EXOSC5

protein-coding

exosome component 5, the group of Exosome complex

Gene summary

Predicted to enable RNA binding activity. Involved in DNA deamination; RNA processing; and mRNA catabolic process. Acts upstream of or within defense response to virus. Located in cytosol; euchromatin; and nucleolus. Part of exosome (RNase complex). [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_020158.4

Inheritance

AR

ClinVar variants

P:6U:57B:7

Top phenotype

Cerebellar ataxia, brain abnormalities, and cardiac conduction defects

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr19:41,386,371-41,397,362

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~11.0 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

cerebellar ataxia, brain abnormalities, and cardiac conduction defectsSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0859200

Submitter: Labcorp Genetics (formerly Invitae)

cerebellar ataxia, brain abnormalities, and cardiac conduction defectsSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0859200

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Cerebellar ataxia, brain abnormalities, and cardiac conduction defectsAR

Manifestation: Cardiovascular; Craniofacial; Musculoskeletal; Neurologic

Intervention: Cardiovascular

Rationale: Among other findings, the condition can include cardiovascular anomalies, including conduction defects, and awareness may allow early diagnosis and management (eg, with pacemaker)

Refs: 30950035; 32504085; 34089229Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EXOSC5 variants in ClinVar

3 Conditions Cataloged
Inborn genetic diseasesTotal: 43
not providedTotal: 18
Cerebellar ataxia, brain abnormalities, and cardiac conduction defectsTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020158.4. 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
1
clinvar
5
clinvar
6
missense
1
clinvar
2
clinvar
53
clinvar
2
clinvar
58
nonsense
0
start loss
0
frameshift
1
clinvar
2
clinvar
3
splice donor/acceptor (+/-2bp)
1
clinvar
1
clinvar
1
clinvar
3
Total33577070

Highest pathogenic variant AF is 0.000061530576

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_020158.4RefSeqNP_064543.36MANE Select
ENST00000221233.9EnsemblENSP00000221233.36MANE Select
ENST00000593771.2EnsemblENSP00000471557.27Standard
ENST00000593771.3EnsemblENSP00000471557.27Standard

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
  • rRNA catabolic process
  • 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
ENST00000221233
Coding exons
6
Length
11106
Individuals with no LoFs
125734
Homozygous LoFs
0
Heterozygous LoFs
13
Defined
125747
p
0.0000517
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.4841311480.8880.000009331476
Missense (PolyPhen)4960.1810.81421585
Synonymous0.2066668.20.9680.00000453508
Loss of Function1.2959.220.5433.92e-7111

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish0.000130.000092rare
European (Non-Finnish)0.0000630.000062rare
South Asian0.0000980.000098rare
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. {ECO:0000269|PubMed:11782436, ECO:0000269|PubMed:21255825}.;

Recessive Scores

pRec
0.109

Intolerance Scores

LoFtool
0.746
RVIS EVS
-0.29
RVIS percentile EVS
33.2

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
E
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
0.964

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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