NELFE

negative elongation factor complex member E, the group of RNA binding motif containing|MicroRNA protein coding host genes|Negative elongation factor complex members

Basic information

Region (hg38): 6:31952087-31959038

Previous symbols: [ "RDBP" ]

Links

ENSG00000204356NCBI:7936OMIM:154040HGNC:13974Uniprot:P18615AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NELFE gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
44
clinvar
2
clinvar
46
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 44 3 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NELFEprotein_codingprotein_codingENST00000375429 107024
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.006900.9931257370111257480.0000437
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.571772460.7190.00001622451
Missense in Polyphen2339.970.57544460
Synonymous0.9987182.50.8600.00000438758
Loss of Function3.32927.90.3220.00000218236

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00005940.0000594
Ashkenazi Jewish0.00009970.0000992
East Asian0.00005470.0000544
Finnish0.000.00
European (Non-Finnish)0.00004630.0000439
Middle Eastern0.00005470.0000544
South Asian0.00007770.0000653
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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