AGO1

gene
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Also known as hAGO1

Summary

AGO1 (argonaute RISC component 1, HGNC:3262) is a protein-coding gene on chromosome 1p34.3, encoding Protein argonaute-1 (Q9UL18). Required for RNA-mediated gene silencing (RNAi).

This gene encodes a member of the argonaute family of proteins, which associate with small RNAs and have important roles in RNA interference (RNAi) and RNA silencing. This protein binds to microRNAs (miRNAs) or small interfering RNAs (siRNAs) and represses translation of mRNAs that are complementary to them. It is also involved in transcriptional gene silencing (TGS) of promoter regions that are complementary to bound short antigene RNAs (agRNAs), as well as in the degradation of miRNA-bound mRNA targets. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. A recent study showed this gene to be an authentic stop codon readthrough target, and that its mRNA could give rise to an additional C-terminally extended isoform by use of an alternative in-frame translation termination codon.

Source: NCBI Gene 26523 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): complex neurodevelopmental disorder (Definitive, ClinGen) — +1 more curated relationship
  • GWAS associations: 1
  • Clinical variants (ClinVar): 191 total — 1 pathogenic, 13 likely-pathogenic
  • Phenotypes (HPO): 37
  • MANE Select transcript: NM_012199

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:3262
Approved symbolAGO1
Nameargonaute RISC component 1
Location1p34.3
Locus typegene with protein product
StatusApproved
AliaseshAGO1
Ensembl geneENSG00000092847
Ensembl biotypeprotein_coding
OMIM606228
Entrez26523

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 8 protein_coding, 5 nonsense_mediated_decay

ENST00000373204, ENST00000373206, ENST00000635259, ENST00000674426, ENST00000699841, ENST00000699842, ENST00000699843, ENST00000699844, ENST00000910381, ENST00000910382, ENST00000910383, ENST00000931710, ENST00000931711

RefSeq mRNA: 3 — MANE Select: NM_012199 NM_001317122, NM_001317123, NM_012199

CCDS: CCDS398, CCDS81300, CCDS90915

Canonical transcript exons

ENST00000373204 — 19 exons

ExonStartEnd
ENSE000005949483590147435901593
ENSE000007660123589309735893278
ENSE000007660163589403735894171
ENSE000007660753590194835902070
ENSE000007660773590220435902337
ENSE000007660793590693535907119
ENSE000007660813591384235914001
ENSE000007660833591418435914274
ENSE000007660853591534835915542
ENSE000007660863591759335917727
ENSE000007660883591832235918423
ENSE000014597603591949935930532
ENSE000014597613588320935883446
ENSE000016312403591905535919254
ENSE000016442123589431535894402
ENSE000016844833589367435893810
ENSE000017954423589512235895269
ENSE000036698343589255735892677
ENSE000036914143588842735888610

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 89.91.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.1619 / max 225.1369, expressed in 1815 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
213212.89221789
21339.29251771
21311.2002105
21350.7770305

Top tissues by expression

285 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
ganglionic eminenceUBERON:000402389.91gold quality
cervix squamous epitheliumUBERON:000692289.37silver quality
visceral pleuraUBERON:000240189.06gold quality
tendon of biceps brachiiUBERON:000818888.63gold quality
pleuraUBERON:000097788.54gold quality
parietal pleuraUBERON:000240088.44gold quality
ventricular zoneUBERON:000305387.04gold quality
adrenal tissueUBERON:001830385.66gold quality
hair follicleUBERON:000207385.61silver quality
monocyteCL:000057685.43gold quality
leukocyteCL:000073885.40gold quality
mononuclear cellCL:000084285.39gold quality
medial globus pallidusUBERON:000247784.75gold quality
tibiaUBERON:000097984.65gold quality
stromal cell of endometriumCL:000225584.44gold quality
esophagus squamous epitheliumUBERON:000692084.22gold quality
ileal mucosaUBERON:000033184.15gold quality
middle temporal gyrusUBERON:000277183.45gold quality
parotid glandUBERON:000183183.42gold quality
squamous epitheliumUBERON:000691483.32gold quality
embryoUBERON:000092283.07gold quality
colonic epitheliumUBERON:000039782.79gold quality
epithelial cell of pancreasCL:000008382.56silver quality
metanephric glomerulusUBERON:000473682.48gold quality
nephron tubuleUBERON:000123182.43gold quality
renal glomerulusUBERON:000007482.38gold quality
germinal epithelium of ovaryUBERON:000130482.30gold quality
tibialis anteriorUBERON:000138582.29silver quality
bloodUBERON:000017882.24gold quality
myocardiumUBERON:000234982.18silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes6.79

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

3 targets.

