INTS1 (integrator complex subunit 1)

Gene

• Entrez ID: 26173
• Gene name: Integrator complex subunit 1
• Gene symbol: INTS1
• Synonyms (NCBI Gene): 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: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

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

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Malignant tumor of esophagus	Likely pathogenic	rs1053594617	RCV005937389	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental delay	Likely pathogenic	rs1357982637, rs770569947	RCV001007904 RCV001007905	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
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	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Cervical cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial pancreatic carcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTS1-related disorder	Likely benign; Conflicting classifications of pathogenicity; Uncertain significance; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Uncertain significance; Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Uncertain significance; Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Breast Carcinoma	Breast Carcinoma	BEFREE	1975511		★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	29565490		★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	GENOMICS_ENGLAND_DG	17544522		★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	BEFREE	30622326		★☆☆☆☆ Found in Text Mining only
Chronic Obstructive Airway Disease	Chronic Obstructive Pulmonary Disease	BEFREE	28245136		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	24815830		★☆☆☆☆ Found in Text Mining only
Congenital chromosomal disease	Congenital Chromosomal Disease	BEFREE	1309486, 17893227		★☆☆☆☆ Found in Text Mining only
Conventional (Clear Cell) Renal Cell Carcinoma	Renal Carcinoma	BEFREE	15705910, 30826166		★☆☆☆☆ Found in Text Mining only
Dysmorphic features	Dysmorphic Features	BEFREE	30622326		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	GENOMICS_ENGLAND_DG	17544522		★☆☆☆☆ Found in Text Mining only
Glomerulonephritis	Glomerulonephritis	Pubtator	40629603	Associate	★☆☆☆☆ Found in Text Mining only
Idiopathic Pulmonary Fibrosis	Pulmonary Fibrosis	BEFREE	29345973		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	30622326		★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	BEFREE	23257782, 9058730		★☆☆☆☆ Found in Text Mining only
Liposarcoma, Myxoid	liposarcoma	BEFREE	2515180		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	29565490		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	24241165, 29565490, 3281802		★☆☆☆☆ Found in Text Mining only
Mesothelioma Malignant	Mesothelioma	Pubtator	34294080	Associate	★☆☆☆☆ Found in Text Mining only
MICROPHTHALMIA, SYNDROMIC 7	Syndromic microphthalmia	BEFREE	2515180		★☆☆☆☆ Found in Text Mining only
Miller Dieker syndrome	Miller Dieker Syndrome	BEFREE	18094713		★☆☆☆☆ Found in Text Mining only
MYELODYSPLASTIC SYNDROME	Myelodysplastic Syndrome	BEFREE	17893227, 18094713, 20573398, 23257782, 23596104, 24813620, 27655690, 29572506		★☆☆☆☆ Found in Text Mining only
Myelofibrosis	Myelofibrosis	BEFREE	30390311		★☆☆☆☆ Found in Text Mining only
Myotonia Fluctuans (disorder)	Myotonia Fluctuans	BEFREE	30390311		★☆☆☆☆ Found in Text Mining only
Myxoid/Round Cell Liposarcoma	Myxoid Liposarcoma	BEFREE	2515180		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	15705910, 30826166		★☆☆☆☆ Found in Text Mining only
Neurodevelopmental Disorders	Neurodevelopmental Disorders	BEFREE	31428919		★☆☆☆☆ Found in Text Mining only
Primary Myelofibrosis	Myelofibrosis	BEFREE	30390311		★☆☆☆☆ Found in Text Mining only
Renal Cell Carcinoma	Renal Carcinoma	BEFREE	15705910		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	34925643	Associate	★☆☆☆☆ Found in Text Mining only
X-linked sideroblastic anemia	Sideroblastic Anemia, X-Linked	BEFREE	28123038		★☆☆☆☆ Found in Text Mining only