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	26173
Gene name	Integrator complex subunit 1
Gene symbol	INTS1
Synonyms (NCBI Gene)	INT1NDCAGFNET28
Chromosome	7
Chromosome location	7p22.3
Summary	INTS1 is a subunit of the Integrator complex, which associates with the C-terminal domain of RNA polymerase II large subunit (POLR2A; MIM 180660) and mediates 3-prime end processing of small nuclear RNAs U1 (RNU1; MIM 180680) and U2 (RNU2; MIM 180690) (Ba

Show/Hide all (8)

SNP ID	Visualize variation	Clinical significance	Consequence
rs200649090	G>A	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs770569947	T>G	Likely-pathogenic	Splice acceptor variant
rs1030646527	T>A,C	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs1162809128	G>A	Pathogenic	Coding sequence variant, missense variant, genic downstream transcript variant
rs1284335313	G>A	Pathogenic	Genic downstream transcript variant, stop gained, coding sequence variant
rs1286686353	G>T	Pathogenic	Genic downstream transcript variant, non coding transcript variant, stop gained, coding sequence variant
rs1357982637	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1562487424	->G	Pathogenic	Genic downstream transcript variant, coding sequence variant, non coding transcript variant, frameshift variant

Show/Hide all (20)

miRTarBase ID	miRNA	Experiments	Reference
MIRT052201	hsa-let-7b-5p	CLASH	23622248
MIRT039713	hsa-miR-615-3p	CLASH	23622248
MIRT039713	hsa-miR-615-3p	CLASH	23622248
MIRT039214	hsa-miR-769-5p	CLASH	23622248
MIRT039110	hsa-miR-769-3p	CLASH	23622248
MIRT037241	hsa-miR-877-5p	CLASH	23622248
MIRT440446	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT440446	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT1067906	hsa-miR-3191	CLIP-seq
MIRT1067907	hsa-miR-3917	CLIP-seq
MIRT1067908	hsa-miR-4532	CLIP-seq
MIRT1067909	hsa-miR-4707-5p	CLIP-seq
MIRT1067910	hsa-miR-634	CLIP-seq
MIRT1067907	hsa-miR-3917	CLIP-seq
MIRT1067910	hsa-miR-634	CLIP-seq
MIRT2451891	hsa-miR-1203	CLIP-seq
MIRT2451892	hsa-miR-1538	CLIP-seq
MIRT2451893	hsa-miR-1915	CLIP-seq
MIRT2451894	hsa-miR-4685-5p	CLIP-seq
MIRT2451895	hsa-miR-4745-3p	CLIP-seq

Show/Hide all (24)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001832	Process	Blastocyst growth	IEA
GO:0001833	Process	Inner cell mass cell proliferation	IEA
GO:0005515	Function	Protein binding	IPI	28514442, 33961781
GO:0005634	Component	Nucleus	IDA	29471365, 39032490
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	32647223
GO:0005654	Component	Nucleoplasm	TAS
GO:0007566	Process	Embryo implantation	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IEA
GO:0016180	Process	SnRNA processing	IDA	16239144
GO:0016180	Process	SnRNA processing	NAS	16239144
GO:0031965	Component	Nuclear membrane	IEA
GO:0032039	Component	Integrator complex	IBA
GO:0032039	Component	Integrator complex	IDA	16239144, 29471365, 36920904, 39032490
GO:0032039	Component	Integrator complex	IEA
GO:0032039	Component	Integrator complex	NAS	33548203
GO:0034243	Process	Regulation of transcription elongation by RNA polymerase II	NAS	32697989
GO:0034474	Process	U2 snRNA 3'-end processing	IBA
GO:0034474	Process	U2 snRNA 3'-end processing	IEA
GO:0034474	Process	U2 snRNA 3'-end processing	IEA
GO:0043066	Process	Negative regulation of apoptotic process	IEA
GO:0160232	Component	INTAC complex	IDA	33243860, 34004147, 34762484, 36869814, 38570683
GO:0160240	Process	RNA polymerase II transcription initiation surveillance	IDA	33243860, 34004147, 38570683

MIM	HGNC	e!Ensembl
611345	24555	ENSG00000164880

Q8N201

Protein name

Integrator complex subunit 1 (Int1)

Protein function

Component of the integrator complex, a multiprotein complex that terminates RNA polymerase II (Pol II) transcription in the promoter-proximal region of genes (PubMed:25201415, PubMed:33243860, PubMed:38570683). The integrator complex provides a

