EXOSC1

protein-coding

exosome component 1, the group of Exosome complex

Gene summary

This gene encodes a core component of the exosome. The mammalian exosome is required for rapid degradation of AU rich element-containing RNAs but not for poly(A) shortening. The association of this protein with the exosome is mediated by protein-protein interactions with ribosomal RNA-processing protein 42 and ribosomal RNA-processing protein 46. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2016]

MANE transcript

NM_016046.5

Inheritance

AR

ClinVar variants

P:1U:29

Top phenotype

Pontocerebellar hypoplasia, type 1F

gnomAD constraint

pLI —, LoF o/e 0.94

Max pathogenic AF

—

Genomic locus

chr10:97,435,909-97,446,017

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~10.1 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

pontocerebellar hypoplasia, type 1FLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0030261

Submitter: PanelApp Australia

pontocerebellar hypoplasia, type 1FLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0030261

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Pontocerebellar hypoplasia, type 1FAR

Manifestation: Craniofacial; 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: 33463720Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EXOSC1 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 24
Pontocerebellar hypoplasia, type 1FTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016046.5. 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
1
clinvar
1
missense
1
clinvar
23
clinvar
24
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
5
clinvar
5
Total10290030

Highest pathogenic variant AF is 6.841911e-7

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 59 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_016046.5RefSeqNP_057130.18MANE Select
ENST00000370902.8EnsemblENSP00000359939.38MANE Select
NM_001318362.2RefSeqNP_001305291.17Standard
NM_001318363.2RefSeqNP_001305292.16Standard

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
  • regulation of mRNA stability
  • exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
  • RNA phosphodiester bond hydrolysis, exonucleolytic

Molecular Function

  • RNA binding
  • exoribonuclease activity
  • protein binding

Cellular Component

  • nuclear exosome (RNase complex)
  • exosome (RNase complex)
  • nucleoplasm
  • nucleolus
  • cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000370902
Coding exons
8
Length
9876
Individuals with no LoFs
125677
Homozygous LoFs
0
Heterozygous LoFs
71
Defined
125748
p
0.000282
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.2901081170.9250.000006151254
Missense (PolyPhen)4045.2340.88429470
Synonymous0.4943842.10.9030.00000221372
Loss of Function0.2171313.90.9377.38e-7152

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000180.00018rare
Latino/Admixed American0.000620.00061rare
Ashkenazi Jewish0.00200.0020notable
East Asian0.000160.00016rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.000110.00011rare
South Asian0.000320.00029rare
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. EXOSC1 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC6 and EXOSC8.;

Recessive Scores

pRec
0.156

Intolerance Scores

LoFtool
0.424
RVIS EVS
-0.36
RVIS percentile EVS
28.63

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
E
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
0.973

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.