EXOSC3

protein-coding

exosome 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

NM_016042.4

Inheritance

AR

ClinVar variants

P:53U:91B:112

Top phenotype

Pontocerebellar hypoplasia type 1B

gnomAD constraint

pLI —, LoF o/e 0.65

Max pathogenic AF

—

Genomic locus

chr9:37,759,234-37,832,117

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~72.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

pontocerebellar hypoplasia type 1BDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013853

Submitter: Illumina

pontocerebellar hypoplasia type 1BSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013853

Submitter: PanelApp Australia

pontocerebellar hypoplasia type 1SUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0016396

Submitter: Orphanet

pontocerebellar hypoplasia type 1BSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013853

Submitter: Genomics England PanelApp

pontocerebellar hypoplasia type 1BDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013853

Submitter: G2P

pontocerebellar hypoplasia type 1BSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013853

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Pontocerebellar hypoplasia type 1BAR

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

Refs: 11020648; 12731647; 22544365; 24524299; 25149867Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EXOSC3 variants in ClinVar

18 Conditions Cataloged
Pontocerebellar hypoplasia type 1BTotal: 226
Inborn genetic diseasesTotal: 58
not providedTotal: 37
not specifiedTotal: 21
EXOSC3-related disorderTotal: 12
Pontoneocerebellar hypoplasiaTotal: 9
Abnormal cerebellum morphologyTotal: 1
Hypoplasia of the ponsTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
99
clinvar
2
clinvar
101
missense
2
clinvar
9
clinvar
89
clinvar
11
clinvar
111
nonsense
3
clinvar
5
clinvar
8
start loss
3
clinvar
3
clinvar
6
frameshift
13
clinvar
11
clinvar
2
clinvar
26
splice donor/acceptor (+/-2bp)
4
clinvar
4
Total2132911102256

Highest pathogenic variant AF is 0.0007057202

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_016042.4RefSeqNP_057126.24MANE Select
ENST00000327304.10EnsemblENSP00000323046.44MANE Select
NM_001002269.2RefSeqNP_001002269.13Standard
ENST00000396521.3EnsemblENSP00000379775.33Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
exosc3Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.2241621541.050.000006851745
Missense (PolyPhen)5956.3031.0479681
Synonymous-2.848759.21.470.00000273575
Loss of Function1.08710.80.6465.54e-7131

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000270.00025rare
Latino/Admixed American0.000440.00043rare
Ashkenazi Jewish00.0absent
East Asian0.000930.00092rare
Finnish00.0absent
European (Non-Finnish)0.000110.00011rare
South Asian0.000130.00013rare
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. 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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.