PDB

7CUN , 7PKS , 7YCX , 8RBX , 8RBZ , 8RC4 , 8YJB

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF12432	DUF3677	350 → 430	Protein of unknown function (DUF3677)	Family

Sequence

MNRAKPTTVRRPSAAAKPSGHPPPGDFIALGSKGQANESKTASTLLKPAPSGLPSERKRD
AAAALSSASALTGLTKRPKLSSTPPLSALGRLAEAAVAEKRAISPSIKEPSVVPIEVLPT
VLLDEIEAAELEGNDDRIEGVLCGAVKQLKVTRAKPDSTLYLSLMYLAKIKPNIFATEGV
IEALCSLLRRDASINFKAKGNSLVSVLACNLLMAAYEEDENWPEIFVKVYIEDSLGERIW
VDSPHCKTFVDNIQTAFNTRMPPRSVLLQGEAGRVAGDLGAGSSPHPSLTEEEDSQTELL
IAEEKLSPEQEGQLMPRYEELAESVEEYVLDMLRDQLNRRQPIDNVSRNLLRLLTSTCGY
KEVRLLAVQKLEMWLQNPKLTRPAQDLLMSVCMNCNTHGSEDMDVISHLIKIRLKPKVLL
NHFMLCIRELLSAHKDNLGTTIKLVIFNELSSARNPNNMQVLYTALQHSSELAPKFLAMV
FQDLLTNKDDYLRASRALLREIIKQTKHEINFQAFCLGLMQERKEPQYLEMEFKERFVVH
ITDVLAVSMMLGITAQVKEAGIAWDKGEKRNLEVLRSFQNQIAAIQRDAVWWLHTVVPSI
SKLAPKDYVHCLHKVLFTEQPETYYKWDNWPPESDRNFFLRLCSEVPILEDTLMRILVIG
LSRELPLGPADAMELADHLVKRAAAVQADDVEVLKVGRTQLIDAVLNLCTYHHPENIQLP
PGYQPPNLAISTLYWKAWPLLLVVAAFNPENIGLAAWEEYPTLKMLMEMVMTNNYSYPPC
TLTDEETRTEMLNRELQTAQREKQEILAFEGHLAAASTKQTITESSSLLLSQLTSLDPQG
PPRRPPPHILDQVKSLNQSLRLGHLLCRSRNPDFLLHIIQRQASSQSMPWLADLVQSSEG
SLDVLPVQCLCEFLLHDAVDDAASGEEDDEGESKEQKAKKRQRQQKQRQLLGRLQDLLLG
PKADEQTTCEVLDYFLRRLGSSQVASRVLAMKGLSLVLSEGSLRDGEEKEPPMEEDVGDT
DVLQGYQWLLRDLPRLPLFDSVRSTTALALQQAIHMETDPQTISAYLIYLSQHTPVEEQA
QHSDLALDVARLVVERSTIMSHLFSKLSPSAASDAVLSALLSIFSRYVRRMRQSKEGEEV
YSWSESQDQVFLRWSSGETATMHILVVHAMVILLTLGPPRADDSEFQALLDIWFPEEKPL
PTAFLVDTSEEALLLPDWLKLRMIRSEVLRLVDAALQDLEPQQLLLFVQSFGIPVSSMSK
LLQFLDQAVAHDPQTLEQNIMDKNYMAHLVEVQHERGASGGQTFHSLLTASLPPRRDSTE
APKPKSSPEQPIGQGRIRVGTQLRVLGPEDDLAGMFLQIFPLSPDPRWQSSSPRPVALAL
QQALGQELARVVQGSPEVPGITVRVLQALATLLSSPHGGALVMSMHRSHFLACPLLRQLC
QYQRCVPQDTGFSSLFLKVLLQMLQWLDSPGVEGGPLRAQLRMLASQASAGRRLSDVRGG
LLRLAEALAFRQDLEVVSSTVRAVIATLRSGEQCSVEPDLISKVLQGLIEVRSPHLEELL
TAFFSATADAASPFPACKPVVVVSSLLLQEEEPLAGGKPGADGGSLEAVRLGPSSGLLVD
WLEMLDPEVVSSCPDLQLRLLFSRRKGKGQAQVPSFRPYLLTLFTHQSSWPTLHQCIRVL
LGKSREQRFDPSASLDFLWACIHVPRIWQGRDQRTPQKRREELVLRVQGPELISLVELIL
AEAETRSQDGDTAACSLIQARLPLLLSCCCGDDESVRKVTEHLSGCIQQWGDSVLGRRCR
DLLLQLYLQRPELRVPVPEVLLHSEGAASSSVCKLDGLIHRFITLLADTSDSRALENRGA
DASMACRKLAVAHPLLLLRHLPMIAALLHGRTHLNFQEFRQQNHLSCFLHVLGLLELLQP
HVFRSEHQGALWDCLLSFIRLLLNYRKSSRHLAAFINKFVQFIHKYITYNAPAAISFLQK
HADPLHDLSFDNSDLVMLKSLLAGLSLPSRDDRTDRGLDEEGEEESSAGSLPLVSVSLFT
PLTAAEMAPYMKRLSRGQTVEDLLEVLSDIDEMSRRRPEILSFFSTNLQRLMSSAEECCR
NLAFSLALRSMQNSPSIAAAFLPTFMYCLGSQDFEVVQTALRNLPEYALLCQEHAAVLLH
RAFLVGMYGQMDPSAQISEALRILHMEAVM