TargetRegulation
CCNB1Activation
IL2Activation
RELAActivation

Upstream regulators (CollecTRI, top): DNMT1, ESR1, MYC, SOX4

miRNA regulators (miRDB)

315 targeting AGO1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-4533100.0069.482758
HSA-MIR-4692100.0067.322066
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-12118100.0065.881270
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-3163100.0077.238605
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-3162-3P100.0065.37363
HSA-MIR-188-3P100.0068.761240
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-118499.9968.191458
HSA-MIR-451499.9967.101870
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-371A-3P99.9966.7791
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-1213699.9872.815713
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595

Literature-anchored findings (GeneRIF, showing 40)

  • describes cloning rat sequence and used RNA interference to show that the GERp95 orthologue in C. elegans is important for maturation of germ-line stem cells in the gonad. (PMID:10512872)
  • 2.6 A crystal structure of the PAZ domain from human Argonaute eIF2c1 bound to both ends of a 9-mer siRNA-like duplex (PMID:15152257)
  • These results establish a connection between RNA interference components AGO1 and TRBP2, RNAPII transcription and Polycomb-regulated control of gene expression. (PMID:16936726)
  • AGO1 and AGO2 associate with promoter DNA in cells treated with antigene RNAs (agRNAs), and inhibiting expression of AGO1 or AGO2 reverses transcriptional and post-transcriptional silencing. (PMID:16936728)
  • a unique amino acid sequence in human DICER protein is essential for binding to Argonaute family proteins (PMID:17482383)
  • Results describe a repetitive motif within Tas3, termed the ‘Argonaute hook’, that is conserved from yeast to humans and binds Ago1 and 2 through their PIWI domains in vitro and in vivo. (PMID:17891150)
  • Data show that Argonaute1 and 2 reside in three complexes with distinct Dicer and RNA-induced silencing complex activities, and that the putative RNA-binding protein RBM4 is required for microRNA-guided gene regulation. (PMID:17932509)
  • findings show that miRNA function is effected by AGO1-GW182 complexes and the role of GW182 in silencing goes beyond promoting deadenylation (PMID:18345015)
  • The specificity of RNA interference depends on the concentration of Ago1, Ago3, and Ago4 relative to Ago2. (PMID:18771919)
  • EIF2C1 protein expressed during the differentiation of N-type and S-type cells decreased from one of I-type cells to the central period of differentiation. (PMID:19393748)
  • Data show that Ago1 and Ago2 (which encode argonautes, the key proteins forming the RNA-induced silencing complex (RISC)) had significantly higher expression levels in ER- than in ER+ breast cancer. (PMID:19723326)
  • Study analyzed the association of Argonaute/EIF2C-miRNA complexes with target mRNAs and the degradation of these messages. (PMID:19767416)
  • The authors demonstrate that AGO1 uses only miRNA duplexes when assembling translational repression-competent complexes, whereas AGO2 can use both miRNA and siRNA duplexes. (PMID:19946268)
  • These data suggest that Axl acts as a tumor lymphatic metastasis-associated gene, and may function partly through the regulation of Cyr61. (PMID:20721975)
  • Data show that Ago1, but not Ago2, overexpression in neuroblastoma cells causes slowing of the cell cycle, decreased cellular motility, and a stronger apoptotic response to UV. (PMID:21846468)
  • DGCR8, AGO1, AGO2, PACT, and TARBP1 expression levels were significantly higher in the epithelial skin cancer groups than the healthy controls (P > 0.05). (PMID:22025453)
  • Mammalian PUM2-Ago-eEF1A inhibited translation of nonadenylated and polyadenylated reporter mRNAs in vitro. (PMID:22231398)
  • Ago3 is able to load microRNAs efficiently in the absence of Ago1 and Ago2, despite a significant loss of global microRNA expression (PMID:22474261)
  • Drosha, Dicer, Argonaute 1, and Argonaute 2 are differentially expressed at different metastatic sites in ovarian carcinoma compared with primary carcinomas. (PMID:22647351)
  • Study observed a dramatic difference in AGO1 and AGO2 associated miRNA profiles in blood plasma. The lack of correlation between AGO1 and AGO2 miRNA content in the plasma can be explained by the fact that many tissues contribute to the extracellular miRNA content. (PMID:22858679)
  • AGO1 and AGO2 proteins couple RNA polymerase II elongation to chromatin modification (PMID:22961379)
  • Ago2 and Ago1 can slice, and thus functionally bind, preannealed siRNA-mRNA duplexes. (PMID:23019594)
  • Tumor xenografts and human cancer specimens indicate that AGO1-mediated translational desuppression of VEGF may be associated with tumor angiogenesis and poor prognosis. (PMID:23426184)
  • PIWI-domain mutations in Ago1 may misarrange the catalytic center. Replacing Ago1 cluster 2 by the sequence found in Ago2 fully activated the Ago1 PIWI domain only when the Ago1 PIWI domain was placed into the Ago2 backbone. (PMID:23665583)
  • Aberrant expression of argonaute-1/-2 in human renal cell carcinoma is possibly involved with tumorigenesis and prognosis. (PMID:23696926)
  • Completion of the tetrad, combined with a mutation on a loop adjacent to the active site of hAgo1, results in slicer activity that is substantially enhanced by swapping in the N domain of hAgo2. (PMID:23746446)
  • The Ago1 N domain performed best when juxtaposed with cognate PAZ and MID. This exemplifies the importance of proper intermolecular-domain interactions. (PMID:23748378)
  • Evolutionary amino acid changes to hAGO1 were readily reversible, suggesting that loading of guide RNA and pairing of seed-based miRNA and target RNA constrain its sequence drift. (PMID:23809764)
  • nuclear Ago1 directly interacts with RNA Polymerase II and is widely associated with chromosomal loci throughout the genome with preferential enrichment in promoters of transcriptionally active genes (PMID:24086155)
  • Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing (PMID:25313066)
  • EIF2C2, Dicer, and Drosha are more highly expressed in bladder carcinoma, promote the development of bladder cancer, and suggested a poor prognosis (PMID:25656609)
  • Blocking AGO1, AGO2, or TRBP expression changes expression levels and nuclear distribution of RNAi factors Dicer, TNRC6A (GW182), and TRBP. (PMID:26242502)
  • Low AGO1 expression is associated with melanoma. (PMID:27518285)
  • We selected five single nucleotide polymorphisms (SNPs) (rs7813, rs2740349, rs2291778, rs910924, rs595961) in two key microRNA biosynthesis genes (GEMIN4 and AGO1) and systematically evaluated the association between these SNPs, the gene-environment interaction and lung cancer risk. This is the first study showing that rs7813 and rs595961 could be meaningful as genetic markers for lung cancer risk. (PMID:27669275)
  • E-cadherin silencing relies on the formation of a complex between the paRNA and microRNA-guided Argonaute 1 that, together, recruit SUV39H1 and induce repressive chromatin modifications in the gene promoter (PMID:28555645)
  • In miRNA-mediated gene silencing, the physical interaction between human Argonaute (hAgo) and GW182 (hGW182) is essential for facilitating the downstream silencing of the targeted mRNA. hGW182 can recruit up to three copies of hAgo via its three GW motifs. This may explain the observed cooperativity in miRNA-mediated gene silencing. (PMID:28781232)
  • the polymorphisms of the AGO1 and AGO2 genes, the expression levels of which correlated with the proportion of Th17 cells, were associated with the development and prognosis of Graves’ disease. (PMID:29256262)
  • AGO1 may promote hepatocellular carcinoma metastasis through TGF-beta pathway. (PMID:29487329)
  • AGO1 missense mutation was identified in a patient with syndromic form of intellectual disability/autism spectrum disorder. (PMID:30213762)
  • Effects of the PIWI/MID domain of Argonaute protein on the association of miRNAi’s seed base with the target have been reported. (PMID:30770397)

