NFE2
nuclear factor, erythroid 2, the group of Basic leucine zipper proteins
Basic information
Region (hg38): 12:54292111-54301015
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFE2 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 | |||||
| missense | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 1 | 0 |
Variants in NFE2
This is a list of pathogenic ClinVar variants found in the NFE2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-54292400-C-T | not specified | Uncertain significance (May 18, 2022) | ||
| 12-54292427-C-T | not specified | Uncertain significance (Apr 04, 2023) | ||
| 12-54292460-A-G | not specified | Uncertain significance (Oct 18, 2021) | ||
| 12-54292465-C-T | not specified | Uncertain significance (Feb 01, 2023) | ||
| 12-54292501-T-A | not specified | Uncertain significance (Feb 15, 2023) | ||
| 12-54292621-A-C | not specified | Uncertain significance (Apr 18, 2023) | ||
| 12-54292754-C-G | not specified | Uncertain significance (Jun 09, 2022) | ||
| 12-54292907-G-T | not specified | Uncertain significance (May 09, 2023) | ||
| 12-54292990-C-T | not specified | Uncertain significance (Mar 14, 2023) | ||
| 12-54292993-C-T | not specified | Uncertain significance (Feb 14, 2023) | ||
| 12-54293064-G-A | Likely benign (Feb 01, 2023) | |||
| 12-54293200-T-C | not specified | Uncertain significance (May 06, 2024) | ||
| 12-54293362-T-C | not specified | Uncertain significance (Dec 18, 2023) | ||
| 12-54295172-A-G | not specified | Uncertain significance (May 30, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NFE2 | protein_coding | protein_coding | ENST00000540264 | 2 | 9011 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.667 | 0.332 | 125735 | 0 | 8 | 125743 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.22 | 176 | 228 | 0.772 | 0.0000146 | 2352 |
| Missense in Polyphen | 55 | 86.017 | 0.63941 | 809 | ||
| Synonymous | 0.327 | 91 | 95.1 | 0.957 | 0.00000529 | 831 |
| Loss of Function | 2.71 | 2 | 12.2 | 0.163 | 7.06e-7 | 142 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000296 | 0.0000296 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000547 | 0.0000544 |
| Finnish | 0.0000488 | 0.0000462 |
| European (Non-Finnish) | 0.0000101 | 0.00000879 |
| Middle Eastern | 0.0000547 | 0.0000544 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the NF-E2 complex essential for regulating erythroid and megakaryocytic maturation and differentiation. Binds to the hypersensitive site 2 (HS2) of the beta-globin control region (LCR). This subunit (NFE2) recognizes the TCAT/C sequence of the AP-1-like core palindrome present in a number of erythroid and megakaryocytic gene promoters. Requires MAFK or other small MAF proteins for binding to the NF-E2 motif. May play a role in all aspects of hemoglobin production from globin and heme synthesis to procurement of iron. {ECO:0000269|PubMed:11154691, ECO:0000269|PubMed:16287851}.;
- Pathway
- Hematopoietic Stem Cell Differentiation;Steatosis AOP;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;Gene expression (Transcription);Generic Transcription Pathway;Factors involved in megakaryocyte development and platelet production;RNA Polymerase II Transcription;RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function;Hemostasis;Transcriptional regulation by RUNX1
(Consensus)
Recessive Scores
- pRec
- 0.360
Intolerance Scores
- loftool
- 0.0570
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 33.97
Haploinsufficiency Scores
- pHI
- 0.507
- hipred
- Y
- hipred_score
- 0.598
- ghis
- 0.623
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nfe2
- Phenotype
- skeleton phenotype; immune system phenotype; neoplasm; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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); growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- nfe2
- Affected structure
- nucleate erythrocyte
- Phenotype tag
- abnormal
- Phenotype quality
- low saturation
Gene ontology
- Biological process
- nucleosome disassembly;regulation of transcription by RNA polymerase II;multicellular organism development;blood coagulation;hemostasis;blood circulation;regulation of megakaryocyte differentiation;positive regulation of transcription, DNA-templated
- Cellular component
- nucleus;nucleoplasm;cytoplasm;PML body;protein-DNA complex
- Molecular function
- transcription regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;proximal promoter sequence-specific DNA binding;DNA binding;DNA-binding transcription factor activity;transcription coactivator activity;protein binding;sequence-specific DNA binding;protein N-terminus binding;WW domain binding