EXOSC6

exosome component 6, the group of Exosome complex

Basic information

Region (hg38): 16:70246778-70251940

Links

ENSG00000223496NCBI:118460OMIM:606490HGNC:19055Uniprot:Q5RKV6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EXOSC6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXOSC6 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
0
missense
31
clinvar
31
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 31 0 0

Variants in EXOSC6

This is a list of pathogenic ClinVar variants found in the EXOSC6 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
16-70251102-C-T not specified Uncertain significance (Jun 21, 2021)2407428
16-70251130-C-G not specified Uncertain significance (Mar 02, 2023)2457622
16-70251146-T-C not specified Uncertain significance (Apr 07, 2022)2281504
16-70251161-C-G not specified Uncertain significance (Jun 01, 2023)2555140
16-70251180-C-G EBV-positive nodal T- and NK-cell lymphoma Likely benign (-)2681264
16-70251230-C-G not specified Uncertain significance (Feb 05, 2024)3091216
16-70251245-A-G not specified Uncertain significance (Mar 20, 2023)2526594
16-70251279-C-T not specified Uncertain significance (Jul 22, 2022)2394412
16-70251284-C-T not specified Uncertain significance (Mar 19, 2024)3276843
16-70251285-G-T not specified Uncertain significance (Mar 19, 2024)3276844
16-70251300-G-A not specified Uncertain significance (Dec 27, 2022)2378027
16-70251339-C-T not specified Uncertain significance (Jun 27, 2023)2597356
16-70251371-T-C not specified Uncertain significance (Feb 09, 2023)2482609
16-70251399-C-A not specified Uncertain significance (Nov 18, 2022)2385715
16-70251423-C-T not specified Uncertain significance (Nov 06, 2023)3091214
16-70251470-A-C not specified Uncertain significance (Feb 06, 2023)2458889
16-70251509-T-C not specified Uncertain significance (Oct 12, 2022)2318624
16-70251524-A-T not specified Uncertain significance (Feb 05, 2024)3091213
16-70251543-G-A not specified Uncertain significance (May 27, 2022)2292537
16-70251560-G-A not specified Uncertain significance (Oct 13, 2023)3091212
16-70251567-C-T not specified Uncertain significance (Oct 29, 2021)2383595
16-70251570-G-A not specified Uncertain significance (May 30, 2023)2552974
16-70251576-G-C not specified Uncertain significance (Dec 16, 2022)3091211
16-70251611-A-T not specified Uncertain significance (Dec 27, 2023)3091209
16-70251684-C-G not specified Uncertain significance (Oct 03, 2022)2272458

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EXOSC6protein_codingprotein_codingENST00000435634 11700
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.5250.41800000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.5907763.71.210.000003001556
Missense in Polyphen3322.461.4693640
Synonymous-3.285531.61.740.00000159629
Loss of Function1.3602.160.009.35e-852

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

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:21255825}.;
Pathway
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;Regulation of mRNA stability by proteins that bind AU-rich elements;mRNA decay by 3, to 5, exoribonuclease;Deadenylation-dependent mRNA decay (Consensus)

Haploinsufficiency Scores

pHI
0.108
hipred
Y
hipred_score
0.556
ghis

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.816

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Exosc6
Phenotype

Gene ontology

Biological process
rRNA processing;rRNA catabolic process;nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5';U4 snRNA 3'-end processing;regulation of mRNA stability;exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay;DNA deamination;isotype switching;positive regulation of isotype switching;nuclear mRNA surveillance;polyadenylation-dependent snoRNA 3'-end processing;RNA phosphodiester bond hydrolysis, exonucleolytic
Cellular component
nuclear exosome (RNase complex);cytoplasmic exosome (RNase complex);exosome (RNase complex);nucleoplasm;nucleolus;cytosol
Molecular function
RNA binding;exoribonuclease activity