Cross-species orthologs

13 orthologs

OrganismSymbolGene ID
danio_rerioago1ENSDARG00000092644
mus_musculusAgo1ENSMUSG00000041530
rattus_norvegicusAgo1ENSRNOG00000055915
caenorhabditis_elegansppw-1WBGENE00004093
caenorhabditis_elegansppw-2WBGENE00004094
caenorhabditis_elegansWBGENE00006449
caenorhabditis_elegansWBGENE00007624
caenorhabditis_elegansWBGENE00010263
caenorhabditis_eleganswago-1WBGENE00011061
caenorhabditis_elegansWBGENE00011910
caenorhabditis_eleganssago-2WBGENE00018921
caenorhabditis_elegansWBGENE00020707
caenorhabditis_elegansWBGENE00022877

Paralogs (3): AGO2 (ENSG00000123908), AGO3 (ENSG00000126070), AGO4 (ENSG00000134698)

Protein

Protein identifiers

Protein argonaute-1Q9UL18 (reviewed: Q9UL18)

Alternative names: Argonaute RISC catalytic component 1, Eukaryotic translation initiation factor 2C 1, Putative RNA-binding protein Q99

All UniProt accessions (8): Q9UL18, A0A0U1RQZ8, A0A6I8PTZ8, A0A8V8TNY0, A0A8V8TPF2, A0A8V8TQA7, A0A8V8TQN5, Q5TA58

UniProt curated annotations — full annotation on UniProt →

Function. Required for RNA-mediated gene silencing (RNAi). Binds to short RNAs such as microRNAs (miRNAs) or short interfering RNAs (siRNAs), and represses the translation of mRNAs which are complementary to them. Lacks endonuclease activity and does not appear to cleave target mRNAs. Also required for transcriptional gene silencing (TGS) of promoter regions which are complementary to bound short antigene RNAs (agRNAs).

Subunit / interactions. Interacts with DDB1, DDX5, DDX6, DHX30, DHX36, DDX47, DICER1, AGO2, ELAVL1, HNRNPF, IGF2BP1, ILF3, IMP8, MATR3, MOV10, PABPC1, PRMT5, RBM4, SART3, TNRC6B, UPF1 and YBX1. Associates with polysomes and messenger ribonucleoproteins (mNRPs). Interacts with LIMD1, WTIP and AJUBA. Interacts with APOBEC3F, APOBEC3G and APOBEC3H.

Subcellular location. Cytoplasm. P-body.

Post-translational modifications. Ubiquitinated on surface-exposed lysines by a SCF-like E3 ubiquitin-protein ligase complex containing ZSWIM8 during target-directed microRNA degradation (TDMD), a process that mediates degradation of microRNAs (miRNAs). Ubiquitination by the SCF-like E3 ubiquitin-protein ligase complex containing ZSWIM8 leads to its subsequent degradation, thereby exposing miRNAs for degradation. ZSWIM8 recognizes and binds AGO1 when it is engaged with a TDMD target.

Disease relevance. Neurodevelopmental disorder with language delay and behavioral abnormalities, with or without seizures (NEDLBAS) [MIM:620292] An autosomal dominant neurodevelopmental disorder characterized by global developmental delay with intellectual disability of varying severity, speech and motor delay, and behavioral abnormalities, including autistic features. About half of patients develop seizures. The disease is caused by variants affecting the gene represented in this entry.

Miscellaneous. Lacks RNA cleavage activity due to the absence of the conserved His at position 805, but also because it binds the RNA in a subtly different manner that precludes efficient cleavage.

Similarity. Belongs to the argonaute family. Ago subfamily.

RefSeq proteins (3): NP_001304051, NP_001304052, NP_036331* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003100PAZ_domDomain
IPR003165PiwiDomain
IPR012337RNaseH-like_sfHomologous_superfamily
IPR014811ArgoL1Domain
IPR032472ArgoL2Domain
IPR032473Argonaute_Mid_domDomain
IPR032474Argonaute_NDomain
IPR036085PAZ_dom_sfHomologous_superfamily
IPR036397RNaseH_sfHomologous_superfamily
IPR045246Piwi_ago-likeDomain

Pfam: PF02170, PF02171, PF08699, PF16486, PF16487, PF16488

UniProt features (104 total): strand 36, helix 29, sequence variant 17, turn 8, region of interest 6, mutagenesis site 4, domain 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

8 structures.

PDBMethodResolution (Å)
4KREX-RAY DIFFRACTION1.75
4KRFX-RAY DIFFRACTION2.1
4KXTX-RAY DIFFRACTION2.29
1SI2X-RAY DIFFRACTION2.6
1SI3X-RAY DIFFRACTION2.6
5W6VX-RAY DIFFRACTION2.83
9Q3FELECTRON MICROSCOPY3.3
9Q3GELECTRON MICROSCOPY3.3

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UL18-F191.450.80

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Mutagenesis-validated functional residues (4):

PositionPhenotype
670confers modest rna cleavage activity; when associated with q-675 and h-805.
674confers modest rna cleavage activity; when associated with h-805.
675does not confer enzyme activity by itself. confers low rna cleavage activity; when associated with h-805. confers modest
805does not confer enzyme activity by itself. confers modest rna cleavage activity; when associated with f-674.

Function

Pathways and Gene Ontology

Reactome pathways

66 pathways

IDPathway
R-HSA-165159MTOR signalling
R-HSA-1912408Pre-NOTCH Transcription and Translation
R-HSA-203927MicroRNA (miRNA) biogenesis
R-HSA-2559580Oxidative Stress Induced Senescence
R-HSA-2559585Oncogene Induced Senescence
R-HSA-4086398Ca2+ pathway
R-HSA-426486Small interfering RNA (siRNA) biogenesis
R-HSA-426496Post-transcriptional silencing by small RNAs
R-HSA-5578749Transcriptional regulation by small RNAs
R-HSA-5628897TP53 Regulates Metabolic Genes
R-HSA-5687128MAPK6/MAPK4 signaling
R-HSA-8853884Transcriptional Regulation by VENTX
R-HSA-8934593Regulation of RUNX1 Expression and Activity
R-HSA-8936459RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
R-HSA-8943723Regulation of PTEN mRNA translation
R-HSA-8948700Competing endogenous RNAs (ceRNAs) regulate PTEN translation
R-HSA-8986944Transcriptional Regulation by MECP2
R-HSA-9018519Estrogen-dependent gene expression
R-HSA-9022692Regulation of MECP2 expression and activity
R-HSA-9029569NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux
R-HSA-9725371Nuclear events stimulated by ALK signaling in cancer
R-HSA-9759811Regulation of CDH11 mRNA translation by microRNAs
R-HSA-9764562Regulation of CDH1 mRNA translation by microRNAs
R-HSA-9768778Regulation of NPAS4 mRNA translation
R-HSA-9824594Regulation of MITF-M-dependent genes involved in apoptosis
R-HSA-9839394TGFBR3 expression
R-HSA-9909620Regulation of PD-L1(CD274) translation
R-HSA-1257604PIP3 activates AKT signaling
R-HSA-1266738Developmental Biology
R-HSA-1500931Cell-Cell communication

MSigDB gene sets: 505 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, AGGAAGC_MIR5163P, MYAATNNNNNNNGGC_UNKNOWN, REACTOME_SIGNALING_BY_NOTCH, GOMF_ENDONUCLEASE_ACTIVITY, GOMF_RNA_NUCLEASE_ACTIVITY, MYOGENIN_Q6, TGCGCANK_UNKNOWN, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, TGCACTT_MIR519C_MIR519B_MIR519A, GOMF_NUCLEASE_ACTIVITY, AAGTCCA_MIR422B_MIR422A, TTTGTAG_MIR520D

