ELP6
protein-codingelongator acetyltransferase complex subunit 6, the group of Elongator acetyltransferase complex
Gene summary
Predicted to be involved in positive regulation of cell migration. Predicted to act upstream of or within several processes, including autophagosome maturation; gene expression; and homeostasis of number of retina cells. Located in cytosol and nucleus. Part of elongator holoenzyme complex. [provided by Alliance of Genome Resources, Jul 2025]
- TMEM103
- C3orf75
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~18.1 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 ELP6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001031703.3. 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 | 0 | |||||
| missense | 1 | 40 | 8 | 49 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 1 | 42 | 8 | 0 | 51 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001026873.2 | 7 | MANE Select | |
| Ensembl | ENSP00000296149.4 | 7 | MANE Select | |
| RefSeq | NP_001350886.1 | 4 | Standard | |
| RefSeq | NP_001411139.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Chromatin modifying enzymes
- HATs acetylate histones
- Chromatin organization
Biological Process
- tRNA wobble uridine modification
- biological_process
- positive regulation of cell migration
Molecular Function
- molecular_function
Cellular Component
- nucleus
- cytosol
- Elongator holoenzyme complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000296149
- Coding exons
- 7
- Length
- 18122
- Individuals with no LoFs
- 124738
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 75
- Defined
- 124813
- p
- 0.000300
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.405 | 142 | 156 | 0.909 | 0.00000891 | 1748 |
| Missense (PolyPhen) | 39 | 52.176 | 0.74746 | 667 | ||
| Synonymous | 1.21 | 55 | 67.7 | 0.813 | 0.00000427 | 524 |
| Loss of Function | 1.42 | 7 | 12.4 | 0.565 | 5.25e-7 | 146 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00019 | rare |
| Latino/Admixed American | 0.00014 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00061 | 0.00061 | rare |
| Finnish | 0.00019 | 0.00019 | rare |
| European (Non-Finnish) | 0.00036 | 0.00036 | rare |
| South Asian | 0.00036 | 0.00036 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Acts as subunit of the RNA polymerase II elongator complex, which is a histone acetyltransferase component of the RNA polymerase II (Pol II) holoenzyme and is involved in transcriptional elongation. Elongator may play a role in chromatin remodeling and is involved in acetylation of histones H3 and probably H4. Involved in cell migration.;
Intolerance Scores
- RVIS EVS
- 0.15
- RVIS percentile EVS
- 64.32
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |