NELFE
Basic information
Region (hg38): 6:31952087-31959038
Previous symbols: [ "RDBP" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (46 variants)
- not_provided (4 variants)
- Trichohepatoenteric_syndrome (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NELFE gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002904.6. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 44 | 46 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 44 | 3 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
NELFE | protein_coding | protein_coding | ENST00000375429 | 10 | 7024 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00690 | 0.993 | 125737 | 0 | 11 | 125748 | 0.0000437 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.57 | 177 | 246 | 0.719 | 0.0000162 | 2451 |
Missense in Polyphen | 23 | 39.97 | 0.57544 | 460 | ||
Synonymous | 0.998 | 71 | 82.5 | 0.860 | 0.00000438 | 758 |
Loss of Function | 3.32 | 9 | 27.9 | 0.322 | 0.00000218 | 236 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000594 | 0.0000594 |
Ashkenazi Jewish | 0.0000997 | 0.0000992 |
East Asian | 0.0000547 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000463 | 0.0000439 |
Middle Eastern | 0.0000547 | 0.0000544 |
South Asian | 0.0000777 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Essential component of the NELF complex, a complex that negatively regulates the elongation of transcription by RNA polymerase II. The NELF complex, which acts via an association with the DSIF complex and causes transcriptional pausing, is counteracted by the P-TEFb kinase complex. The NELF complex is involved in HIV-1 latency possibly involving recruitment of PCF11 to paused RNA polymerase II. Provides the strongest RNA binding activity of the NELF complex and may initially recruit the NELF complex to RNA. Binds to the HIV-1 TAR RNA which is located in the long terminal repeat (LTR) of HIV-1. {ECO:0000269|PubMed:10199401, ECO:0000269|PubMed:11940650, ECO:0000269|PubMed:12612062, ECO:0000269|PubMed:18303858, ECO:0000269|PubMed:27282391, ECO:0000305}.;
- Pathway
- Initiation of transcription and translation elongation at the HIV-1 LTR;Disease;Formation of the HIV-1 Early Elongation Complex;Gene expression (Transcription);Formation of HIV-1 elongation complex containing HIV-1 Tat;Tat-mediated elongation of the HIV-1 transcript;Abortive elongation of HIV-1 transcript in the absence of Tat;HIV Transcription Elongation;HIV elongation arrest and recovery;Formation of HIV elongation complex in the absence of HIV Tat;Pausing and recovery of HIV elongation;Generic Transcription Pathway;Tat-mediated HIV elongation arrest and recovery;Pausing and recovery of Tat-mediated HIV elongation;Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;RNA Polymerase II Pre-transcription Events;Formation of RNA Pol II elongation complex ;RNA Polymerase II Transcription;Infectious disease;RNA Polymerase II Transcription Elongation;TP53 Regulates Transcription of DNA Repair Genes;Transcriptional Regulation by TP53;Formation of the Early Elongation Complex
(Consensus)
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- loftool
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 53.51
Haploinsufficiency Scores
- pHI
- 0.497
- hipred
- Y
- hipred_score
- 0.655
- ghis
- 0.532
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- gene_indispensability_score
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nelfe
- Phenotype
Zebrafish Information Network
- Gene name
- nelfe
- Affected structure
- hematopoietic multipotent progenitor cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;negative regulation of transcription elongation from RNA polymerase II promoter;positive regulation of transcription by RNA polymerase II;positive regulation of histone H3-K4 methylation;positive regulation of ERK1 and ERK2 cascade;negative regulation of mRNA polyadenylation
- Cellular component
- nucleus;nucleoplasm;plasma membrane;nuclear body;NELF complex
- Molecular function
- chromatin binding;RNA binding;protein binding