ELL
protein-codingelongation factor for RNA polymerase II, the group of Super elongation complex|Protein phosphatase 1 regulatory subunits
Gene summary
Enables phosphatase binding activity. Involved in positive regulation of DNA-templated transcription and snRNA transcription. Located in euchromatin and nuclear ribonucleoprotein granule. Part of transcription elongation factor complex. [provided by Alliance of Genome Resources, Jun 2026]
- C19orf17
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~79.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ELL variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006532.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 1 | 3 | |||
| missense | 93 | 9 | 102 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 95 | 9 | 1 | 105 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006523.1 | 12 | MANE Select | |
| Ensembl | ENSP00000262809.3 | 12 | MANE Select | |
| Ensembl | ENSP00000475681.2 | 3 | Standard | |
| Ensembl | ENSP00000475648.2 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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
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
Molecular Function
- protein binding
- phosphatase binding
Cellular Component
- nucleoplasm
- transcription elongation factor complex
- Cajal body
- nuclear speck
- transcriptionally active chromatin
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000262809
- Coding exons
- 12
- Length
- 79465
- Individuals with no LoFs
- 125725
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 5
- Defined
- 125730
- p
- 0.0000199
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.03 | 328 | 385 | 0.852 | 0.0000258 | 3972 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.169
Intolerance Scores
- LoFtool
- 0.157
- RVIS EVS
- -0.6
- RVIS percentile EVS
- 18.19
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.990
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |