EXOSC8

protein-coding

exosome component 8, the group of Exosome complex

Gene summary

This gene encodes a 3'-5' exoribonuclease that specifically interacts with mRNAs containing AU-rich elements. The encoded protein is part of the exosome complex that is important for the degradation of numerous RNA species. A pseudogene of this gene is found on chromosome 6. [provided by RefSeq, Mar 2009]

MANE transcript

NM_181503.3

Inheritance

AR

ClinVar variants

P:4U:62B:18

Top phenotype

Pontocerebellar hypoplasia, type 1C

gnomAD constraint

pLI —, LoF o/e 1.17

Max pathogenic AF

—

Genomic locus

chr13:36,998,816-37,025,881

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~27.1 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

pontocerebellar hypoplasia, type 1CLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0014485

Submitter: Ambry Genetics

pontocerebellar hypoplasia, type 1CSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014485

Submitter: PanelApp Australia

pontocerebellar hypoplasia, type 1CMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0014485

Submitter: G2P

pontocerebellar hypoplasia type 1SUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0016396

Submitter: Orphanet

pontocerebellar hypoplasia, type 1CLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0014485

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Pontocerebellar hypoplasia, type 1CAR

Manifestation: Audiologic/Otolaryngologic; Neurologic; Ophthalmologic

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: 24989451Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EXOSC8 variants in ClinVar

5 Conditions Cataloged
not providedTotal: 84
not specifiedTotal: 35
Pontocerebellar hypoplasia, type 1CTotal: 15
EXOSC8-related disorderTotal: 5
Spastic ataxiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_181503.3. 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
14
clinvar
1
clinvar
15
missense
1
clinvar
56
clinvar
1
clinvar
2
clinvar
60
nonsense
1
clinvar
1
clinvar
2
start loss
1
clinvar
1
frameshift
2
clinvar
1
clinvar
3
splice donor/acceptor (+/-2bp)
3
clinvar
3
Total226215384

Highest pathogenic variant AF is 0.0000074515187

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 69 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_181503.3RefSeqNP_852480.111MANE Select
ENST00000389704.4EnsemblENSP00000374354.311MANE Select
ENST00000239893.9EnsemblENSP00000239893.53Standard
ENST00000481013.1EnsemblENSP00000419203.12Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
exosc8Danio 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
  • biological_process
  • rRNA catabolic process
  • nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'

Molecular Function

  • exoribonuclease activity
  • protein binding
  • AU-rich element binding
  • identical 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
ENST00000389704
Coding exons
11
Length
10798
Individuals with no LoFs
125656
Homozygous LoFs
0
Heterozygous LoFs
92
Defined
125748
p
0.000366
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.8461151440.8010.000007031778
Missense (PolyPhen)2240.0690.54905464
Synonymous1.813450.30.6760.00000269524
Loss of Function-0.6602017.11.178.02e-7227

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000750.00074rare
Latino/Admixed American0.000180.00017rare
Ashkenazi Jewish00.0absent
East Asian0.000110.00011rare
Finnish00.0absent
European (Non-Finnish)0.000560.00055rare
South Asian0.000320.00029rare
Other00.0absent

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. EXOSC8 binds to ARE-containing RNAs. {ECO:0000269|PubMed:16912217, ECO:0000269|PubMed:17545563}.;
Disease
DISEASE: Pontocerebellar hypoplasia 1C (PCH1C) [MIM:616081]: A severe autosomal recessive neurodegenerative disease characterized by cerebellar and corpus callosum hypoplasia, abnormal myelination of the central nervous system, and spinal motor neuron disease. Affected individuals manifest failure to thrive, severe muscle weakness, spasticity and psychomotor retardation. Vision and hearing are impaired. {ECO:0000269|PubMed:24989451}. Note=The disease is caused by mutations affecting the gene represented in this entry. EXOSC8 dysfunction causes myelin disruption through an imbalanced supply of myelin proteins due to dysregulation of their ARE-containing mRNAs (PubMed:24989451). {ECO:0000269|PubMed:24989451}.;

Recessive Scores

pRec
0.137

Intolerance Scores

LoFtool
0.831
RVIS EVS
0.1
RVIS percentile EVS
61.49

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
E
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
0.930

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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