ETF1
Basic information
Region (hg38): 5:138506095-138543236
Previous symbols: [ "SUP45L1", "ERF1", "ERF" ]
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 ETF1 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 | 0 | |||||
| missense | 2 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 2 | 0 | 0 |
Variants in ETF1
This is a list of pathogenic ClinVar variants found in the ETF1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-138508784-C-T | not specified | Uncertain significance (Sep 25, 2024) | ||
| 5-138512774-A-G | not specified | Uncertain significance (Feb 15, 2023) | ||
| 5-138518814-C-T | not specified | Uncertain significance (Dec 20, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ETF1 | protein_coding | protein_coding | ENST00000360541 | 10 | 37206 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.996 | 0.00400 | 125738 | 0 | 2 | 125740 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 4.39 | 45 | 234 | 0.192 | 0.0000120 | 2854 |
| Missense in Polyphen | 11 | 84.217 | 0.13061 | 1107 | ||
| Synonymous | 0.267 | 81 | 84.1 | 0.963 | 0.00000444 | 807 |
| Loss of Function | 4.27 | 2 | 25.1 | 0.0796 | 0.00000144 | 303 |
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 | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000179 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. Component of the transient SURF complex which recruits UPF1 to stalled ribosomes in the context of nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. {ECO:0000269|PubMed:7990965}.;
- Pathway
- mRNA surveillance pathway - Homo sapiens (human);Translation Factors;Eukaryotic Translation Termination;Translation;Metabolism of proteins;Metabolism of RNA;Nonsense-Mediated Decay (NMD);Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC);Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
(Consensus)
Recessive Scores
- pRec
- 0.375
Intolerance Scores
- loftool
- rvis_EVS
- -0.32
- rvis_percentile_EVS
- 31.46
Haploinsufficiency Scores
- pHI
- 0.988
- hipred
- Y
- hipred_score
- 0.748
- ghis
- 0.623
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.983
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Etf1
- Phenotype
Zebrafish Information Network
- Gene name
- etf1b
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- curved ventral
Gene ontology
- Biological process
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translational termination;regulation of translational termination;protein methylation
- Cellular component
- nucleus;cytoplasm;cytosol;translation release factor complex
- Molecular function
- RNA binding;translation release factor activity;protein binding;translation termination factor activity;translation release factor activity, codon specific;ribosome binding;sequence-specific mRNA binding