MTOR

mechanistic target of rapamycin kinase, the group of MTOR complex 2|Armadillo like helical domain containing|MTOR complex 1

Basic information

Region (hg38): 1:11106535-11262556

Previous symbols: [ "FRAP", "FRAP2", "FRAP1" ]

Links

ENSG00000198793NCBI:2475OMIM:601231HGNC:3942Uniprot:P42345AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome (Definitive), mode of inheritance: AD
  • macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome (Strong), mode of inheritance: AD
  • macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome (Supportive), mode of inheritance: AD
  • macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome (Definitive), mode of inheritance: AD
  • overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Smith-Kingsmore syndromeADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Musculoskeletal; Neurologic25851998; 26542245; 27753196; 27830187

ClinVar

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

  • not provided (10 variants)
  • Macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome (9 variants)
  • Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes (8 variants)
  • CEBALID syndrome (7 variants)
  • Isolated focal cortical dysplasia type II (7 variants)
  • Papillary renal cell carcinoma type 1 (6 variants)
  • Glioblastoma (5 variants)
  • Breast neoplasm (3 variants)
  • Malignant neoplasm of body of uterus (2 variants)
  • Neoplasm of uterine cervix (2 variants)
  • Inborn genetic diseases (2 variants)
  • Neoplasm of the large intestine (2 variants)
  • Renal carcinoma (2 variants)
  • Papillary renal cell carcinoma, sporadic (2 variants)
  • Malignant melanoma of skin (2 variants)
  • Transitional cell carcinoma of the bladder (1 variants)
  • Hemimegalencephaly (1 variants)
  • Intellectual disability (1 variants)
  • Macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome;Isolated focal cortical dysplasia type II (1 variants)
  • MTOR-related megalencephaly and pigmentary mosaicism in skin (1 variants)
  • Rare genetic intellectual disability (1 variants)
  • Intellectual disability, severe (1 variants)
  • Macrocephaly (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTOR 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
16
clinvar
573
clinvar
39
clinvar
628
missense
20
clinvar
13
clinvar
656
clinvar
120
clinvar
120
clinvar
929
nonsense
1
clinvar
20
clinvar
6
clinvar
27
start loss
0
frameshift
26
clinvar
2
clinvar
28
inframe indel
15
clinvar
5
clinvar
1
clinvar
21
splice donor/acceptor (+/-2bp)
8
clinvar
8
splice region
43
115
21
179
non coding
26
clinvar
374
clinvar
183
clinvar
583
Total 20 14 767 1080 343

Highest pathogenic variant AF is 0.00000657

Variants in MTOR

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

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

Position Type Phenotype Significance ClinVar
1-11106656-T-C Benign (Aug 23, 2019)1237596
1-11107422-G-A Likely benign (Nov 27, 2018)1189891
1-11107484-G-C Benign (Nov 09, 2020)1274284
1-11107498-C-A Uncertain significance (Feb 09, 2022)2095355
1-11107503-A-G Benign (Jun 14, 2021)640092
1-11107512-G-C Likely benign (Jan 14, 2022)1907789
1-11107518-A-C Likely benign (Jul 18, 2023)1603095
1-11107541-G-C Benign (Mar 10, 2021)1277670
1-11107703-C-T Benign (Jul 27, 2018)1267226
1-11107772-C-T Benign (Jul 26, 2018)1225480
1-11107853-C-T Benign (Jul 26, 2018)1283465
1-11107991-T-A Benign (Jul 03, 2018)1276271
1-11108041-A-G Likely benign (Oct 05, 2018)1218120
1-11108166-G-A Likely benign (Aug 16, 2022)1610693
1-11108170-G-A Likely benign (Mar 03, 2023)2098491
1-11108175-A-G Uncertain significance (Jun 05, 2023)862815
1-11108177-T-C Benign (Dec 09, 2023)2179712
1-11108186-A-G Likely benign (Jul 15, 2023)1976892
1-11108187-A-G Uncertain significance (Jul 26, 2019)1307206
1-11108201-G-A Likely benign (Sep 06, 2023)1554544
1-11108202-A-G Uncertain significance (May 27, 2023)2742768
1-11108216-T-G Likely benign (Nov 26, 2022)2868649
1-11108219-C-T Likely benign (Nov 27, 2023)1140243
1-11108220-G-C Uncertain significance (Feb 22, 2021)1374970
1-11108222-T-C MTOR-related disorder Benign (Jan 30, 2024)696762