GO Biological Process (14): nuclear-transcribed mRNA catabolic process (GO:0000956), miRNA metabolic process (GO:0010586), positive regulation of gene expression (GO:0010628), negative regulation of angiogenesis (GO:0016525), pre-miRNA processing (GO:0031054), regulatory ncRNA-mediated post-transcriptional gene silencing (GO:0035194), miRNA processing (GO:0035196), miRNA-mediated gene silencing by inhibition of translation (GO:0035278), regulation of mRNA stability (GO:0043488), positive regulation of transcription by RNA polymerase II (GO:0045944), RISC complex assembly (GO:0070922), positive regulation of non-canonical NF-kappaB signal transduction (GO:1901224), regulation of translation (GO:0006417), regulatory ncRNA-mediated gene silencing (GO:0031047)

GO Molecular Function (11): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), RNA polymerase II complex binding (GO:0000993), core promoter sequence-specific DNA binding (GO:0001046), RNA binding (GO:0003723), double-stranded RNA binding (GO:0003725), single-stranded RNA binding (GO:0003727), miRNA binding (GO:0035198), transcription cis-regulatory region binding (GO:0000976), nucleic acid binding (GO:0003676), protein binding (GO:0005515), regulatory RNA binding (GO:0061980)

GO Cellular Component (9): P-body (GO:0000932), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), RISC complex (GO:0016442), cytoplasmic ribonucleoprotein granule (GO:0036464), RISC-loading complex (GO:0070578), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-14 pathways:

CategoryPathways
Gene Silencing by RNA4
Cellular Senescence2
Generic Transcription Pathway2
Transcriptional regulation by RUNX12
Signal Transduction1
Pre-NOTCH Expression and Processing1
Beta-catenin independent WNT signaling1
Transcriptional Regulation by TP531
MAPK family signaling cascades1
PTEN Regulation1
Regulation of PTEN mRNA translation1
ESR-mediated signaling1
Transcriptional Regulation by MECP21
NR1H2 and NR1H3-mediated signaling1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA binding3
cellular anatomical structure3
regulatory ncRNA-mediated gene silencing2
binding2
cytoplasm2
mRNA catabolic process1
RNA metabolic process1
gene expression1
regulation of gene expression1
positive regulation of macromolecule biosynthetic process1
angiogenesis1
regulation of angiogenesis1
negative regulation of blood vessel morphogenesis1
miRNA processing1
post-transcriptional gene silencing1
regulatory ncRNA processing1
negative regulation of translation1
miRNA-mediated post-transcriptional gene silencing1
regulation of RNA stability1
regulation of mRNA catabolic process1
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
positive regulation of DNA-templated transcription1
protein-RNA complex assembly1
non-canonical NF-kappaB signal transduction1
regulation of non-canonical NF-kappaB signal transduction1
positive regulation of intracellular signal transduction1
translation1
post-transcriptional regulation of gene expression1
regulation of protein metabolic process1
negative regulation of gene expression1
RNA polymerase II transcription regulatory region sequence-specific DNA binding1
cis-regulatory region sequence-specific DNA binding1
RNA polymerase core enzyme binding1
transcription cis-regulatory region binding1
nucleic acid binding1
regulatory RNA binding1
transcription regulatory region nucleic acid binding1
sequence-specific double-stranded DNA binding1
cytoplasmic ribonucleoprotein granule1

Protein interactions and networks

STRING

2578 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
AGO1DICER1Q9UPY3999
AGO1TNRC6AQ8NDV7998
AGO1AGO2Q9UKV8982
AGO1DDX6P26196978
AGO1AGO4Q9HCK5975
AGO1FMR1Q06787971
AGO1MOV10Q9HCE1968
AGO1TARBP2Q15633963
AGO1TNRC6BQ9UPQ9948
AGO1DROSHAQ9NRR4939
AGO1DDX20Q9UHI6927
AGO1HSP90AA1P07900916
AGO1TRIM32Q13049881
AGO1AGO3Q9H9G7858
AGO1HDAC1Q13547853

IntAct

88 interactions, top by confidence:

ABTypeScore
TNRC6AAGO2psi-mi:“MI:0914”(association)0.960
AGO1TNRC6Apsi-mi:“MI:0914”(association)0.900
TNRC6AAGO1psi-mi:“MI:0915”(physical association)0.900
TNRC6AAGO1psi-mi:“MI:0403”(colocalization)0.900
AGO1DICER1psi-mi:“MI:0915”(physical association)0.830
AGO2DDX6psi-mi:“MI:0914”(association)0.810
AGO1HSP90AB1psi-mi:“MI:0915”(physical association)0.740
H2AXPPM1Gpsi-mi:“MI:0914”(association)0.730
AGO2AGO1psi-mi:“MI:0407”(direct interaction)0.720
AGO1TNRC6Bpsi-mi:“MI:0407”(direct interaction)0.680
AGO1TNRC6Bpsi-mi:“MI:0915”(physical association)0.680
AGO1TNRC6Bpsi-mi:“MI:0403”(colocalization)0.680
DNAJC7PLD2psi-mi:“MI:0914”(association)0.640
PABPC1AGO2psi-mi:“MI:0914”(association)0.640
PPP5CAGO1psi-mi:“MI:0915”(physical association)0.620
PRNPAGO1psi-mi:“MI:0915”(physical association)0.610
AGO1TNRC6Cpsi-mi:“MI:0915”(physical association)0.600
AGO1TNRC6Cpsi-mi:“MI:0403”(colocalization)0.600
PPP5CIRS4psi-mi:“MI:0914”(association)0.570
AGO1LIMD1psi-mi:“MI:0915”(physical association)0.570
AGO1LIMD1psi-mi:“MI:0407”(direct interaction)0.570
AGO1LIMD1psi-mi:“MI:0403”(colocalization)0.570
AGO2FKBP5psi-mi:“MI:0914”(association)0.530
AGO1AIPpsi-mi:“MI:0914”(association)0.530
TRMT13STAG1psi-mi:“MI:0914”(association)0.530

