ELOA2
protein-codingelongin A2, the group of Elongin complex
Gene summary
This gene encodes the transcriptionally active subunit of the SIII (or elongin) transcription elongation factor complex, which also includes two regulatory subunits, elongins B and C. This complex acts to increase the rate of RNA chain elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites along the DNA template. Whereas a related protein with similar function, elongin A, is ubiquitously expressed, the encoded protein is specifically expressed in the testis, suggesting it may have a role in spermatogenesis. [provided by RefSeq, Jul 2008]
- TCEB3B
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.1 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 ELOA2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016427.3. 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 | 5 | 5 | ||||
| missense | 196 | 29 | 2 | 227 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 196 | 34 | 2 | 232 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057511.2 | 1 | MANE Select | |
| Ensembl | ENSP00000331302.4 | 1 | MANE Select |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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
Biological Process
- regulation of transcription by RNA polymerase II
- transcription by RNA polymerase II
- transcription elongation from RNA polymerase II promoter
- regulation of DNA-templated transcription, elongation
Molecular Function
- protein binding
Cellular Component
- nucleoplasm
- elongin complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000332567
- Coding exons
- 1
- Length
- 3046
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -3.32 | 656 | 456 | 1.44 | 0.0000336 | 4858 |
| Missense (PolyPhen) | 161 | 111.03 | 1.4501 | 1293 | ||
| Synonymous | -2.85 | 251 | 200 | 1.26 | 0.0000167 | 1548 |
| Loss of Function |
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 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: SIII, also known as elongin, is a general transcription elongation factor that increases the RNA polymerase II transcription elongation past template-encoded arresting sites. Subunit A2 is transcriptionally active but its transcription activity is not enhanced by binding to the dimeric complex of the SIII regulatory subunits B and C (elongin BC complex). {ECO:0000269|PubMed:10692460}.;
Intolerance Scores
- RVIS EVS
- 2.28
- RVIS percentile EVS
- 98.26
Essentials
- Essential (gene trap)
- N