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MTORprotein_codingprotein_codingENST00000361445 57155973
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.002.31e-111257170311257480.000123
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense7.027311.49e+30.4890.000088016753
Missense in Polyphen173563.680.306916334
Synonymous0.7575485710.9600.00003304987
Loss of Function9.95191510.1260.000009131535

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001190.000119
Ashkenazi Jewish0.00009920.0000992
East Asian0.0001630.000163
Finnish0.00004630.0000462
European (Non-Finnish)0.0001500.000149
Middle Eastern0.0001630.000163
South Asian0.0001960.000196
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Serine/threonine protein kinase which is a central regulator of cellular metabolism, growth and survival in response to hormones, growth factors, nutrients, energy and stress signals. MTOR directly or indirectly regulates the phosphorylation of at least 800 proteins. Functions as part of 2 structurally and functionally distinct signaling complexes mTORC1 and mTORC2 (mTOR complex 1 and 2). Activated mTORC1 up-regulates protein synthesis by phosphorylating key regulators of mRNA translation and ribosome synthesis. This includes phosphorylation of EIF4EBP1 and release of its inhibition toward the elongation initiation factor 4E (eiF4E). Moreover, phosphorylates and activates RPS6KB1 and RPS6KB2 that promote protein synthesis by modulating the activity of their downstream targets including ribosomal protein S6, eukaryotic translation initiation factor EIF4B, and the inhibitor of translation initiation PDCD4. Stimulates the pyrimidine biosynthesis pathway, both by acute regulation through RPS6KB1- mediated phosphorylation of the biosynthetic enzyme CAD, and delayed regulation, through transcriptional enhancement of the pentose phosphate pathway which produces 5-phosphoribosyl-1- pyrophosphate (PRPP), an allosteric activator of CAD at a later step in synthesis, this function is dependent on the mTORC1 complex. Regulates ribosome synthesis by activating RNA polymerase III-dependent transcription through phosphorylation and inhibition of MAF1 an RNA polymerase III-repressor. In parallel to protein synthesis, also regulates lipid synthesis through SREBF1/SREBP1 and LPIN1. To maintain energy homeostasis mTORC1 may also regulate mitochondrial biogenesis through regulation of PPARGC1A. mTORC1 also negatively regulates autophagy through phosphorylation of ULK1. Under nutrient sufficiency, phosphorylates ULK1 at 'Ser- 758', disrupting the interaction with AMPK and preventing activation of ULK1. Also prevents autophagy through phosphorylation of the autophagy inhibitor DAP. mTORC1 exerts a feedback control on upstream growth factor signaling that includes phosphorylation and activation of GRB10 a INSR-dependent signaling suppressor. Among other potential targets mTORC1 may phosphorylate CLIP1 and regulate microtubules. As part of the mTORC2 complex MTOR may regulate other cellular processes including survival and organization of the cytoskeleton. Plays a critical role in the phosphorylation at 'Ser-473' of AKT1, a pro-survival effector of phosphoinositide 3-kinase, facilitating its activation by PDK1. mTORC2 may regulate the actin cytoskeleton, through phosphorylation of PRKCA, PXN and activation of the Rho-type guanine nucleotide exchange factors RHOA and RAC1A or RAC1B. mTORC2 also regulates the phosphorylation of SGK1 at 'Ser-422' (PubMed:12087098, PubMed:12150925, PubMed:12150926, PubMed:12231510, PubMed:12718876, PubMed:14651849, PubMed:15268862, PubMed:15467718, PubMed:15545625, PubMed:15718470, PubMed:18497260, PubMed:18762023, PubMed:18925875, PubMed:20516213, PubMed:20537536, PubMed:21659604, PubMed:23429703, PubMed:23429704, PubMed:25799227, PubMed:26018084). Regulates osteoclastogenesis by adjusting the expression of CEBPB isoforms (By similarity). {ECO:0000250|UniProtKB:Q9JLN9, ECO:0000269|PubMed:12087098, ECO:0000269|PubMed:12150925, ECO:0000269|PubMed:12150926, ECO:0000269|PubMed:12231510, ECO:0000269|PubMed:12718876, ECO:0000269|PubMed:14651849, ECO:0000269|PubMed:15268862, ECO:0000269|PubMed:15467718, ECO:0000269|PubMed:15545625, ECO:0000269|PubMed:15718470, ECO:0000269|PubMed:18497260, ECO:0000269|PubMed:18762023, ECO:0000269|PubMed:18925875, ECO:0000269|PubMed:20516213, ECO:0000269|PubMed:20537536, ECO:0000269|PubMed:21659604, ECO:0000269|PubMed:23429703, ECO:0000269|PubMed:23429704, ECO:0000269|PubMed:25799227, ECO:0000269|PubMed:26018084}.;
Disease
DISEASE: Smith-Kingsmore syndrome (SKS) [MIM:616638]: An autosomal dominant syndrome characterized by intellectual disability, macrocephaly, seizures, umbilical hernia, and facial dysmorphic features. {ECO:0000269|PubMed:25851998, ECO:0000269|PubMed:26542245, ECO:0000269|PubMed:27830187}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Focal cortical dysplasia 2 (FCORD2) [MIM:607341]: A form of focal cortical dysplasia, a malformation of cortical development that results in medically refractory epilepsy in the pediatric population and in adults. FCORD2 is a severe form, with onset usually in childhood, characterized by disrupted cortical lamination and specific cytological abnormalities. It is classified in 2 subtypes: type IIA characterized by dysmorphic neurons and lack of balloon cells; type IIB with dysmorphic neurons and balloon cells. {ECO:0000269|PubMed:25799227, ECO:0000269|PubMed:25878179, ECO:0000269|PubMed:26018084, ECO:0000269|PubMed:27830187}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
