Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	5393
Gene name	Exosome component 9
Gene symbol	EXOSC9
Synonyms (NCBI Gene)	PCH1DPM/Scl-75PMSCL1RRP45Rrp45pp5p6
Chromosome	4
Chromosome location	4q27
Summary	This gene encodes a component of the human exosome, a exoribonuclease complex which processes and degrades RNA in the nucleus and cytoplasm. This component may play a role in mRNA degradation and the polymyositis/scleroderma autoantigen complex. Alternati

Show/Hide all (2)

SNP ID	Visualize variation	Clinical significance	Consequence
rs139632595	T>C	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs372318863	C>G,T	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant, missense variant

Show/Hide all (56)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000175	Function	3'-5'-RNA exonuclease activity	NAS	11879549
GO:0000176	Component	Nuclear exosome (RNase complex)	IBA
GO:0000176	Component	Nuclear exosome (RNase complex)	IDA	22791713
GO:0000176	Component	Nuclear exosome (RNase complex)	NAS	11879549, 20531386
GO:0000177	Component	Cytoplasmic exosome (RNase complex)	IBA
GO:0000177	Component	Cytoplasmic exosome (RNase complex)	NAS	20531386
GO:0000178	Component	Exosome (RNase complex)	IDA	20531389
GO:0000178	Component	Exosome (RNase complex)	IEA
GO:0000178	Component	Exosome (RNase complex)	NAS	20531386
GO:0000228	Component	Nuclear chromosome	IDA	24105744
GO:0000467	Process	Exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IBA
GO:0000956	Process	Nuclear-transcribed mRNA catabolic process	IMP	17545563
GO:0003723	Function	RNA binding	HDA	22658674
GO:0003723	Function	RNA binding	IEA
GO:0003723	Function	RNA binding	NAS	11879549
GO:0004532	Function	RNA exonuclease activity	IDA	17174896
GO:0005515	Function	Protein binding	IPI	12788944, 15231747, 20531386, 24105744, 24981860, 26496610, 30021884, 33961781
GO:0005634	Component	Nucleus	IDA	17545563, 20531386, 22791713
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	TAS	2007859
GO:0005654	Component	Nucleoplasm	IDA	24105744
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005730	Component	Nucleolus	IDA	22791713
GO:0005730	Component	Nucleolus	IDA	20531386, 22791713, 24105744
GO:0005730	Component	Nucleolus	IEA
GO:0005730	Component	Nucleolus	TAS	2007859
GO:0005737	Component	Cytoplasm	IDA	17545563
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IDA	20531386
GO:0005829	Component	Cytosol	TAS
GO:0006364	Process	RRNA processing	IEA
GO:0006364	Process	RRNA processing	NAS	11879549
GO:0006396	Process	RNA processing	IDA	17174896, 20531386
GO:0006396	Process	RNA processing	IEA
GO:0006401	Process	RNA catabolic process	IDA	17174896, 20531386
GO:0006401	Process	RNA catabolic process	IEA
GO:0006402	Process	MRNA catabolic process	IMP	11782436
GO:0006955	Process	Immune response	NAS	11879549
GO:0016075	Process	RRNA catabolic process	IBA
GO:0030307	Process	Positive regulation of cell growth	IMP	17545563
GO:0034473	Process	U1 snRNA 3'-end processing	IBA
GO:0034475	Process	U4 snRNA 3'-end processing	IBA
GO:0034476	Process	U5 snRNA 3'-end processing	IBA
GO:0035925	Function	MRNA 3'-UTR AU-rich region binding	IBA
GO:0035925	Function	MRNA 3'-UTR AU-rich region binding	IDA	11782436
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0061629	Function	RNA polymerase II-specific DNA-binding transcription factor binding	IEA
GO:0070062	Component	Extracellular exosome	HDA	18570454
GO:0071028	Process	Nuclear mRNA surveillance	IBA
GO:0071028	Process	Nuclear mRNA surveillance	IMP	17545563
GO:0071035	Process	Nuclear polyadenylation-dependent rRNA catabolic process	IBA
GO:0071035	Process	Nuclear polyadenylation-dependent rRNA catabolic process	IMP	16455498
GO:0071038	Process	TRAMP-dependent tRNA surveillance pathway	IBA
GO:0101019	Component	Nucleolar exosome (RNase complex)	NAS	20531386
GO:1905354	Component	Exoribonuclease complex	IEA

MIM	HGNC	e!Ensembl
606180	9137	ENSG00000123737

Q06265

Protein name

Exosome complex component RRP45 (Autoantigen PM/Scl 1) (Exosome component 9) (P75 polymyositis-scleroderma overlap syndrome-associated autoantigen) (Polymyositis/scleroderma autoantigen 1) (Polymyositis/scleroderma autoantigen 75 kDa) (PM/Scl-75)

