INTS1 (integrator complex subunit 1)

Gene

• Entrez ID: 26173
• Gene name: Integrator complex subunit 1
• Gene symbol: INTS1
• Synonyms: INT1, NDCAGF, NET28
• 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

SNPs

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

miRNA

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

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005654	Component	Nucleoplasm	TAS
GO:0016020	Component	Membrane	HDA	19946888
GO:0016021	Component	Integral component of membrane	IEA
GO:0016180	Process	SnRNA processing	IDA	16239144
GO:0031965	Component	Nuclear membrane	IEA
GO:0032039	Component	Integrator complex	IBA	21873635
GO:0032039	Component	Integrator complex	IDA	16239144
GO:0034474	Process	U2 snRNA 3'-end processing	IBA	21873635
GO:0042795	Process	SnRNA transcription by RNA polymerase II	TAS

Other IDs

• MIM: 611345
• HGNC: 24555
• e!Ensembl: ENSG00000164880

Protein

• UniProt ID: 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

Pathways

Reactome:

RNA polymerase II transcribes snRNA genes

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Cataract	Cataract	rs118203965, rs118203966, rs104893685, rs121908938, rs104894175, rs121909048, rs28937573, rs121909049, rs121909050, rs74315488, rs80358200, rs80358203, rs121434643, rs56141211, rs132630322, rs121917775, rs121917735, rs121917736, rs137853199, rs137853200, rs121917867, rs121917869, rs121913555, rs104893736, rs121909595, rs121909596, rs121909597, rs28931605, rs121909598, rs104893618, rs1695062782, rs74315486, rs74315487, rs74315490, rs74315489, rs745938679, rs1566402656, rs74315439, rs74315441, rs121912973, rs121917823, rs1593332981, rs121917825, rs121917827, rs113994108, rs387906963, rs387906964, rs1240503246, rs387906965, rs387906966, rs750207077, rs387907336, rs387907337, rs387907342, rs140332366, rs397514703, rs398122937, rs398122378, rs398122392, rs398122944, rs137853924, rs398122947, rs397515623, rs397515624, rs397515625, rs397515626, rs398122948, rs587778872, rs398123066, rs587777601, rs370424081, rs786205221, rs786205222, rs864309684, rs864309688, rs864309701, rs864309689, rs864309690, rs864309681, rs864309686, rs864309696, rs864309693, rs864309687, rs864309691, rs864309692, rs864309695, rs864309678, rs864309685, rs864309700, rs864309698, rs864309683, rs864309682, rs864309679, rs111534978, rs864309680, rs864309702, rs864622780, rs756898971, rs869312732, rs775038545, rs878852983, rs1114167312, rs1114167313, rs1114167314, rs1114167315, rs1114167307, rs886041410, rs886041412, rs1057518738, rs1057517926, rs1057518878, rs1057519616, rs12799308, rs1064793935, rs1064797219, rs1085307126, rs1085307127, rs765628635, rs1114167427, rs1114167433, rs1554744860, rs1554743428, rs747093432, rs1411557416, rs1555179713, rs1481963503, rs1555549755, rs1456161420, rs1555547008, rs1555889308, rs1555888762, rs766522434, rs1264025914, rs1553585262, rs1567671947, rs1337897299, rs764945940, rs1307969607, rs949335475, rs1184095219, rs776129797, rs1569203234, rs1567668570, rs749141857, rs764098604, rs1184398243, rs1578956689, rs1568480054, rs1564745688, rs1564722302, rs1564723150, rs1571175950, rs1569602837, rs1576552712, rs1575369255, rs981126461, rs1570403798, rs200557771, rs1477743112, rs1651879427, rs1651881222, rs1651919374, rs2024441691, rs148284531, rs1246080692	17544522
Developmental delay	Global developmental delay	rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291, rs886041382, rs1057518991, rs1057518699, rs753254213, rs748294403, rs762552974, rs1135401795, rs1553121073, rs1553122926, rs1364690005, rs1554086554, rs1554210415, rs1554168326, rs1554776342, rs1553873247, rs1567860112, rs779009256, rs1557447255, rs1564568350, rs780011005, rs1597464953, rs1200336864, rs1569513017, rs1587459606, rs1570332505, rs748888652, rs1575155995, rs2087029320, rs1589669105, rs1601769604, rs1184981709, rs749201074	17544522