NELFA

negative elongation factor complex member A, the group of Negative elongation factor complex members|MicroRNA protein coding host genes

Basic information

Region (hg38): 4:1982717-2041903

Previous symbols: [ "WHSC2" ]

Links

ENSG00000185049 ∙ NCBI:7469 ∙ OMIM:606026 ∙ HGNC:12768 ∙ Uniprot:Q9H3P2 ∙ 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 NELFA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NELFA 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				26	5	31
missense			25	5	3	33
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				3		3
Total	0	0	26	34	8

Variants in NELFA

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

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

Position	Type	Phenotype	Significance	ClinVar
4-1983359-G-A		not specified	Uncertain significance (Jun 26, 2023)
4-1983411-T-C		not specified	Uncertain significance (Jul 02, 2024)
4-1983432-C-A		not specified	Likely benign (Apr 07, 2023)
4-1983477-C-T		not specified	Uncertain significance (Sep 06, 2022)
4-1983478-G-T		not specified	Uncertain significance (Apr 04, 2024)
4-1983636-G-A			Likely benign (Oct 24, 2018)
4-1983642-C-T			Likely benign (May 01, 2023)
4-1983663-G-A			Benign/Likely benign (Oct 01, 2023)
4-1983860-G-A			Benign (Aug 01, 2023)
4-1983891-T-C		not specified	Uncertain significance (Sep 20, 2023)
4-1983899-C-T			Likely benign (May 30, 2018)
4-1983918-G-A		not specified	Uncertain significance (Oct 20, 2024)
4-1983940-C-T		not specified	Likely benign (Oct 20, 2023)
4-1983941-G-A			Benign (Dec 31, 2019)
4-1983948-G-A		not specified	Uncertain significance (Aug 30, 2021)
4-1983980-C-T			Likely benign (Jan 19, 2018)
4-1983984-G-A		not specified	Uncertain significance (Jan 19, 2024)
4-1983990-G-A			Likely benign (Dec 31, 2019)
4-1983991-T-G		not specified	Uncertain significance (Dec 28, 2023)
4-1983994-G-C		not specified	Uncertain significance (Jul 09, 2021)
4-1983999-G-A		not specified	Uncertain significance (Aug 08, 2023)
4-1984029-G-A		not specified	Uncertain significance (Oct 29, 2021)
4-1984032-C-T		not specified	Uncertain significance (Sep 30, 2024)
4-1984046-C-T			Likely benign (Jan 11, 2018)
4-1984047-G-A		not specified	Uncertain significance (Aug 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NELFA	protein_coding	protein_coding	ENST00000382882	11	59190

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.135	0.865	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.82	256	352	0.727	0.0000227	3417
Missense in Polyphen		55	109.49	0.50234		975
Synonymous	-2.17	213	176	1.21	0.0000137	1142
Loss of Function	3.29	6	23.0	0.260	0.00000124	256

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000906
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000144	0.000139
European (Non-Finnish)	0.0000638	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
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. In vitro, the NELFA:NELFCD subcomplex binds to ssDNA and ssRNA in a sequence- and structure-dependent manner. Probably required to interact with the RNA polymerase II complex. {ECO:0000269|PubMed:10199401, ECO:0000269|PubMed:12563561, ECO:0000269|PubMed:12612062, 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: 0.146

Intolerance Scores

• rvis_EVS: -1.11
• rvis_percentile_EVS: 6.83

Haploinsufficiency Scores

• pHI: 0.160
• hipred: Y
• hipred_score: 0.780
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• 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: Nelfa

Gene ontology

• Biological process: transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;multicellular organism development;negative regulation of transcription elongation from RNA polymerase II promoter
• Cellular component: nucleoplasm;cytosol;nuclear body;NELF complex
• Molecular function: protein binding