Protein 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 maturat

PDB

2NN6 , 6D6Q , 6D6R , 6H25 , 9G8M , 9G8N , 9G8O , 9G8P

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01138	RNase_PH	31 → 163		Domain
PF03725	RNase_PH_C	189 → 255		Domain

Sequence

MKETPLSNCERRFLLRAIEEKKRLDGRQTYDYRNIRISFGTDYGCCIVELGKTRVLGQVS
CELVSPKLNRATEGILFFNLELSQMAAPAFEPGRQSDLLVKLNRLMERCLRNSKCIDTES
LCVVAGEKVWQIRVDLHLLNHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEER
DPVPLSIHHMPICVSFAFFQQGTYLLVDPNEREERVMDGLLVIAMNKHREICTIQSSGGI
MLLKDQVLRCSKIAGVKVAEITELILKALENDQKVRKEGGKFGFAESIANQRITAFKMEK
APIDTSDVEEKAEEIIAEAEPPSEVVSTPVLWTPGTAQIGEGVENSWGDLEDSEKEDDEG
GGDQAIILDGIKMDTGVEVSDIGSQDAPIILSDSEEEEMIILEPDKNPKKIRTQTTSAKQ
EKAPSKKPVKRRKKKRAAN

Sequence length

439

Interactions

View interactions

	KEGG		Reactome
	RNA degradation		ATF4 activates genes in response to endoplasmic reticulum stress mRNA decay by 3' to 5' exoribonuclease Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA KSRP (KHSRP) binds and destabilizes mRNA Major pathway of rRNA processing in the nucleolus and cytosol

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Cerebral atrophy	Likely pathogenic; Pathogenic	rs139632595	RCV001260241	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Pontocerebellar hypoplasia, type 1D	Pathogenic; Likely pathogenic	rs781301648, rs1726969482, rs2149033494, rs139632595, rs372318863	RCV002250388 RCV002250389 RCV002250390 RCV000664415 RCV000664416	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Pontoneocerebellar hypoplasia	Likely pathogenic; Pathogenic	rs139632595	RCV004798852	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Thymoma	Likely pathogenic	rs1377012763	RCV005928352	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (21)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Acute myeloid leukemia	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL PONTOCEREBELLAR HYPOPLASIA TYPE 1	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EXOSC9-related disorder	Benign; Uncertain significance; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial pancreatic carcinoma	Benign; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Uncertain significance; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS, KNEE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Pontocerebellar atrophy	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PONTOCEREBELLAR HYPOPLASIA TYPE 1	—	GWAS catalog, Orphanet GWAS catalog, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (25)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Breast Neoplasms	Breast neoplasm	Pubtator	37887339	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Byzanthine arch palate	High palate	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebellar atrophy	Cerebellar atrophy	BEFREE	29727687, 31768969		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebellar atrophy	Cerebellar atrophy	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebellar atrophy	Cerebellar atrophy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebellar Hypoplasia	Cerebellar Hypoplasia	BEFREE	30690203		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral atrophy	Cerebral Atrophy	HPO_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cerebral atrophy	Cerebral Atrophy	CLINVAR_DG			★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Congenital Epicanthus	Congenital Epicanthus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Deglutition Disorders	Dysphagia	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Mucopolysaccharidoses	Mucopolysaccharidosis	Pubtator	35456399	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Oropharyngeal Dysphagia	Oropharyngeal Dysphagia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Peripheral motor neuropathy	Motor nerve neuritis	BEFREE	30690203		★★★★★ ★☆☆☆☆ Found in Text Mining only
Polymyositis	Polymyositis	LHGDN	14872500		★★★★★ ★☆☆☆☆ Found in Text Mining only
Pontocerebellar Hypoplasia Type 1	Pontoneocerebellar hypoplasia	ORPHANET_DG	29727687		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Pontocerebellar hypoplasia type 1	Pontoneocerebellar hypoplasia	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PONTOCEREBELLAR HYPOPLASIA, TYPE 1D	Erythermalgia	UNIPROT_DG	29727687		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PONTOCEREBELLAR HYPOPLASIA, TYPE 1D	Erythermalgia	BEFREE	30690203		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PONTOCEREBELLAR HYPOPLASIA, TYPE 1D	Erythermalgia	GENOMICS_ENGLAND_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PONTOCEREBELLAR HYPOPLASIA, TYPE 1D	Erythermalgia	CLINVAR_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Respiratory Failure	Respiratory Failure	BEFREE	30690203		★★★★★ ★☆☆☆☆ Found in Text Mining only

EXOSC9 (exosome component 9)