PI3K-Akt signaling pathway - Homo sapiens (human);Gastric cancer - Homo sapiens (human);mTOR signaling pathway - Homo sapiens (human);Adipocytokine signaling pathway - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Central carbon metabolism in cancer - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Type II diabetes mellitus - Homo sapiens (human);Insulin resistance - Homo sapiens (human);HIF-1 signaling pathway - Homo sapiens (human);Jak-STAT signaling pathway - Homo sapiens (human);Longevity regulating pathway - multiple species - Homo sapiens (human);Acute myeloid leukemia - Homo sapiens (human);Breast cancer - Homo sapiens (human);ErbB signaling pathway - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Autophagy - other - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Glioma - Homo sapiens (human);Thyroid hormone signaling pathway - Homo sapiens (human);Prostate cancer - Homo sapiens (human);Longevity regulating pathway - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Pancreatic cancer - Homo sapiens (human);Colorectal cancer - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Leucine Stimulation on Insulin Signaling;Glutaminolysis and Cancer;AMP-activated Protein Kinase (AMPK) Signaling;Target Of Rapamycin (TOR) Signaling;MicroRNAs in cardiomyocyte hypertrophy;Type II diabetes mellitus;Sterol Regulatory Element-Binding Proteins (SREBP) signalling;Integrated Breast Cancer Pathway;Angiogenesis overview;SREBF and miR33 in cholesterol and lipid homeostasis;RANKL-RANK (Receptor activator of NFKB (ligand)) Signaling Pathway;Leptin signaling pathway;Human Thyroid Stimulating Hormone (TSH) signaling pathway;Follicle Stimulating Hormone (FSH) signaling pathway;Prolactin Signaling Pathway;Thymic Stromal LymphoPoietin (TSLP) Signaling Pathway;Oncostatin M Signaling Pathway;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Alpha 6 Beta 4 signaling pathway;Integrated Lung Cancer Pathway;Polycystic Kidney Disease Pathway;JAK-STAT;Cardiac Hypertrophic Response;Extracellular vesicle-mediated signaling in recipient cells;MECP2 and Associated Rett Syndrome;Wnt Signaling Pathway;BDNF-TrkB Signaling;PI3K-AKT-mTOR signaling pathway and therapeutic opportunities;Factors and pathways affecting insulin-like growth factor (IGF1)-Akt signaling;ATM Signaling Network in Development and Disease;4-hydroxytamoxifen, Dexamethasone, and Retinoic Acids Regulation of p27 Expression;VEGFA-VEGFR2 Signaling Pathway;Angiopoietin Like Protein 8 Regulatory Pathway;ESC Pluripotency Pathways;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;miRNA regulation of prostate cancer signaling pathways;Steatosis AOP;Pathways in clear cell renal cell carcinoma;PI3K-AKT-mTOR - VitD3 Signalling;PI3K-Akt Signaling Pathway;Somatroph axis (GH) and its relationship to dietary restriction and aging;Caloric restriction and aging;EGF-EGFR Signaling Pathway;Insulin Signaling;Interferon type I signaling pathways;Senescence and Autophagy in Cancer;ErbB Signaling Pathway;Disease;Signal Transduction;Gene expression (Transcription);HSF1-dependent transactivation;mtor signaling pathway;regulation of eif-4e and p70s6 kinase;stat3 signaling pathway;b cell survival pathway;VEGFA-VEGFR2 Pathway;skeletal muscle hypertrophy is regulated via akt-mtor pathway;ctcf: first multivalent nuclear factor;Generic Transcription Pathway;Alpha6Beta4Integrin;CD28 dependent PI3K/Akt signaling;Cellular responses to stress;CD28 co-stimulation;Costimulation by the CD28 family;RNA Polymerase II Transcription;mTORC1-mediated signalling;Energy dependent regulation of mTOR by LKB1-AMPK;mTOR signalling;Oncostatin_M;Immune System;Adaptive Immune System;KitReceptor;insulin Mam;TP53 Regulates Metabolic Genes;Macroautophagy;Cellular responses to external stimuli;IL-7 signaling;EGFR1;CXCR4-mediated signaling events;ErbB1 downstream signaling;Regulation of PTEN gene transcription;Regulation of TP53 Degradation;Regulation of TP53 Expression and Degradation;PTEN Regulation;PIP3 activates AKT signaling;JAK STAT pathway and regulation;IL2;Cellular response to heat stress;EPO signaling;Regulation of TP53 Activity;Transcriptional Regulation by TP53;IFN-gamma pathway;Signaling by VEGF;EGFR-dependent Endothelin signaling events;Constitutive Signaling by AKT1 E17K in Cancer;PI3K/AKT Signaling in Cancer;Signaling by Receptor Tyrosine Kinases;VEGF;ErbB2/ErbB3 signaling events;Intracellular signaling by second messengers;mTOR signaling pathway;Diseases of signal transduction;CDC42 signaling events;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);Regulation of Telomerase;IL2 signaling events mediated by PI3K;CXCR3-mediated signaling events;Class I PI3K signaling events mediated by Akt;IL4-mediated signaling events;IL12-mediated signaling events;LKB1 signaling events;VEGFR2 mediated vascular permeability;insulin (Consensus)

