EXOSC6

exosome component 6, the group of Exosome complex

Basic information

Region (hg38): 16:70246778-70251940

Links

ENSG00000223496 ∙ NCBI:118460 ∙ OMIM:606490 ∙ HGNC:19055 ∙ Uniprot:Q5RKV6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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			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)
16-70251130-C-G		not specified	Uncertain significance (Mar 02, 2023)
16-70251146-T-C		not specified	Uncertain significance (Apr 07, 2022)
16-70251161-C-G		not specified	Uncertain significance (Jun 01, 2023)
16-70251180-C-G		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
16-70251230-C-G		not specified	Uncertain significance (Feb 05, 2024)
16-70251245-A-G		not specified	Uncertain significance (Mar 20, 2023)
16-70251279-C-T		not specified	Uncertain significance (Jul 22, 2022)
16-70251284-C-T		not specified	Uncertain significance (Mar 19, 2024)
16-70251285-G-T		not specified	Uncertain significance (Mar 19, 2024)
16-70251300-G-A		not specified	Uncertain significance (Dec 27, 2022)
16-70251339-C-T		not specified	Uncertain significance (Jun 27, 2023)
16-70251371-T-C		not specified	Uncertain significance (Feb 09, 2023)
16-70251399-C-A		not specified	Uncertain significance (Nov 18, 2022)
16-70251423-C-T		not specified	Uncertain significance (Nov 06, 2023)
16-70251470-A-C		not specified	Uncertain significance (Feb 06, 2023)
16-70251509-T-C		not specified	Uncertain significance (Oct 12, 2022)
16-70251524-A-T		not specified	Uncertain significance (Feb 05, 2024)
16-70251543-G-A		not specified	Uncertain significance (May 27, 2022)
16-70251560-G-A		not specified	Uncertain significance (Oct 13, 2023)
16-70251567-C-T		not specified	Uncertain significance (Oct 29, 2021)
16-70251570-G-A		not specified	Uncertain significance (May 30, 2023)
16-70251576-G-C		not specified	Uncertain significance (Dec 16, 2022)
16-70251611-A-T		not specified	Uncertain significance (Dec 27, 2023)
16-70251684-C-G		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EXOSC6	protein_coding	protein_coding	ENST00000435634	1	1700

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.525	0.418	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.590	77	63.7	1.21	0.00000300	1556
Missense in Polyphen		33	22.46	1.4693		640
Synonymous	-3.28	55	31.6	1.74	0.00000159	629
Loss of Function	1.36	0	2.16	0.00	9.35e-8	52

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Exosc6

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