ELL3

elongation factor for RNA polymerase II 3, the group of Super elongation complex

Basic information

Region (hg38): 15:43772605-43777315

Links

ENSG00000128886 ∙ NCBI:80237 ∙ OMIM:609885 ∙ HGNC:23113 ∙ Uniprot:Q9HB65 ∙ 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 ELL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELL3 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in ELL3

This is a list of pathogenic ClinVar variants found in the ELL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-43773199-G-A		not specified	Uncertain significance (Feb 05, 2024)
15-43773339-C-T		not specified	Uncertain significance (Oct 06, 2021)
15-43774204-C-T		not specified	Likely benign (Aug 30, 2021)
15-43774212-T-G		not specified	Uncertain significance (Dec 23, 2022)
15-43774612-A-C		not specified	Uncertain significance (Jul 20, 2022)
15-43774625-C-T		not specified	Uncertain significance (Jul 13, 2022)
15-43774740-C-G		not specified	Uncertain significance (Mar 15, 2024)
15-43774770-G-A		not specified	Uncertain significance (Jun 30, 2023)
15-43775311-C-T		not specified	Uncertain significance (Apr 26, 2023)
15-43775317-G-A		not specified	Uncertain significance (Dec 09, 2023)
15-43775344-C-G		not specified	Uncertain significance (Nov 20, 2023)
15-43775541-C-T		not specified	Uncertain significance (May 20, 2024)
15-43775585-C-T		not specified	Uncertain significance (May 09, 2022)
15-43775597-T-A		not specified	Uncertain significance (Mar 20, 2023)
15-43775804-G-C		not specified	Uncertain significance (Feb 12, 2024)
15-43775821-G-T		not specified	Uncertain significance (Aug 23, 2021)
15-43775857-C-T		not specified	Uncertain significance (Dec 13, 2022)
15-43775918-C-T		not specified	Uncertain significance (Jul 13, 2021)
15-43776135-C-T		not specified	Uncertain significance (Apr 25, 2023)
15-43776544-C-T		not specified	Uncertain significance (Sep 17, 2021)
15-43776783-C-A		not specified	Uncertain significance (Feb 05, 2024)
15-43776784-A-C		not specified	Uncertain significance (Dec 07, 2021)
15-43776786-T-A		not specified	Uncertain significance (Aug 17, 2021)
15-43776868-G-C		not specified	Uncertain significance (Nov 29, 2023)
15-43776886-C-G		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELL3	protein_coding	protein_coding	ENST00000319359	11	4944

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.70e-12	0.200	125653	0	94	125747	0.000374

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.470	196	215	0.910	0.0000110	2552
Missense in Polyphen		62	76.261	0.813		902
Synonymous	0.546	71	77.1	0.921	0.00000341	768
Loss of Function	0.908	21	26.0	0.808	0.00000119	294

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000750	0.000750
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000415	0.000413
Middle Eastern	0.000381	0.000381
South Asian	0.000492	0.000490
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enhancer-binding elongation factor that specifically binds enhancers in embryonic stem cells (ES cells), marks them, and is required for their future activation during stem cell specification. Does not only bind to enhancer regions of active genes, but also marks the enhancers that are in a poised or inactive state in ES cells and is required for establishing proper RNA polymerase II occupancy at developmentally regulated genes in a cohesin-dependent manner. Probably required for priming developmentally regulated genes for later recruitment of the super elongation complex (SEC), for transcriptional activation during differentiation. Required for recruitment of P-TEFb within SEC during differentiation. Probably preloaded on germ cell chromatin, suggesting that it may prime gene activation by marking enhancers as early as in the germ cells. Promoting epithelial-mesenchymal transition (EMT) (By similarity). 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. 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). {ECO:0000250, ECO:0000269|PubMed:10882741, ECO:0000269|PubMed:22195968}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0831

Intolerance Scores

• loftool: 0.925
• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.38

Haploinsufficiency Scores

• pHI: 0.0925
• hipred: N
• hipred_score: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.963

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ell3

Gene ontology

• Biological process: DNA-templated transcription, elongation;transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;spermatogenesis;regulation of epithelial to mesenchymal transition;positive regulation of DNA-templated transcription, elongation;snRNA transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II;stem cell differentiation;positive regulation of neurogenesis;negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator;positive regulation of neural precursor cell proliferation
• Cellular component: nucleus;nucleoplasm;nucleolus;transcription elongation factor complex
• Molecular function: protein binding;enhancer binding