NRF1
Basic information
Region (hg38): 7:129611719-129757082
Links
Phenotypes
GenCC
Source:
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 NRF1 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 | 3 | |||||
| missense | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 0 | 3 |
Variants in NRF1
This is a list of pathogenic ClinVar variants found in the NRF1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-129657406-G-T | not specified | Uncertain significance (May 26, 2023) | ||
| 7-129657466-A-G | not specified | Uncertain significance (May 16, 2024) | ||
| 7-129657483-G-A | Benign (Jun 26, 2018) | |||
| 7-129671445-C-T | Benign (Dec 31, 2019) | |||
| 7-129709138-TG-T | Uncertain significance (Aug 01, 2022) | |||
| 7-129717227-A-C | not specified | Uncertain significance (Nov 09, 2022) | ||
| 7-129717360-A-G | not specified | Uncertain significance (May 31, 2023) | ||
| 7-129727250-C-T | Benign (Aug 08, 2018) | |||
| 7-129727323-G-A | not specified | Uncertain significance (Dec 06, 2022) | ||
| 7-129727335-G-A | not specified | Uncertain significance (Dec 16, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NRF1 | protein_coding | protein_coding | ENST00000393232 | 10 | 145368 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000782 | 125514 | 0 | 2 | 125516 | 0.00000797 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 4.51 | 83 | 305 | 0.272 | 0.0000180 | 3225 |
| Missense in Polyphen | 17 | 81.846 | 0.20771 | 786 | ||
| Synonymous | 0.747 | 110 | 120 | 0.913 | 0.00000790 | 1048 |
| Loss of Function | 4.46 | 1 | 25.1 | 0.0399 | 0.00000114 | 277 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.00000882 | 0.00000882 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor that activates the expression of the EIF2S1 (EIF2-alpha) gene. Links the transcriptional modulation of key metabolic genes to cellular growth and development. Implicated in the control of nuclear genes required for respiration, heme biosynthesis, and mitochondrial DNA transcription and replication.;
- Pathway
- Huntington,s disease - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Energy Metabolism;Mitochondrial biogenesis;Simplified Interaction Map Between LOXL4 and Oxidative Stress Pathway;Mitochondrial Gene Expression;Transcriptional activation of mitochondrial biogenesis;Mitochondrial biogenesis;Organelle biogenesis and maintenance
(Consensus)
Intolerance Scores
- loftool
- 0.0375
- rvis_EVS
- -0.45
- rvis_percentile_EVS
- 24
Haploinsufficiency Scores
- pHI
- 0.248
- hipred
- Y
- hipred_score
- 0.816
- ghis
- 0.643
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- 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
- Nrf1
- Phenotype
- cellular 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);
Zebrafish Information Network
- Gene name
- nrf1
- Affected structure
- photoreceptor cell
- Phenotype tag
- abnormal
- Phenotype quality
- apoptotic
Gene ontology
- Biological process
- generation of precursor metabolites and energy;regulation of transcription by RNA polymerase II;mitochondrion organization;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleus;nucleoplasm;cytosol;extracellular exosome
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II core promoter sequence-specific DNA binding;core promoter sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;protein binding;protein homodimerization activity