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

ENSG00000204356 ∙ NCBI:7936 ∙ OMIM:154040 ∙ HGNC:13974 ∙ Uniprot:P18615 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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		1
missense			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel					2	2
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			5	1	2	8
Total	0	0	32	3	4

Variants in NELFE

This is a list of pathogenic ClinVar variants found in the NELFE region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-31952140-T-C			Benign (Nov 10, 2018)
6-31952179-T-C			Benign (Nov 10, 2018)
6-31952321-T-C		not specified	Uncertain significance (Sep 12, 2023)
6-31952342-T-C		not specified	Uncertain significance (Jun 11, 2024)
6-31952369-G-A		not specified	Uncertain significance (Aug 10, 2021)
6-31953767-A-T		not specified	Uncertain significance (Apr 20, 2024)
6-31953789-T-C		not specified	Uncertain significance (Dec 27, 2023)
6-31954129-G-A		not specified	Uncertain significance (Jul 14, 2021)
6-31954379-T-C		not specified	Uncertain significance (Apr 25, 2023)
6-31954380-C-T		not specified	Uncertain significance (Aug 28, 2023)
6-31954394-A-G		not specified	Uncertain significance (Nov 08, 2021)
6-31954557-C-T		not specified	Uncertain significance (Nov 18, 2022)
6-31954558-G-A		not specified	Uncertain significance (May 31, 2022)
6-31954568-CTCTCGG-C			Benign (May 23, 2018)
6-31954596-C-T		not specified	Uncertain significance (Sep 06, 2023)
6-31954630-C-T		not specified	Uncertain significance (Mar 23, 2022)
6-31954633-G-C		not specified	Uncertain significance (Jul 12, 2023)
6-31954637-C-T			Likely benign (Feb 13, 2018)
6-31954651-G-A		not specified	Uncertain significance (Oct 27, 2021)
6-31954663-TGTCTCGATCCCG-T			Benign (Apr 09, 2018)
6-31954668-C-T		not specified	Uncertain significance (Nov 08, 2022)
6-31954692-C-T		not specified	Uncertain significance (Nov 21, 2023)
6-31954729-G-A		not specified	Uncertain significance (Aug 04, 2023)
6-31954734-C-T		not specified	Uncertain significance (Jul 14, 2021)
6-31954750-G-C		not specified	Uncertain significance (Oct 17, 2023)

GnomAD

Source: gnomAD

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: 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

• 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 Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nelfe

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