AGO3

argonaute RISC catalytic component 3, the group of Argonaute RISC component family

Basic information

Region (hg38): 1:35930718-36072500

Previous symbols: [ "EIF2C3" ]

Links

ENSG00000126070 ∙ NCBI:192669 ∙ OMIM:607355 ∙ HGNC:18421 ∙ Uniprot:Q9H9G7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AGO3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGO3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				15	5	20
missense			18		1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	1		2
Total	0	0	19	16	6

Variants in AGO3

This is a list of pathogenic ClinVar variants found in the AGO3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-35945708-G-C		not specified	Uncertain significance (Aug 17, 2022)
1-35967050-A-G		not specified	Uncertain significance (Dec 03, 2021)
1-35967061-G-A		not specified	Uncertain significance (Jul 20, 2021)
1-35972102-G-T		not specified	Uncertain significance (Jan 19, 2024)
1-35972140-G-C			Likely benign (Mar 29, 2018)
1-35972146-G-A			Likely benign (Dec 14, 2018)
1-35972150-G-A		not specified	Uncertain significance (Nov 10, 2021)
1-35972221-G-A		AGO3-related disorder	Benign (Mar 28, 2018)
1-35973426-C-T		AGO3-related disorder	Likely benign (Jun 21, 2019)
1-35973475-C-T		not specified	Uncertain significance (Aug 09, 2021)
1-36004355-T-C			Uncertain significance (Oct 19, 2020)
1-36004366-A-G			Likely benign (Jul 06, 2018)
1-36008945-G-A		AGO3-related disorder	Likely benign (Apr 09, 2018)
1-36008987-G-A		AGO3-related disorder	Likely benign (Aug 19, 2019)
1-36009017-A-G			Benign (Dec 31, 2019)
1-36009028-C-T		AGO3-related disorder	Uncertain significance (Sep 07, 2023)
1-36009521-A-G		not specified	Uncertain significance (May 04, 2022)
1-36013651-A-G		not specified	Uncertain significance (Nov 12, 2021)
1-36013667-A-G		not specified	Uncertain significance (May 24, 2023)
1-36013689-G-A		AGO3-related disorder	Benign/Likely benign (Apr 01, 2022)
1-36013737-C-G			Likely benign (Apr 03, 2018)
1-36013919-G-A		AGO3-related disorder	Uncertain significance (Mar 04, 2023)
1-36013999-G-T		not specified	Uncertain significance (May 31, 2023)
1-36014041-A-G		not specified	Uncertain significance (Mar 04, 2024)
1-36027134-G-A		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGO3	protein_coding	protein_coding	ENST00000373191	19	141783

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000258	125739	0	6	125745	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	5.26	170	501	0.339	0.0000279	5596
Missense in Polyphen		42	171.35	0.24512		1974
Synonymous	1.55	143	169	0.848	0.00000901	1689
Loss of Function	5.84	4	47.4	0.0843	0.00000268	545

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000670	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for RNA-mediated gene silencing (RNAi). Binds to short RNAs such as microRNAs (miRNAs) and represses the translation of mRNAs which are complementary to them. Proposed to be involved in stabilization of small RNA derivates (riRNA) derived from processed RNA polymerase III-transcribed Alu repeats containing a DR2 retinoic acid response element (RARE) in stem cells and in the subsequent riRNA-dependent degradation of a subset of RNA polymerase II-transcribed coding mRNAs by recruiting a mRNA decapping complex involving EDC4. Possesses RNA slicer activity but only on select RNAs bearing 5'- and 3'-flanking sequences to the region of guide-target complementarity (PubMed:29040713). {ECO:0000255|HAMAP-Rule:MF_03032, ECO:0000269|PubMed:18771919, ECO:0000269|PubMed:23064648, ECO:0000269|PubMed:29040713}.
• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Competing endogenous RNAs (ceRNAs) regulate PTEN translation;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;Oncogene Induced Senescence;Oxidative Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;RNA Polymerase II Transcription;Pre-NOTCH Transcription and Translation;Pre-NOTCH Expression and Processing;Signaling by NOTCH;TP53 Regulates Metabolic Genes;Cellular responses to external stimuli;Regulation of PTEN mRNA translation;PTEN Regulation;PIP3 activates AKT signaling;Signaling by Nuclear Receptors;Transcriptional Regulation by TP53;Regulation of RUNX1 Expression and Activity;Estrogen-dependent gene expression;ESR-mediated signaling;Intracellular signaling by second messengers;MicroRNA (miRNA) biogenesis;Transcriptional regulation by RUNX1;Small interfering RNA (siRNA) biogenesis;Post-transcriptional silencing by small RNAs;Gene Silencing by RNA (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: -1
• rvis_percentile_EVS: 8.32

Haploinsufficiency Scores

• pHI: 0.155
• hipred: Y
• hipred_score: 0.825
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ago3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: mRNA catabolic process;Wnt signaling pathway, calcium modulating pathway;RNA secondary structure unwinding;positive regulation of gene expression;negative regulation of gene expression;pre-miRNA processing;posttranscriptional gene silencing by RNA;production of miRNAs involved in gene silencing by miRNA;miRNA mediated inhibition of translation;mRNA cleavage involved in gene silencing by miRNA;miRNA loading onto RISC involved in gene silencing by miRNA;regulation of megakaryocyte differentiation;regulation of stem cell proliferation;RNA phosphodiester bond hydrolysis, endonucleolytic;mRNA cleavage involved in gene silencing by siRNA;positive regulation of NIK/NF-kappaB signaling
• Cellular component: condensed nuclear chromosome;P-body;nucleoplasm;cytoplasm;cytosol;membrane;RISC complex;micro-ribonucleoprotein complex;cytoplasmic ribonucleoprotein granule;RISC-loading complex
• Molecular function: RNA binding;double-stranded RNA binding;single-stranded RNA binding;endoribonuclease activity;protein binding;miRNA binding;metal ion binding;endoribonuclease activity, cleaving miRNA-paired mRNA