EXOSC3
protein-codingexosome component 3, the group of Exosome complex
Gene summary
This gene encodes a non-catalytic component of the human exosome, a complex with 3'-5' exoribonuclease activity that plays a role in numerous RNA processing and degradation activities. Related pseudogenes of this gene are found on chromosome 19 and 21. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jun 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~72.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0013853
Submitter: Illumina
Inheritance Pattern: AR
Disease ID:MONDO:0013853
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0016396
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0013853
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0013853
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0013853
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to EXOSC3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016042.4. 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 | 99 | 2 | 101 | |||
| missense | 2 | 9 | 89 | 11 | 111 | |
| nonsense | 3 | 5 | 8 | |||
| start loss | 3 | 3 | 6 | |||
| frameshift | 13 | 11 | 2 | 26 | ||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 21 | 32 | 91 | 110 | 2 | 256 |
Highest pathogenic variant AF is 0.0007057202
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057126.2 | 4 | MANE Select | |
| Ensembl | ENSP00000323046.4 | 4 | MANE Select | |
| RefSeq | NP_001002269.1 | 3 | Standard | |
| Ensembl | ENSP00000379775.3 | 3 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| exosc3 | Danio rerio | Structure: motor neuron Quality: branchiness abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- RNA degradation - Homo sapiens (human)
- Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA
- KSRP (KHSRP) binds and destabilizes mRNA
- Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA
- Metabolism of RNA
Biological Process
- exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
- rRNA processing
- nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'
- U4 snRNA 3'-end processing
- regulation of mRNA stability
Molecular Function
- 3'-5'-exoribonuclease activity
- RNA binding
- exoribonuclease activity
- protein binding
Cellular Component
- nuclear exosome (RNase complex)
- cytoplasmic exosome (RNase complex)
- exosome (RNase complex)
- nucleus
- nucleoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000327304
- Coding exons
- 4
- Length
- 34460
- Individuals with no LoFs
- 125695
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 53
- Defined
- 125748
- p
- 0.000211
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.224 | 162 | 154 | 1.05 | 0.00000685 | 1745 |
| Missense (PolyPhen) | 59 | 56.303 | 1.0479 | 681 | ||
| Synonymous | -2.84 | 87 | 59.2 | 1.47 | 0.00000273 | 575 |
| Loss of Function | 1.08 | 7 | 10.8 | 0.646 | 5.54e-7 | 131 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00027 | 0.00025 | rare |
| Latino/Admixed American | 0.00044 | 0.00043 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00093 | 0.00092 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00011 | 0.00011 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. EXOSC3 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC9 and EXOSC5. {ECO:0000269|PubMed:11782436, ECO:0000269|PubMed:17545563, ECO:0000269|PubMed:19056938, ECO:0000269|PubMed:21255825}.;
- Disease
- DISEASE: Pontocerebellar hypoplasia 1B (PCH1B) [MIM:614678]: A severe autosomal recessive neurologic disorder characterized by a combination of cerebellar and spinal motor neuron degeneration beginning at birth. There is diffuse muscle weakness, progressive microcephaly, global developmental delay, and brainstem involvement. {ECO:0000269|PubMed:22544365}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- LoFtool
- 0.320
- RVIS EVS
- 0.62
- RVIS percentile EVS
- 83.25
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.924
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |