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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	51010
Gene name	Exosome component 3
Gene symbol	EXOSC3
Synonyms (NCBI Gene)	CGI-102PCH1BRRP40Rrp40pbA3J10.7hRrp-40p10
Chromosome	9
Chromosome location	9p13.2
Summary	This gene encodes a non-catalytic component of the human exosome, a complex with 3`-5` exoribonuclease activity that plays a role in numerous RNA processing and degradation activities. Related pseudogenes of this gene are found on chromosome 19 and 21. Al

Show/Hide all (12)

SNP ID	Visualize variation	Clinical significance	Consequence
rs141138948	T>C,G	Pathogenic, pathogenic-likely-pathogenic	Coding sequence variant, missense variant
rs370087266	T>C	Uncertain-significance, pathogenic	Intron variant
rs374550999	C>A,G	Likely-pathogenic	Missense variant, coding sequence variant
rs387907195	C>G	Pathogenic	Missense variant, coding sequence variant
rs387907196	C>G	Pathogenic	Missense variant, coding sequence variant
rs587780333	C>-	Pathogenic	Coding sequence variant, frameshift variant
rs672601331	AGTAAACACC>-	Pathogenic	Coding sequence variant, frameshift variant
rs730882145	C>A,T	Pathogenic	Missense variant, coding sequence variant, intron variant
rs797045567	C>T	Uncertain-significance, likely-pathogenic	Coding sequence variant, missense variant, intron variant
rs886041316	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs1057518124	A>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1160669103	->TTAA	Pathogenic	Coding sequence variant, inframe indel, stop gained, intron variant

Show/Hide all (44)

miRTarBase ID	miRNA	Experiments
MIRT973204	hsa-miR-181a	CLIP-seq
MIRT973205	hsa-miR-181b	CLIP-seq
MIRT973206	hsa-miR-181c	CLIP-seq
MIRT973207	hsa-miR-181d	CLIP-seq
MIRT973208	hsa-miR-369-3p	CLIP-seq
MIRT973209	hsa-miR-374c	CLIP-seq
MIRT973210	hsa-miR-4262	CLIP-seq
MIRT973211	hsa-miR-655	CLIP-seq
MIRT973212	hsa-miR-150	CLIP-seq
MIRT973213	hsa-miR-188-3p	CLIP-seq
MIRT973214	hsa-miR-4713-5p	CLIP-seq
MIRT973215	hsa-miR-4719	CLIP-seq
MIRT973216	hsa-miR-4768-5p	CLIP-seq
MIRT973217	hsa-miR-532-3p	CLIP-seq
MIRT973218	hsa-miR-628-5p	CLIP-seq
MIRT973219	hsa-miR-944	CLIP-seq
MIRT1988353	hsa-miR-1275	CLIP-seq
MIRT1988354	hsa-miR-3182	CLIP-seq
MIRT1988355	hsa-miR-4303	CLIP-seq
MIRT1988356	hsa-miR-4525	CLIP-seq
MIRT1988357	hsa-miR-4665-5p	CLIP-seq
MIRT1988358	hsa-miR-4682	CLIP-seq
MIRT1988359	hsa-miR-4694-3p	CLIP-seq
MIRT1988360	hsa-miR-4723-5p	CLIP-seq
MIRT1988361	hsa-miR-496	CLIP-seq
MIRT1988362	hsa-miR-522	CLIP-seq
MIRT1988363	hsa-miR-625	CLIP-seq
MIRT2222815	hsa-miR-1228	CLIP-seq
MIRT973204	hsa-miR-181a	CLIP-seq
MIRT973205	hsa-miR-181b	CLIP-seq
MIRT973206	hsa-miR-181c	CLIP-seq
MIRT973207	hsa-miR-181d	CLIP-seq
MIRT2222816	hsa-miR-3163	CLIP-seq
MIRT2222817	hsa-miR-340	CLIP-seq
MIRT2222818	hsa-miR-3607-3p	CLIP-seq
MIRT2222819	hsa-miR-3661	CLIP-seq
MIRT973208	hsa-miR-369-3p	CLIP-seq
MIRT973209	hsa-miR-374c	CLIP-seq
MIRT2222820	hsa-miR-377	CLIP-seq
MIRT973210	hsa-miR-4262	CLIP-seq
MIRT2222821	hsa-miR-548aa	CLIP-seq
MIRT2222822	hsa-miR-548c-3p	CLIP-seq
MIRT2222823	hsa-miR-631	CLIP-seq
MIRT973211	hsa-miR-655	CLIP-seq

Show/Hide all (46)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000175	Function	3'-5'-RNA exonuclease activity	NAS	11110791
GO:0000176	Component	Nuclear exosome (RNase complex)	IBA
GO:0000176	Component	Nuclear exosome (RNase complex)	IDA	11110791
GO:0000176	Component	Nuclear exosome (RNase complex)	NAS	20531386
GO:0000177	Component	Cytoplasmic exosome (RNase complex)	IBA
GO:0000177	Component	Cytoplasmic exosome (RNase complex)	IDA	11110791
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: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:0000791	Component	Euchromatin	IMP	20699273
GO:0000956	Process	Nuclear-transcribed mRNA catabolic process	IBA
GO:0003723	Function	RNA binding	IBA
GO:0003723	Function	RNA binding	IEA
GO:0004532	Function	RNA exonuclease activity	IDA	17174896
GO:0005515	Function	Protein binding	IPI	11719186, 12419256, 14731398, 15231747, 16396833, 17185417, 17545563, 18334637, 20531386, 20531389, 21255825, 21876179, 23756462, 24981860, 26496610, 28514442, 32296183, 33961781
GO:0005634	Component	Nucleus	IDA	17545563, 20531386
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005730	Component	Nucleolus	IDA	20531386, 20531389
GO:0005730	Component	Nucleolus	IEA
GO:0005737	Component	Cytoplasm	IDA	17545563
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IDA	20531386
GO:0005829	Component	Cytosol	TAS
GO:0006259	Process	DNA metabolic process	IEA
GO:0006364	Process	RRNA processing	IDA	11110791
GO:0006364	Process	RRNA processing	IEA
GO:0006396	Process	RNA processing	IDA	17174896, 20531386
GO:0006401	Process	RNA catabolic process	IDA	17174896, 20531386
GO:0006402	Process	MRNA catabolic process	IMP	11782436
GO:0010467	Process	Gene expression	IEA
GO:0010468	Process	Regulation of gene expression	IEA
GO:0034475	Process	U4 snRNA 3'-end processing	IBA
GO:0045006	Process	DNA deamination	IDA	21255825
GO:0045190	Process	Isotype switching	IEA
GO:0045190	Process	Isotype switching	ISS
GO:0045830	Process	Positive regulation of isotype switching	IEA
GO:0071034	Process	CUT catabolic process	IBA
GO:0071034	Process	CUT catabolic process	IMP	19056938
GO:0071035	Process	Nuclear polyadenylation-dependent rRNA catabolic process	IBA
GO:0071038	Process	TRAMP-dependent tRNA surveillance pathway	IBA
GO:0071051	Process	Poly(A)-dependent snoRNA 3'-end processing	IBA
GO:0101019	Component	Nucleolar exosome (RNase complex)	NAS	20531386

MIM	HGNC	e!Ensembl
606489	17944	ENSG00000107371

Q9NQT5

Protein name

Exosome complex component RRP40 (Exosome component 3) (Ribosomal RNA-processing protein 40) (p10)

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
PF15985	KH_6	197 → 245	KH domain	Domain

Sequence

MAEPASVAAESLAGSRARAARTVLGQVVLPGEELLLPEQEDAEGPGGAVERPLSLNARAC
SRVRVVCGPGLRRCGDRLLVTKCGRLRHKEPGSGSGGGVYWVDSQQKRYVPVKGDHVIGI
VTAKSGDIFKVDVGGSEPASLSYLSFEGATKRNRPNVQVGDLIYGQFVVANKDMEPEMVC
IDSCGRANGMGVIGQDGLLFKVTLGLIRKLLAPDCEIIQEVGKLYPLEIVFGMNGRIWVK
AKTIQQTLILANILEACEHMTSDQRKQIFSRLAES

Sequence length

275

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

257

Show/Hide Causal Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the nervous system	Pathogenic	rs141138948	RCV001836713
Congenital myopathy	Likely pathogenic; Pathogenic	rs387907196	RCV004586024
Congenital pontocerebellar hypoplasia type 1	Pathogenic	rs141138948	RCV005364888
EXOSC3-related disorder	Pathogenic	rs141138948	RCV004757111
Hypotonia	Pathogenic	rs141138948	RCV000761614
Pontocerebellar hypoplasia type 1B	Pathogenic; Likely pathogenic	rs2118980242, rs1198691735, rs1296865764, rs769374744, rs587780333, rs374550999, rs2118980158, rs2118977758, rs149049356, rs730882145, rs1325914775, rs114878910, rs1395561739, rs2489890955, rs797045567 View all (18 more)	RCV001783217 RCV003827688 RCV001781059 RCV004720318 RCV000117004 RCV000117005 RCV002032143 RCV002211035 RCV003102289 RCV000161917 RCV002470377 RCV003072623 RCV003530273 RCV002801869 RCV000625808 RCV003225691 RCV000499694 RCV003530937 RCV003531289 RCV003529833 RCV003529892 RCV003646413 RCV003646533 RCV003646646 RCV003646743 RCV003646792 RCV003647073 RCV003647130 RCV003867910 RCV003876594 RCV000024366 RCV000024368 RCV000024369 RCV000024370 RCV002499349 RCV003770230
Pontoneocerebellar hypoplasia	Likely pathogenic; Pathogenic	rs769374744, rs374550999, rs149049356, rs1395561739, rs886041316, rs1427979807, rs1325914775	RCV001797933 RCV000825519 RCV002308518 RCV002510386 RCV002509341 RCV004018282 RCV003331076
See cases	Pathogenic	rs141138948	RCV003156064

Show/Hide Text Mining Associations (20)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Abnormalities Drug Induced	Associate	23284067
Atypical Hemolytic Uremic Syndrome	Associate	35522339
Carcinoma Non Small Cell Lung	Associate	39176091
Colorectal Neoplasms	Associate	34626022
Contracture	Associate	23284067
Conversion Disorder	Associate	23284067
COVID 19	Associate	35522339
Cysts	Associate	24524299
Death	Associate	24524299
Depression Postpartum	Associate	23284067
Fetal Growth Retardation	Associate	23284067
Heredodegenerative Disorders Nervous System	Associate	28053271, 35522339
Kidney Failure Chronic	Associate	30499177
Lung Neoplasms	Associate	39176091
Neoplasms	Associate	34626022, 39176091
Nerve Degeneration	Associate	28053271
Perinatal Death	Associate	23284067
Pontocerebellar Hypoplasia	Associate	24524299, 28053271, 34089229
Pontocerebellar Hypoplasia Type 1	Associate	23284067
Psychomotor Disorders	Associate	23284067

EXOSC3 (exosome component 3)