EXOSC2

protein-coding

exosome 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

NM_014285.7

Inheritance

AR

ClinVar variants

P:8U:133B:70

Top phenotype

Short stature, hearing loss, retinitis pigmentosa, and distinctive facies

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr9:130,693,721-130,707,288

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~13.6 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

retinitis pigmentosa-hearing loss-premature aging-short stature-facial dysmorphism syndromeLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0044634

Submitter: Ambry Genetics

retinitis pigmentosa-hearing loss-premature aging-short stature-facial dysmorphism syndromeMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0044634

Submitter: PanelApp Australia

retinitis pigmentosa-hearing loss-premature aging-short stature-facial dysmorphism syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0044634

Submitter: Labcorp Genetics (formerly Invitae)

retinitis pigmentosa-hearing loss-premature aging-short stature-facial dysmorphism syndromeLIMITED

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).

retinitis pigmentosa-hearing loss-premature aging-short stature-facial dysmorphism syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0044634

Submitter: Orphanet

retinitis pigmentosa-hearing loss-premature aging-short stature-facial dysmorphism syndromeLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0044634

Submitter: G2P

Clinical Genomic Database (CGD)

Short stature, hearing loss, retinitis pigmentosa, and distinctive faciesAR

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

Refs: 26843489Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EXOSC2 variants in ClinVar

6 Conditions Cataloged
not providedTotal: 270
not specifiedTotal: 81
Retinitis pigmentosa-hearing loss-premature aging-short stature-facial dysmorphism syndromeTotal: 14
EXOSC2-related disorderTotal: 9
Retinal dystrophyTotal: 1
Neurodevelopmental delayTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
63
clinvar
1
clinvar
64
missense
4
clinvar
116
clinvar
5
clinvar
1
clinvar
126
nonsense
2
clinvar
3
clinvar
5
start loss
0
frameshift
9
clinvar
9
splice donor/acceptor (+/-2bp)
2
clinvar
5
clinvar
7
Total08133682211

Highest pathogenic variant AF is 0.00009916159

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_014285.7RefSeqNP_055100.29MANE Select
ENST00000372358.10EnsemblENSP00000361433.59MANE Select
NM_001282708.1RefSeqNP_001269637.18Standard
NM_001282709.1RefSeqNP_001269638.18Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.3901531670.9150.000008661893
Missense (PolyPhen)3351.4750.64109524
Synonymous0.6025763.10.9040.00000348578
Loss of Function1.281116.60.6628.65e-7196

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000430.00043rare
Latino/Admixed American0.000170.00017rare
Ashkenazi Jewish0.0000990.000099rare
East Asian0.000430.00044rare
Finnish0.0000930.000092rare
European (Non-Finnish)0.000490.00049rare
South Asian0.0000650.000065rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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