EXOSC7

exosome component 7, the group of Exosome complex

Basic information

Region (hg38): 3:44975241-45036066

Links

ENSG00000075914 ∙ NCBI:23016 ∙ OMIM:606488 ∙ HGNC:28112 ∙ Uniprot:Q15024 ∙ 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 EXOSC7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EXOSC7 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in EXOSC7

This is a list of pathogenic ClinVar variants found in the EXOSC7 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-44976281-G-T		not specified	Uncertain significance (May 30, 2023)
3-44976299-G-C		not specified	Uncertain significance (Sep 19, 2023)
3-44989149-C-T		not specified	Uncertain significance (Jan 29, 2024)
3-44989150-G-A		not specified	Uncertain significance (Apr 17, 2023)
3-44989180-G-A		not specified	Uncertain significance (Feb 14, 2024)
3-44989188-G-A		not specified	Uncertain significance (May 17, 2023)
3-44989227-G-A		not specified	Uncertain significance (Feb 10, 2022)
3-44989593-C-T		not specified	Uncertain significance (Jun 09, 2022)
3-44997098-C-T		not specified	Uncertain significance (Mar 26, 2024)
3-44997163-C-T		not specified	Uncertain significance (Mar 29, 2024)
3-44997184-A-G		not specified	Uncertain significance (Jul 06, 2021)
3-44997196-A-C		not specified	Uncertain significance (Jun 16, 2023)
3-45001542-T-C		not specified	Uncertain significance (Aug 22, 2023)
3-45005319-G-A		not specified	Uncertain significance (Nov 09, 2021)
3-45005354-C-G		not specified	Uncertain significance (Feb 16, 2023)
3-45005371-G-A		not specified	Uncertain significance (Dec 13, 2022)
3-45007433-A-G		not specified	Uncertain significance (Aug 26, 2022)
3-45007541-G-C		not specified	Uncertain significance (Mar 12, 2024)
3-45007567-A-G		not specified	Uncertain significance (Aug 13, 2021)
3-45007567-A-T		not specified	Uncertain significance (Dec 18, 2023)
3-45011299-G-A		not specified	Uncertain significance (Aug 04, 2023)
3-45026394-G-A		not specified	Uncertain significance (Jun 22, 2021)
3-45026426-G-A		not specified	Uncertain significance (Sep 29, 2022)
3-45035536-G-A		not specified	Uncertain significance (Jun 24, 2022)
3-45035684-G-C		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EXOSC7	protein_coding	protein_coding	ENST00000265564	8	60826

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000104	0.812	125683	0	65	125748	0.000258

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.237	175	166	1.05	0.00000913	1880
Missense in Polyphen		41	41.578	0.98609		455
Synonymous	1.43	51	65.8	0.775	0.00000380	569
Loss of Function	1.30	10	15.5	0.644	9.05e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000556	0.000551
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000109	0.000109
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000352	0.000352
Middle Eastern	0.000109	0.000109
South Asian	0.000327	0.000327
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.
• 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)

Recessive Scores

• pRec: 0.269

Intolerance Scores

• loftool: 0.827
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.635
• hipred: Y
• hipred_score: 0.713
• ghis: 0.584

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.958

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Exosc7

Gene ontology

• Biological process: exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);rRNA processing;RNA catabolic process;rRNA catabolic process;nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5';U1 snRNA 3'-end processing;U4 snRNA 3'-end processing;U5 snRNA 3'-end processing;regulation of mRNA stability;exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay;nuclear mRNA surveillance;nuclear polyadenylation-dependent rRNA catabolic process;nuclear polyadenylation-dependent tRNA catabolic process;nuclear polyadenylation-dependent mRNA catabolic process
• Cellular component: nuclear exosome (RNase complex);cytoplasmic exosome (RNase complex);exosome (RNase complex);nucleoplasm;nucleolus;cytosol
• Molecular function: 3'-5'-exoribonuclease activity;RNA binding;exoribonuclease activity;protein binding;AU-rich element binding