EXOSC10

exosome component 10, the group of Exosome complex

Basic information

Region (hg38): 1:11066618-11099869

Previous symbols: [ "PMSCL2" ]

Links

ENSG00000171824 ∙ NCBI:5394 ∙ OMIM:605960 ∙ HGNC:9138 ∙ Uniprot:Q01780 ∙ 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 EXOSC10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXOSC10 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					1	1
missense			43	2		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	43	2	1

Variants in EXOSC10

This is a list of pathogenic ClinVar variants found in the EXOSC10 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-11066734-T-C		not specified	Uncertain significance (Apr 25, 2022)
1-11068021-C-T		not specified	Uncertain significance (May 24, 2024)
1-11068039-T-C		not specified	Uncertain significance (Nov 27, 2023)
1-11068042-T-G		not specified	Uncertain significance (Aug 28, 2023)
1-11068080-C-T		not specified	Uncertain significance (Jan 04, 2022)
1-11068691-T-C		not specified	Uncertain significance (Jan 23, 2023)
1-11069598-G-C		not specified	Uncertain significance (Apr 22, 2024)
1-11070913-C-T			Likely benign (Apr 01, 2023)
1-11070917-C-T		not specified	Uncertain significance (Jan 18, 2023)
1-11070943-T-C		not specified	Uncertain significance (Oct 06, 2023)
1-11072089-G-C		not specified	Uncertain significance (Apr 19, 2023)
1-11073927-C-T			Likely benign (Feb 01, 2024)
1-11073948-T-C			Likely benign (Jan 01, 2023)
1-11073972-G-C		not specified	Uncertain significance (Oct 27, 2022)
1-11073981-G-C		not specified	Uncertain significance (Mar 21, 2024)
1-11074272-C-T		not specified	Uncertain significance (Dec 15, 2023)
1-11076853-T-A		not specified	Uncertain significance (May 30, 2023)
1-11077376-A-G		not specified	Uncertain significance (Nov 07, 2022)
1-11077413-C-G		not specified	Uncertain significance (Jul 12, 2023)
1-11077440-A-T		not specified	Uncertain significance (Jan 06, 2023)
1-11077633-C-T		not specified	Uncertain significance (Oct 13, 2023)
1-11079734-C-T		not specified	Uncertain significance (Jun 07, 2024)
1-11079779-G-T		not specified	Uncertain significance (Feb 28, 2024)
1-11080866-T-C		not specified	Uncertain significance (Dec 06, 2021)
1-11081096-C-T		not specified	Uncertain significance (Aug 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EXOSC10	protein_coding	protein_coding	ENST00000376936	25	33264

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.97e-14	0.999	125668	0	80	125748	0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.870	453	508	0.891	0.0000283	5840
Missense in Polyphen		129	172.88	0.74617		2029
Synonymous	-0.0408	194	193	1.00	0.0000114	1644
Loss of Function	3.19	32	58.3	0.549	0.00000321	619

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000782	0.000782
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000491	0.000489
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000283	0.000281
Middle Eastern	0.000491	0.000489
South Asian	0.000429	0.000425
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative 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. EXOSC10 has 3'-5' exonuclease activity (By similarity). EXOSC10 is required for nucleolar localization of C1D and probably mediates the association of MTREX, C1D and MPP6 wth the RNA exosome involved in the maturation of 5.8S rRNA. {ECO:0000250, ECO:0000269|PubMed:14527413, ECO:0000269|PubMed:16455498, ECO:0000269|PubMed:17412707, ECO:0000269|PubMed:17545563, ECO:0000269|PubMed:18172165, ECO:0000269|PubMed:19056938, ECO:0000269|PubMed:20368444, ECO:0000269|PubMed:20699273}.
• Pathway: RNA degradation - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.306

Intolerance Scores

• loftool: 0.0801
• rvis_EVS: -1.24
• rvis_percentile_EVS: 5.49

Haploinsufficiency Scores

• pHI: 0.377
• hipred: Y
• hipred_score: 0.648
• ghis: 0.626

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.963

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Exosc10
• Phenotype: normal phenotype

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;maturation of 5.8S rRNA;nuclear-transcribed mRNA catabolic process;rRNA processing;dosage compensation by inactivation of X chromosome;negative regulation of telomere maintenance via telomerase;nuclear mRNA surveillance;CUT catabolic process;nuclear polyadenylation-dependent rRNA catabolic process;histone mRNA catabolic process;nuclear retention of unspliced pre-mRNA at the site of transcription;RNA phosphodiester bond hydrolysis, exonucleolytic;regulation of telomerase RNA localization to Cajal body
• Cellular component: nuclear exosome (RNase complex);exosome (RNase complex);nucleus;nucleoplasm;nucleolus;cytoplasm;cytosol;membrane;transcriptionally active chromatin
• Molecular function: nucleotide binding;3'-5'-exoribonuclease activity;RNA binding;exoribonuclease activity;protein binding;telomerase RNA binding