BioGRID (256): AGO1 (Affinity Capture-RNA), AGO1 (Affinity Capture-RNA), AGO1 (Affinity Capture-MS), AGO1 (Co-fractionation), AGO1 (Reconstituted Complex), CYLD (Affinity Capture-RNA), TAX1BP1 (Affinity Capture-RNA), OTUD7B (Affinity Capture-RNA), AGO1 (Affinity Capture-MS), AGO1 (Affinity Capture-MS), AGO1 (Affinity Capture-MS), AGO1 (Affinity Capture-MS), AGO1 (Affinity Capture-Western), AGO1 (Affinity Capture-MS), AGO1 (Affinity Capture-MS)

ESM2 similar proteins: A2CEI6, A3KPK0, A6P7L8, A8D8P8, A8KBF3, A9ZSZ2, O04379, O48771, O76922, O77503, O89040, Q0JF58, Q4G033, Q4KLV6, Q5NBN9, Q5Z5B2, Q5ZLG4, Q5ZMW0, Q69VD5, Q6DCX2, Q6DJB9, Q6EU14, Q6K972, Q6QME8, Q6T5B7, Q6YSJ5, Q6Z4F1, Q7PLK0, Q7XSA2, Q7Y001, Q7Z3Z3, Q7Z3Z4, Q84VQ0, Q851R2, Q8CDG1, Q8CGT6, Q8CJF8, Q8CJF9, Q8CJG0, Q8CJG1

Diamond homologs: A3KPK0, O04379, O48771, O74957, O77503, P34681, Q0JF58, Q10F39, Q4KLV6, Q5NBN9, Q5Z5B2, Q5ZLG4, Q5ZMW0, Q69UP6, Q69VD5, Q6DCX2, Q6DJB9, Q6EU14, Q6H6C3, Q6K972, Q6QME8, Q6T5B7, Q6YSJ5, Q6Z4F1, Q75HC2, Q7XSA2, Q7XTS3, Q7XTS4, Q7Y001, Q84VQ0, Q851R2, Q852N2, Q8CJF8, Q8CJF9, Q8CJG0, Q8CJG1, Q9C793, Q9H9G7, Q9HCK5, Q9QZ81

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 86 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Regulation of MITF-M-dependent genes involved in apoptosis657.7×6e-08
Regulation of RUNX1 Expression and Activity550.9×2e-06
TGFBR3 expression534.6×1e-05
Regulation of MECP2 expression and activity527.9×3e-05
Transcriptional Regulation by MECP2524.0×6e-05
NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux523.4×7e-05
MTOR signalling520.1×1e-04
Transcriptional Regulation by VENTX520.1×1e-04

GO biological processes:

GO termPartnersFoldFDR
miRNA-mediated gene silencing by inhibition of translation888.7×1e-11
positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay684.3×8e-09

Disease & clinical

Clinical variants and AI predictions

ClinVar

191 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic1
Likely pathogenic13
Uncertain significance123
Likely benign19
Benign7

Top pathogenic / likely-pathogenic (14)

Variant IDHGVSClassification
976687NM_012199.5(AGO1):c.650-2A>GPathogenic
1299669NM_012199.5(AGO1):c.583G>A (p.Glu195Lys)Likely pathogenic
1300187NM_012199.5(AGO1):c.2252A>T (p.His751Leu)Likely pathogenic
1300188NM_012199.5(AGO1):c.2389A>T (p.Ile797Phe)Likely pathogenic
148904GRCh38/hg38 1p34.3(chr1:34753938-36055310)x1Likely pathogenic
1750732NM_012199.5(AGO1):c.595G>T (p.Gly199Cys)Likely pathogenic
2531391NM_012199.5(AGO1):c.1354G>A (p.Ala452Thr)Likely pathogenic
3254954NM_012199.5(AGO1):c.1249C>A (p.Gln417Lys)Likely pathogenic
3276168NM_012199.5(AGO1):c.1066G>A (p.Asp356Asn)Likely pathogenic
3366942NM_012199.5(AGO1):c.1594C>T (p.Arg532Cys)Likely pathogenic
4024530NM_012199.5(AGO1):c.2466-1G>ALikely pathogenic
4082190NM_012199.5(AGO1):c.1067A>G (p.Asp356Gly)Likely pathogenic
547981NM_012199.5(AGO1):c.566C>T (p.Pro189Leu)Likely pathogenic
984614NM_012199.5(AGO1):c.569T>C (p.Leu190Pro)Likely pathogenic

