EXOSC5
protein-codingexosome component 5, the group of Exosome complex
Gene summary
Predicted to enable RNA binding activity. Involved in DNA deamination; RNA processing; and mRNA catabolic process. Acts upstream of or within defense response to virus. Located in cytosol; euchromatin; and nucleolus. Part of exosome (RNase complex). [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~11.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0859200
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0859200
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Craniofacial; Musculoskeletal; Neurologic
Intervention: Cardiovascular
Rationale: Among other findings, the condition can include cardiovascular anomalies, including conduction defects, and awareness may allow early diagnosis and management (eg, with pacemaker)
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to EXOSC5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020158.4. 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 | 1 | 5 | 6 | |||
| missense | 1 | 2 | 53 | 2 | 58 | |
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 2 | 3 | |||
| splice donor/acceptor (+/-2bp) | 1 | 1 | 1 | 3 | ||
| Total | 3 | 3 | 57 | 7 | 0 | 70 |
Highest pathogenic variant AF is 0.000061530576
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_064543.3 | 6 | MANE Select | |
| Ensembl | ENSP00000221233.3 | 6 | MANE Select | |
| Ensembl | ENSP00000471557.2 | 7 | Standard | |
| Ensembl | ENSP00000471557.2 | 7 | Standard |
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
- rRNA processing
- rRNA catabolic process
- 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
- ENST00000221233
- Coding exons
- 6
- Length
- 11106
- Individuals with no LoFs
- 125734
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 125747
- p
- 0.0000517
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.484 | 131 | 148 | 0.888 | 0.00000933 | 1476 |
| Missense (PolyPhen) | 49 | 60.181 | 0.81421 | 585 | ||
| Synonymous | 0.206 | 66 | 68.2 | 0.968 | 0.00000453 | 508 |
| Loss of Function | 1.29 | 5 | 9.22 | 0.543 | 3.92e-7 | 111 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00013 | 0.000092 | rare |
| European (Non-Finnish) | 0.000063 | 0.000062 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
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. {ECO:0000269|PubMed:11782436, ECO:0000269|PubMed:21255825}.;
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- LoFtool
- 0.746
- RVIS EVS
- -0.29
- RVIS percentile EVS
- 33.2
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.964
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |