ELL2

elongation factor for RNA polymerase II 2, the group of Super elongation complex

Basic information

Region (hg38): 5:95885098-95961851

Links

ENSG00000118985 ∙ NCBI:22936 ∙ OMIM:601874 ∙ HGNC:17064 ∙ Uniprot:O00472 ∙ 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 ELL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELL2 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					3	3
Total	0	0	17	1	3

Variants in ELL2

This is a list of pathogenic ClinVar variants found in the ELL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-95891112-T-G		not specified	Uncertain significance (Feb 14, 2023)
5-95898272-T-C		not specified	Uncertain significance (May 14, 2024)
5-95898298-A-C		not specified	Uncertain significance (Jun 21, 2022)
5-95898356-T-G		not specified	Uncertain significance (Dec 14, 2021)
5-95898387-T-C		not specified	Uncertain significance (Dec 27, 2023)
5-95898432-G-T		not specified	Uncertain significance (Nov 15, 2023)
5-95898510-C-T		not specified	Uncertain significance (Jun 07, 2024)
5-95898545-G-A		not specified	Uncertain significance (Sep 12, 2023)
5-95898552-G-A		not specified	Uncertain significance (Oct 16, 2023)
5-95898612-T-C		not specified	Likely benign (May 13, 2024)
5-95898651-T-G		not specified	Uncertain significance (Oct 22, 2021)
5-95898807-G-A		not specified	Uncertain significance (Jun 02, 2024)
5-95900743-G-A		not specified	Uncertain significance (Jul 15, 2021)
5-95900769-G-A		not specified	Uncertain significance (Apr 08, 2022)
5-95906560-T-G		not specified	Uncertain significance (Jun 27, 2023)
5-95906764-C-G		not specified	Uncertain significance (Aug 02, 2021)
5-95913795-T-A		not specified	Uncertain significance (Dec 28, 2023)
5-95913848-C-T		not specified	Uncertain significance (Dec 08, 2023)
5-95917404-C-G			Benign (Jul 13, 2018)
5-95919425-T-A		not specified	Uncertain significance (Mar 29, 2022)
5-95919514-T-C		not specified	Uncertain significance (Oct 06, 2021)
5-95924158-C-T			Benign (Jan 09, 2019)
5-95929852-G-A			Benign (Jan 09, 2019)
5-95943025-T-C			Likely benign (Jul 27, 2018)
5-95961624-T-C		not specified	Uncertain significance (Apr 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELL2	protein_coding	protein_coding	ENST00000237853	12	76974

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00176	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	261	341	0.765	0.0000175	4162
Missense in Polyphen		36	70.837	0.50821		940
Synonymous	-0.960	143	129	1.11	0.00000671	1221
Loss of Function	4.73	3	31.7	0.0945	0.00000172	400

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000898	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
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. 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). Plays a role in immunoglobulin secretion in plasma cells: directs efficient alternative mRNA processing, influencing both proximal poly(A) site choice and exon skipping, as well as immunoglobulin heavy chain (IgH) alternative processing. Probably acts by regulating histone modifications accompanying transition from membrane- specific to secretory IgH mRNA expression. {ECO:0000269|PubMed:20159561, ECO:0000269|PubMed:20471948, ECO:0000269|PubMed:22195968, ECO:0000269|PubMed:23251033}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.141
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.91

Haploinsufficiency Scores

• pHI: 0.444
• hipred: Y
• hipred_score: 0.647
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.810

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ell2
• Phenotype: immune system phenotype; skeleton phenotype; vision/eye phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: transcription elongation from RNA polymerase II promoter;snRNA transcription by RNA polymerase II
• Cellular component: nucleoplasm;transcription elongation factor complex
• Molecular function: protein binding