SpliceAI

3319 predictions. Top by Δscore:

VariantEffectΔscore
1:35888426:GCT:Gacceptor_gain1.0000
1:35888607:ACCGG:Adonor_loss1.0000
1:35888608:CCG:Cdonor_gain1.0000
1:35888608:CCGG:Cdonor_loss1.0000
1:35888609:CGGT:Cdonor_loss1.0000
1:35888610:GGT:Gdonor_loss1.0000
1:35888611:G:GAdonor_loss1.0000
1:35888611:G:GGdonor_gain1.0000
1:35888612:T:TCdonor_loss1.0000
1:35892556:GGGAA:Gacceptor_gain1.0000
1:35892676:GG:Gdonor_gain1.0000
1:35892677:GG:Gdonor_gain1.0000
1:35892677:GGTAA:Gdonor_loss1.0000
1:35892678:G:GAdonor_loss1.0000
1:35892678:G:GGdonor_gain1.0000
1:35892679:TAA:Tdonor_loss1.0000
1:35893085:A:AGacceptor_gain1.0000
1:35893086:C:Gacceptor_gain1.0000
1:35893092:T:Aacceptor_gain1.0000
1:35894034:CA:Cacceptor_loss1.0000
1:35894035:A:AGacceptor_gain1.0000
1:35894036:G:GCacceptor_gain1.0000
1:35894036:GT:Gacceptor_gain1.0000
1:35894036:GTC:Gacceptor_gain1.0000
1:35894036:GTCT:Gacceptor_gain1.0000
1:35894036:GTCTC:Gacceptor_gain1.0000
1:35894168:AAGGG:Adonor_loss1.0000
1:35894169:AGGGT:Adonor_loss1.0000
1:35894170:GG:Gdonor_gain1.0000
1:35894171:GG:Gdonor_gain1.0000

AlphaMissense

5619 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:35888524:T:AN41K1.000
1:35888524:T:GN41K1.000
1:35888610:G:CR70P1.000
1:35892624:G:CD93H1.000
1:35892625:A:TD93V1.000
1:35892627:G:AG94R1.000
1:35892627:G:CG94R1.000
1:35892628:G:AG94E1.000
1:35892628:G:TG94V1.000
1:35892642:T:GY99D1.000
1:35893142:T:CF126L1.000
1:35893143:T:CF126S1.000
1:35893144:T:AF126L1.000
1:35893144:T:GF126L1.000
1:35893149:T:AV128D1.000
1:35893699:T:CF180L1.000
1:35893701:C:AF180L1.000
1:35893701:C:GF180L1.000
1:35893756:G:CG199R1.000
1:35893757:G:AG199D1.000
1:35893757:G:TG199V1.000
1:35893799:T:CL213P1.000
1:35894049:C:AA221D1.000
1:35894051:T:CF222L1.000
1:35894053:T:AF222L1.000
1:35894053:T:GF222L1.000
1:35894145:G:CR253P1.000
1:35894154:T:CF256S1.000
1:35894318:T:CL263P1.000
1:35894324:T:AV265E1.000

dbSNP variants (sampled 300 via entrez): RS1000050388 (1:35928283 T>C), RS1000051127 (1:35897989 T>C), RS1000081545 (1:35879968 T>A), RS1000206497 (1:35924089 G>A), RS1000221753 (1:35893252 G>A), RS1000242529 (1:35870569 A>C), RS1000280959 (1:35930003 T>A,C,G), RS1000374151 (1:35930873 G>A,C), RS1000404100 (1:35925005 C>G), RS1000435153 (1:35924744 G>A), RS1000444839 (1:35890351 A>C,G,T), RS1000466575 (1:35900427 T>C), RS1000473891 (1:35930134 C>T), RS1000485133 (1:35880324 G>A), RS1000571739 (1:35873843 A>C)

Disease associations

OMIM: gene MIM:606228 | disease phenotypes: MIM:620292

GenCC curated gene-disease

DiseaseClassificationInheritance
neurodevelopmental disorder with language delay and behavioral abnormalities, with or without seizuresStrongAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
complex neurodevelopmental disorderDefinitiveAD

Mondo (3): intellectual disability (MONDO:0001071), neurodevelopmental disorder with language delay and behavioral abnormalities, with or without seizures (MONDO:0859531), neurodevelopmental disorder (MONDO:0700092)

Orphanet (1): NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

37 total (30 of 37 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000219Thin upper lip vermilion
HP:0000286Epicanthus
HP:0000311Round face
HP:0000348High forehead
HP:0000400Macrotia
HP:0000414Bulbous nose
HP:0000431Wide nasal bridge
HP:0000486Strabismus
HP:0000494Downslanted palpebral fissures
HP:0000506Telecanthus
HP:0000718Aggressive behavior
HP:0000729Autistic behavior
HP:0000733Motor stereotypy
HP:0000739Anxiety
HP:0000750Delayed speech and language development
HP:0000752Hyperactivity
HP:0001249Intellectual disability
HP:0001250Seizure
HP:0001252Hypotonia
HP:0001263Global developmental delay
HP:0001270Motor delay
HP:0002020Gastroesophageal reflux
HP:0002069Bilateral tonic-clonic seizure
HP:0002133Status epilepticus
HP:0002342Moderate intellectual disability
HP:0002360Sleep disturbance
HP:0002373Febrile seizure (within the age range of 3 months to 6 years)
HP:0002384Focal impaired awareness seizure
HP:0003196Short nose

