign (Sep 01, 2024)
9-91410250-A-G		not specified	Uncertain significance (May 03, 2023)
9-91410299-C-A		not specified	Uncertain significance (Jul 21, 2021)
9-91410344-A-G		not specified	Uncertain significance (Oct 05, 2023)
9-91410398-C-T		not specified	Uncertain significance (Apr 12, 2023)
9-91410399-G-A			Benign (Feb 08, 2018)
9-91410574-T-C		not specified	Uncertain significance (Oct 12, 2021)
9-91410616-G-A		not specified	Uncertain significance (Nov 12, 2021)
9-91410643-G-A		not specified	Uncertain significance (Dec 27, 2023)
9-91410659-T-A		NFIL3-related disorder	Likely benign (Feb 28, 2022)
9-91410680-T-C		not specified	Likely benign (Sep 10, 2024)
9-91410710-C-T			Benign (Apr 07, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NFIL3	protein_coding	protein_coding	ENST00000297689	1	14818

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.820	0.180	125736	0	5	125741	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	172	242	0.710	0.0000133	3031
Missense in Polyphen		39	78.291	0.49814		1033
Synonymous	0.00795	97	97.1	0.999	0.00000572	906
Loss of Function	3.03	2	14.4	0.139	8.58e-7	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000352
Middle Eastern	0.0000556	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional regulator that recognizes and binds to the sequence 5'-[GA]TTA[CT]GTAA[CT]-3', a sequence present in many cellular and viral promoters. Represses transcription from promoters with activating transcription factor (ATF) sites. Represses promoter activity in osteoblasts (By similarity). Represses transcriptional activity of PER1 (By similarity). Represses transcriptional activity of PER2 via the B- site on the promoter (By similarity). Activates transcription from the interleukin-3 promoter in T-cells. Competes for the same consensus-binding site with PAR DNA-binding factors (DBP, HLF and TEF) (By similarity). Component of the circadian clock that acts as a negative regulator for the circadian expression of PER2 oscillation in the cell-autonomous core clock (By similarity). Protects pro-B cells from programmed cell death (By similarity). {ECO:0000250, ECO:0000269|PubMed:1620116, ECO:0000269|PubMed:7565758, ECO:0000269|PubMed:8836190}.
• Pathway: IL-4 Signaling Pathway;Development and heterogeneity of the ILC family (Consensus)

Recessive Scores

• pRec: 0.233

Intolerance Scores

• loftool: 0.0243
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.327
• hipred: Y
• hipred_score: 0.654
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.976

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nfil3
• Phenotype: hematopoietic system phenotype; vision/eye phenotype; digestive/alimentary phenotype; immune system phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: nfil3
• Affected structure: myeloid lineage restricted progenitor cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;transcription by RNA polymerase II;immune response;circadian rhythm;positive regulation of gene expression;cellular response to interleukin-4
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;transcription corepressor activity;protein binding