EXOSC2
protein-codingexosome component 2, the group of Exosome complex
Gene summary
Predicted to enable RNA binding activity. Involved in RNA catabolic process; RNA processing; and positive regulation of cell growth. Located in cytosol; nucleolus; and nucleoplasm. Part of nuclear exosome (RNase complex). Implicated in short stature, hearing loss, retinitis pigmentosa, and distinctive facies. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~13.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0044634
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0044634
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0044634
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0044634
Submitter: ClinGen
The *EXOSC2* gene (exocyst complex component 2) is located on chromosome 9 at 9q34.12 and encodes a protein that is part of exosome complex, a multi-protein complex capable of degrading various types of RNA molecules. *EXOSC2* was first reported in relation to retinitis pigmentosa-hearing loss-premature aging-short stature-facial dysmorphism syndrome in 2016 (PMID:26843489: Di Donato et al. 2016). Six variants (5 missense, 1 splice-site) reported in four probands across three publications have been included in this curation (PMIDs: 26843489, 36344539, 36069504). The mechanism of disease is predicted to be loss of function. This gene-disease pair is also supported by experimental evidence, namely a zebrafish KO model (PMID: 33333712). In summary, there is limited evidence supporting the relationship between *EXOSC2* and retinitis pigmentosa-hearing loss-premature aging-short stature-facial dysmorphism syndrome. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the ClinGen Syndromic Disorders GCEP on the meeting date March 21st, 2025 (SOP Version 11).
Inheritance Pattern: AR
Disease ID:MONDO:0044634
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0044634
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic
Intervention: Audiologic/Otolaryngologic
Rationale: Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to EXOSC2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014285.7. 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 | 63 | 1 | 64 | |||
| missense | 4 | 116 | 5 | 1 | 126 | |
| nonsense | 2 | 3 | 5 | |||
| start loss | 0 | |||||
| frameshift | 9 | 9 | ||||
| splice donor/acceptor (+/-2bp) | 2 | 5 | 7 | |||
| Total | 0 | 8 | 133 | 68 | 2 | 211 |
Highest pathogenic variant AF is 0.00009916159
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055100.2 | 9 | MANE Select | |
| Ensembl | ENSP00000361433.5 | 9 | MANE Select | |
| RefSeq | NP_001269637.1 | 8 | Standard | |
| RefSeq | NP_001269638.1 | 8 | 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
- exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
- rRNA processing
- positive regulation of cell growth
- nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'
- U4 snRNA 3'-end processing
Molecular Function
- 3'-5'-exoribonuclease activity
- RNA binding
- exoribonuclease activity
- protein binding
- 7S RNA 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
- ENST00000372358
- Coding exons
- 9
- Length
- 11141
- Individuals with no LoFs
- 125665
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 83
- Defined
- 125748
- p
- 0.000330
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.390 | 153 | 167 | 0.915 | 0.00000866 | 1893 |
| Missense (PolyPhen) | 33 | 51.475 | 0.64109 | 524 | ||
| Synonymous | 0.602 | 57 | 63.1 | 0.904 | 0.00000348 | 578 |
| Loss of Function | 1.28 | 11 | 16.6 | 0.662 | 8.65e-7 | 196 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00043 | 0.00043 | rare |
| Latino/Admixed American | 0.00017 | 0.00017 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00043 | 0.00044 | rare |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00049 | 0.00049 | rare |
| South Asian | 0.000065 | 0.000065 | 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. EXOSC2 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC4 and EXOSC7. {ECO:0000269|PubMed:17545563}.;
- Disease
- DISEASE: Short stature, hearing loss, retinitis pigmentosa, and distinctive facies (SHRF) [MIM:617763]: An autosomal recessive disorder characterized by childhood myopia, early onset retinitis pigmentosa, progressive sensorineural hearing loss, hypothyroidism, short stature, brachydactyly, recognisable facial gestalt, premature ageing and mild intellectual disability. {ECO:0000269|PubMed:26843489}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.116
Intolerance Scores
- LoFtool
- 0.391
- RVIS EVS
- -0.23
- RVIS percentile EVS
- 37.32
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.997
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |