NELFCD

negative elongation factor complex member C/D, the group of Armadillo like helical domain containing|Negative elongation factor complex members

Basic information

Region (hg38): 20:58981208-58995133

Previous symbols: [ "TH1L" ]

Links

ENSG00000101158 ∙ NCBI:51497 ∙ OMIM:605297 ∙ HGNC:15934 ∙ Uniprot:Q8IXH7 ∙ 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 NELFCD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NELFCD 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						0
missense			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	21	0	1

Variants in NELFCD

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

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

Position	Type	Phenotype	Significance	ClinVar
20-58981287-C-T		not specified	Uncertain significance (Feb 02, 2024)
20-58981290-G-A		not specified	Uncertain significance (Jul 20, 2021)
20-58981301-G-C		not specified	Uncertain significance (Jun 13, 2023)
20-58981307-A-G		not specified	Uncertain significance (Feb 01, 2023)
20-58981319-G-A		not specified	Uncertain significance (Sep 29, 2022)
20-58981359-A-G		not specified	Uncertain significance (Mar 07, 2023)
20-58986131-G-T		not specified	Uncertain significance (Feb 03, 2022)
20-58987804-C-G		not specified	Uncertain significance (Apr 07, 2022)
20-58988969-A-G		not specified	Uncertain significance (Apr 23, 2024)
20-58989901-C-T		not specified	Uncertain significance (Dec 22, 2023)
20-58989904-T-C		not specified	Uncertain significance (Apr 06, 2024)
20-58989912-G-A		not specified	Uncertain significance (Jan 26, 2022)
20-58990918-A-G		not specified	Uncertain significance (Oct 14, 2023)
20-58991036-C-G		not specified	Uncertain significance (Jun 03, 2022)
20-58991046-A-G		not specified	Uncertain significance (May 30, 2023)
20-58991053-T-C		not specified	Uncertain significance (Feb 17, 2022)
20-58991378-C-A		not specified	Uncertain significance (Jul 30, 2023)
20-58991417-G-T		not specified	Uncertain significance (Aug 02, 2021)
20-58991423-A-G		not specified	Uncertain significance (Oct 13, 2023)
20-58993122-C-T			Benign (Jun 27, 2018)
20-58993452-A-G		not specified	Uncertain significance (Nov 08, 2022)
20-58993721-A-G		not specified	Uncertain significance (Feb 22, 2023)
20-58993760-C-T		not specified	Uncertain significance (Dec 20, 2023)
20-58994221-C-T		not specified	Uncertain significance (May 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NELFCD	protein_coding	protein_coding	ENST00000602795	15	13926

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.176	0.824	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.29	216	334	0.647	0.0000189	3922
Missense in Polyphen		58	112.01	0.51782		1316
Synonymous	0.796	125	137	0.913	0.00000860	1157
Loss of Function	4.00	8	32.7	0.245	0.00000173	369

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000293	0.000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000158	0.000158
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
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, the NELFA:NELFCD subcomplex binds to ssDNA and ssRNA in a sequence- and structure- dependent manner. {ECO:0000269|PubMed:10199401, ECO:0000269|PubMed:12612062, ECO:0000269|PubMed:27282391, ECO:0000305|PubMed:23884411}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;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;AndrogenReceptor;TP53 Regulates Transcription of DNA Repair Genes;Transcriptional Regulation by TP53;Formation of the Early Elongation Complex (Consensus)

Recessive Scores

• pRec: 0.423

Intolerance Scores

• rvis_EVS: -1.2
• rvis_percentile_EVS: 5.76

Haploinsufficiency Scores

• pHI: 0.207
• hipred: Y
• hipred_score: 0.704
• ghis: 0.658

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: 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: Nelfcd

Gene ontology

• Biological process: transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;negative regulation of transcription, DNA-templated
• Cellular component: nucleoplasm;membrane;NELF complex
• Molecular function: RNA binding;protein binding