NFE2L3

NFE2 like bZIP transcription factor 3, the group of Basic leucine zipper proteins

Basic information

Region (hg38): 7:26152197-26187137

Links

ENSG00000050344 ∙ NCBI:9603 ∙ OMIM:604135 ∙ HGNC:7783 ∙ Uniprot:Q9Y4A8 ∙ 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 NFE2L3 gene.

• Inborn genetic diseases (38 variants)
• not provided (4 variants)
• Keratoconus (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFE2L3 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			38	2	1	41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	3	1

Variants in NFE2L3

This is a list of pathogenic ClinVar variants found in the NFE2L3 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-26152630-C-A		not specified	Uncertain significance (Jan 23, 2023)
7-26152649-G-T		not specified	Uncertain significance (May 25, 2022)
7-26152668-A-G		not specified	Uncertain significance (Oct 05, 2021)
7-26152710-C-T		not specified	Uncertain significance (Sep 13, 2023)
7-26152715-C-T		not specified	Uncertain significance (Aug 17, 2021)
7-26152781-G-T		not specified	Uncertain significance (Jan 29, 2024)
7-26152794-G-A		not specified	Uncertain significance (May 18, 2023)
7-26152835-G-C		not specified	Uncertain significance (Nov 22, 2022)
7-26152844-G-A		not specified	Uncertain significance (Aug 26, 2022)
7-26152847-G-A		not specified	Uncertain significance (Jun 21, 2021)
7-26152974-C-A		not specified	Uncertain significance (Dec 21, 2022)
7-26152974-C-T		not specified	Uncertain significance (Jan 23, 2024)
7-26153037-A-C		not specified	Uncertain significance (Jul 26, 2022)
7-26153048-G-A		not specified	Uncertain significance (Jul 12, 2022)
7-26177970-G-A		not specified	Uncertain significance (Apr 10, 2023)
7-26177976-G-T		not specified	Uncertain significance (Oct 25, 2022)
7-26178021-G-C		not specified	Uncertain significance (Sep 01, 2021)
7-26178073-C-T		not specified	Uncertain significance (Nov 09, 2023)
7-26183702-G-C		not specified	Uncertain significance (Dec 21, 2022)
7-26183723-C-T		not specified	Uncertain significance (Mar 29, 2022)
7-26183735-T-C		not specified	Uncertain significance (Oct 18, 2021)
7-26183746-T-C		not specified	Likely benign (Dec 15, 2023)
7-26183761-T-C		not specified	Uncertain significance (Sep 26, 2023)
7-26184594-C-G		not specified	Uncertain significance (Apr 19, 2023)
7-26184630-A-G		Keratoconus	Likely benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NFE2L3	protein_coding	protein_coding	ENST00000056233	4	34886

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.18e-11	0.136	125471	1	276	125748	0.00110

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.75	512	323	1.59	0.0000157	4508
Missense in Polyphen		102	62.167	1.6407		909
Synonymous	-4.64	195	128	1.52	0.00000640	1380
Loss of Function	0.504	17	19.4	0.876	9.23e-7	270

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00223	0.00223
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.00316	0.00316
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000759	0.000756
Middle Eastern	0.00316	0.00316
South Asian	0.00213	0.00209
Other	0.00212	0.00212

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Activates erythroid-specific, globin gene expression.

Recessive Scores

• pRec: 0.0952

Intolerance Scores

• loftool: 0.630
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.43

Haploinsufficiency Scores

• pHI: 0.506
• hipred: N
• hipred_score: 0.153
• ghis: 0.452

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.534

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nfe2l3
• Phenotype: normal 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: negative regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;positive regulation of transcription, DNA-templated
• Cellular component: nucleus;cytoplasm
• Molecular function: transcription 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 transcription factor activity;transcription coactivator activity;protein binding