GeneBe

ELL

elongation factor for RNA polymerase II, the group of Super elongation complex|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 19:18442663-18522116

Previous symbols: [ "C19orf17" ]

Links

ENSG00000105656 ∙ NCBI:8178 ∙ OMIM:600284 ∙ HGNC:23114 ∙ Uniprot:P55199 ∙ 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 ELL gene.

  • not_specified (81 variants)
  • not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELL gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006532.4. 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
73
clinvar
8
clinvar
 81
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 73 8 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ELLprotein_codingprotein_codingENST00000262809 1279465
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.9850.0146125725051257300.0000199
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.033283850.8520.00002583972
Missense in Polyphen74129.120.573091383
Synonymous-1.041941761.100.00001281268
Loss of Function4.44430.50.1310.00000187318

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.00002700.0000264
Middle Eastern0.0001090.000109
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Elongation factor component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA. Elongation factor component of the little elongation complex (LEC), a complex required to regulate small nuclear RNA (snRNA) gene transcription by RNA polymerase II and III (PubMed:22195968, PubMed:23932780). Specifically required for stimulating the elongation step of RNA polymerase II- and III-dependent snRNA gene transcription (PubMed:23932780). ELL also plays an early role before its assembly into in the SEC complex by stabilizing RNA polymerase II recruitment/initiation and entry into the pause site. Required to stabilize the pre-initiation complex and early elongation. {ECO:0000269|PubMed:16006523, ECO:0000269|PubMed:20159561, ECO:0000269|PubMed:20471948, ECO:0000269|PubMed:22195968, ECO:0000269|PubMed:22252557, ECO:0000269|PubMed:23932780, ECO:0000269|PubMed:8596958}.;
Pathway
Interactome of polycomb repressive complex 2 (PRC2);Disease;Gene expression (Transcription);Formation of HIV-1 elongation complex containing HIV-1 Tat;Tat-mediated elongation of the HIV-1 transcript;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 transcribes snRNA genes;RNA Polymerase II Transcription;Infectious disease;RNA Polymerase II Transcription Elongation;TP53 Regulates Transcription of DNA Repair Genes;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

pRec
0.169

Intolerance Scores

loftool
0.157
rvis_EVS
-0.6
rvis_percentile_EVS
18.19

Haploinsufficiency Scores

pHI
0.484
hipred
Y
hipred_score
0.825
ghis
0.524

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.990

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ell
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);

Gene ontology

Biological process
in utero embryonic development;transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;negative regulation of phosphatase activity;positive regulation of DNA-templated transcription, elongation;positive regulation of transcription elongation from RNA polymerase II promoter;snRNA transcription by RNA polymerase II;snRNA transcription by RNA polymerase III;positive regulation of transcription by RNA polymerase III
Cellular component
nucleoplasm;transcription elongation factor complex;Cajal body;nuclear speck;transcriptionally active chromatin;histone locus body
Molecular function
protein binding;phosphatase binding