NELFB

negative elongation factor complex member B, the group of Negative elongation factor complex members

Basic information

Region (hg38): 9:137255327-137273542

Previous symbols: [ "COBRA1" ]

Links

ENSG00000188986 ∙ NCBI:25920 ∙ OMIM:611180 ∙ HGNC:24324 ∙ Uniprot:Q8WX92 ∙ 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 NELFB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NELFB 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			46			46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	1	0

Variants in NELFB

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

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

Position	Type	Phenotype	Significance	ClinVar
9-137255546-G-A		not specified	Uncertain significance (Dec 21, 2023)
9-137255917-G-C		not specified	Uncertain significance (Oct 17, 2023)
9-137255931-T-G		not specified	Uncertain significance (Oct 20, 2024)
9-137255958-G-A		not specified	Uncertain significance (Feb 27, 2023)
9-137256343-A-C		not specified	Uncertain significance (Apr 25, 2022)
9-137256396-G-C		not specified	Uncertain significance (Feb 08, 2025)
9-137256424-C-T		not specified	Uncertain significance (Nov 09, 2021)
9-137256834-A-G		not specified	Uncertain significance (Jan 19, 2024)
9-137256846-T-A		not specified	Uncertain significance (Oct 16, 2024)
9-137256915-A-C		not specified	Uncertain significance (Jun 18, 2021)
9-137256944-C-A		not specified	Uncertain significance (Aug 21, 2023)
9-137263041-T-C		not specified	Uncertain significance (May 05, 2023)
9-137263128-G-A		not specified	Uncertain significance (Apr 18, 2023)
9-137263146-C-T		not specified	Uncertain significance (Jan 10, 2023)
9-137263209-A-T		not specified	Uncertain significance (Jan 22, 2025)
9-137263212-C-A		not specified	Uncertain significance (Mar 20, 2023)
9-137264260-G-A		not specified	Uncertain significance (Dec 07, 2024)
9-137264261-A-T		not specified	Uncertain significance (Dec 07, 2024)
9-137264273-G-C		not specified	Uncertain significance (May 04, 2022)
9-137264333-A-G		not specified	Uncertain significance (Dec 12, 2023)
9-137265959-G-A		not specified	Uncertain significance (Apr 25, 2022)
9-137266340-G-A		not specified	Uncertain significance (Sep 24, 2024)
9-137266358-C-T		not specified	Uncertain significance (Jun 16, 2024)
9-137266972-C-T		not specified	Uncertain significance (Feb 27, 2023)
9-137267011-A-G		not specified	Uncertain significance (Dec 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NELFB	protein_coding	protein_coding	ENST00000343053	13	18374

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00339	0.996	125724	0	19	125743	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.66	271	360	0.753	0.0000227	3751
Missense in Polyphen		85	128.05	0.6638		1340
Synonymous	-1.41	196	172	1.14	0.0000120	1188
Loss of Function	3.09	9	26.0	0.346	0.00000126	294

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000190	0.000181
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

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. Binds RNA which may help to stabilize the NELF complex on nucleic acid. In vitro, binds weakly to the HIV-1 TAR RNA which is located in the long terminal repeat (LTR) of HIV-1. May be able to induce chromatin unfolding. {ECO:0000269|PubMed:10199401, ECO:0000269|PubMed:12612062, ECO:0000269|PubMed:23884411, ECO:0000269|PubMed:27282391}.
• 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: 0.275

Intolerance Scores

• rvis_EVS: -1.35
• rvis_percentile_EVS: 4.56

Haploinsufficiency Scores

• pHI: 0.132
• hipred: Y
• hipred_score: 0.714
• ghis: 0.627

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• 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: Nelfb
• Phenotype: embryo 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: nelfb
• 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
• Cellular component: nucleoplasm;cytoplasm;NELF complex
• Molecular function: RNA binding;protein binding