Sequence length

2190

Interactions

View interactions

	Reactome
			RNA polymerase II transcribes snRNA genes

121

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Malignant tumor of esophagus	Likely pathogenic	rs1053594617	RCV005937389
Neurodevelopmental delay	Likely pathogenic	rs1357982637, rs770569947	RCV001007904 RCV001007905
Neurodevelopmental disorder with cataracts, poor growth, and dysmorphic facies	Likely pathogenic; Pathogenic	rs2128539437, rs774959930, rs2128532901, rs1053594617, rs1286686353, rs1562487424, rs1162809128, rs1030646527, rs1284335313, rs770569947	RCV001374601 RCV001839163 RCV002273355 RCV003989373 RCV000850268 RCV000850270 RCV000850271 RCV000850272 RCV000850273 RCV003147575
See cases	Likely pathogenic	rs2128544907	RCV002253190

Show/Hide Unknown Diseases (12)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Cervical cancer	Benign; Likely benign	rs201734949	RCV005902885
Colon adenocarcinoma	Benign; Likely benign	rs201734949	RCV005902882
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	rs1188419101	RCV004557734
Familial pancreatic carcinoma	Benign; Likely benign	rs199689668	RCV005920676
Gastric cancer	Likely benign; Benign	rs201348159, rs60791229	RCV005911953 RCV005871049
INTS1-related disorder	Likely benign; Conflicting classifications of pathogenicity; Uncertain significance; Benign	rs181410589, rs138397380, rs138307850, rs1001924549, rs201873966, rs370186628, rs371444064, rs200983063, rs181128403, rs201652864, rs201106690, rs1263916093, rs780312974, rs2483381110, rs182741272 View all (23 more)	RCV003943336 RCV003973374 RCV003896210 RCV003896211 RCV003939015 RCV003966419 RCV003966420 RCV003929165 RCV003923969 RCV003929603 RCV003981755 RCV003896441 RCV003897315 RCV003904311 RCV003892306 RCV003977167 RCV003911433 RCV003909841 RCV003934020 RCV003943891 RCV003934568 RCV003951881 RCV003934438 RCV003949567 RCV003949257 RCV003949304 RCV003947001 RCV003954327 RCV003954368 RCV003961977 RCV003971522 RCV003936130 RCV003918584 RCV003948367 RCV003910530 RCV003922955 RCV003902874 RCV003950746
Malignant tumor of urinary bladder	Benign; Likely benign	rs201734949	RCV005902883
Nonpapillary renal cell carcinoma	Uncertain significance; Benign; Likely benign	rs200026887, rs201734949	RCV005911091 RCV005902884
Ovarian serous cystadenocarcinoma	Likely benign	rs201348159	RCV005911954
Thymoma	Benign; Likely benign	rs199689668	RCV005920678
Uterine carcinosarcoma	Benign; Likely benign	rs199689668	RCV005920677
Uterine corpus endometrial carcinoma	Uncertain significance; Benign; Likely benign	rs182750375, rs201734949	RCV005929888 RCV005902886

Show/Hide Text Mining Associations (6)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenomyosis	Associate	40527793
Glomerulonephritis	Associate	40629603
Leukemia Large Granular Lymphocytic	Associate	40629603
Mesothelioma Malignant	Associate	34294080
Neoplasms	Associate	24241165
Stomach Neoplasms	Associate	34925643

INTS1 (integrator complex subunit 1)