GWAS associations

1 associations (top):

StudyTraitp-value
GCST012047_1Fasting glucose9.000000e-07

MeSH disease descriptors (2)

DescriptorNameTree numbers
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D065886Neurodevelopmental DisordersF03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs595961AGO10.000

CTD chemical–gene interactions

36 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects binding, increases reaction, decreases expression2
Cisplatinaffects cotreatment, increases expression, decreases expression2
Dronabinolincreases expression2
Tretinoinincreases expression2
Aflatoxin B1decreases methylation, increases methylation2
dicrotophosincreases expression1
methylmercuric chloridedecreases expression1
cobaltous chloridedecreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
ICG 001increases expression1
abrinedecreases expression1
Grape Seed Proanthocyanidinsaffects cotreatment, increases expression1
jinfukangaffects cotreatment, increases expression1
LDN 193189affects cotreatment, increases expression1
(+)-JQ1 compoundincreases expression1
Vorinostatdecreases expression1
Air Pollutantsaffects response to substance1
Vehicle Emissionsaffects response to substance1
Benzeneincreases expression1
Carbamazepineaffects expression1
Catechinaffects cotreatment, increases expression1
Estradiolaffects expression1
Ivermectindecreases expression1
Leadaffects expression1
Ribonucleotidesaffects binding1
Thimerosaldecreases expression1
Thiramdecreases expression1
Urethaneincreases expression1

Cellosaurus cell lines

5 cell lines: 5 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B1J7Abcam HeLa AGO1 KOCancer cell lineFemale
CVCL_SB94HAP1 AGO1 (-) 1Cancer cell lineMale
CVCL_SB95HAP1 AGO1 (-) 2Cancer cell lineMale
CVCL_SB96HAP1 AGO1 (-) 3Cancer cell lineMale
CVCL_SB97HAP1 AGO1 (-) 4Cancer cell lineMale

Clinical trials (associated diseases)

197 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02270736PHASE3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02304302PHASE2COMPLETEDDown Syndrome Memantine Follow-up Study
NCT03862950PHASE2COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226PHASE2UNKNOWNStudy to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856PHASE2COMPLETEDEvaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT05273320PHASE1COMPLETEDClinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361PHASE1ENROLLING_BY_INVITATIONSensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764PHASE1COMPLETEDUse of MRI and cTBS for Catatonia in Autism
NCT06586827PHASE1COMPLETEDImpact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940PHASE1NOT_YET_RECRUITINGEscalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT03479476PHASE2/PHASE3COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796PHASE1/PHASE2COMPLETEDEffects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672EARLY_PHASE1RECRUITINGClinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948Not specifiedCOMPLETEDHealthy Lifestyles for People With Intellectual Disabilities
NCT01087320Not specifiedRECRUITINGGenome Medical Sequencing for Gene Discovery
NCT01652963Not specifiedUNKNOWNPicture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395Not specifiedCOMPLETEDMental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554Not specifiedCOMPLETEDResearch and Characterization of New Genes Involved in Intellectual Disability
NCT01915381Not specifiedCOMPLETEDImproving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623Not specifiedCOMPLETEDPivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773Not specifiedCOMPLETEDSupport Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849Not specifiedCOMPLETEDInter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041Not specifiedCOMPLETEDSedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438Not specifiedCOMPLETEDEstablishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study
NCT02451761Not specifiedCOMPLETEDApparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability
NCT02461420Not specifiedACTIVE_NOT_RECRUITINGMapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome
NCT02461459Not specifiedACTIVE_NOT_RECRUITINGAutism Spectrum Disorder (ASD) and Intellectual Disability (ID) Determinants in Tuberous Sclerosis Complex (TSC)
NCT02486081Not specifiedCOMPLETEDDevelopment and Application-Smart Football for Movement Evaluation and Training in the Special Education Population
NCT02504502Not specifiedCOMPLETEDEnhancing Genomic Laboratory Reports to Enhance Communication and Empower Patients
NCT02513277Not specifiedCOMPLETEDDiabetes Screening & Prevention for People With Learning (Intellectual) Disabilities:STOP Diabetes Study
NCT02561754Not specifiedCOMPLETEDWeight Management for Adolescents With IDD
NCT02591446Not specifiedCOMPLETEDTranscranial Magnetic Stimulation Studies in Autism Spectrum Disorders
NCT02714868Not specifiedCOMPLETEDEvaluation of Project TEAM (Teens Making Environmental and Activity Modifications)
NCT02721394Not specifiedUNKNOWNFCT With Young Children With ID in the UK: A Feasibility Project V.1
NCT02746614Not specifiedCOMPLETEDPsychomotor Therapy Effects in Adaptive Behavior and Motor Proficiency in Intellectual Disability
NCT02836405Not specifiedCOMPLETEDTMS for the Investigation of Brain Plasticity in Autism Spectrum Disorders