ELL

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

Basic information

Region (hg38): 19:18442662-18522116

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.

• Inborn genetic diseases (26 variants)
• not provided (2 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.

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			24	2	1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	2

Variants in ELL

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

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

Position	Type	Phenotype	Significance	ClinVar
19-18444858-T-C		not specified	Uncertain significance (Nov 10, 2022)
19-18445259-C-T		not specified	Uncertain significance (Apr 10, 2023)
19-18446350-C-T		not specified	Uncertain significance (Sep 14, 2022)
19-18446353-C-T		not specified	Uncertain significance (Jul 05, 2022)
19-18446778-G-C		not specified	Uncertain significance (Dec 06, 2023)
19-18450542-C-T		not specified	Uncertain significance (Jun 23, 2023)
19-18450550-G-C		not specified	Uncertain significance (Sep 12, 2023)
19-18450560-G-A		not specified	Uncertain significance (Sep 12, 2023)
19-18450663-G-A			Benign (Jul 22, 2021)
19-18450665-C-G		not specified	Uncertain significance (Mar 06, 2023)
19-18450666-C-T		not specified	Likely benign (Mar 30, 2022)
19-18450726-G-A		not specified	Uncertain significance (Jun 22, 2023)
19-18450770-G-A		not specified	Uncertain significance (Mar 04, 2024)
19-18450822-T-C		not specified	Likely benign (Dec 13, 2023)
19-18450836-G-A		not specified	Uncertain significance (Apr 22, 2022)
19-18450870-C-T		not specified	Likely benign (Jul 14, 2021)
19-18450948-C-T		not specified	Uncertain significance (May 15, 2023)
19-18450962-G-A		not specified	Uncertain significance (Nov 18, 2022)
19-18450972-G-A		not specified	Uncertain significance (Apr 28, 2023)
19-18451562-G-C		not specified	Uncertain significance (Dec 21, 2023)
19-18451578-G-A		not specified	Uncertain significance (Jan 08, 2024)
19-18451628-C-T			Benign (Jun 08, 2020)
19-18451640-C-G		not specified	Uncertain significance (Apr 12, 2022)
19-18458215-C-A		not specified	Uncertain significance (Oct 20, 2021)
19-18461600-G-A		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELL	protein_coding	protein_coding	ENST00000262809	12	79465

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.985	0.0146	125725	0	5	125730	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	328	385	0.852	0.0000258	3972
Missense in Polyphen		74	129.12	0.57309		1383
Synonymous	-1.04	194	176	1.10	0.0000128	1268
Loss of Function	4.44	4	30.5	0.131	0.00000187	318

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000270	0.0000264
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

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

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

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