Recessive Scores

pRec
0.171

Intolerance Scores

loftool
0.246
rvis_EVS
-3.49
rvis_percentile_EVS
0.34

Haploinsufficiency Scores

pHI
0.975
hipred
Y
hipred_score
0.800
ghis
0.619

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.802

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Mtor
Phenotype
respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; renal/urinary system phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; muscle phenotype;

Zebrafish Information Network

Gene name
mtor
Affected structure
cardiac muscle cell
Phenotype tag
abnormal
Phenotype quality
decreased size

Gene ontology

Biological process
regulation of cell growth;negative regulation of protein phosphorylation;positive regulation of protein phosphorylation;positive regulation of endothelial cell proliferation;T-helper 1 cell lineage commitment;heart morphogenesis;heart valve morphogenesis;regulation of glycogen biosynthetic process;energy reserve metabolic process;'de novo' pyrimidine nucleobase biosynthetic process;protein phosphorylation;cell cycle arrest;germ cell development;brain development;cell aging;response to nutrient;long-term memory;regulation of cell size;visual learning;cellular response to starvation;post-embryonic development;negative regulation of autophagy;positive regulation of lamellipodium assembly;positive regulation of gene expression;positive regulation of epithelial to mesenchymal transition;positive regulation of myotube differentiation;positive regulation of neuron maturation;negative regulation of muscle atrophy;response to activity;regulation of macroautophagy;negative regulation of macroautophagy;phosphorylation;peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;spinal cord development;protein catabolic process;positive regulation of actin filament polymerization;negative regulation of protein ubiquitination;ruffle organization;regulation of myelination;cellular response to nutrient levels;TOR signaling;regulation of fatty acid beta-oxidation;regulation of response to food;activation of protein kinase B activity;positive regulation of phosphoprotein phosphatase activity;response to insulin;regulation of actin cytoskeleton organization;cellular response to amino acid starvation;social behavior;multicellular organism growth;TORC1 signaling;wound healing;response to cocaine;regulation of GTPase activity;response to amino acid;anoikis;response to morphine;regulation of carbohydrate utilization;positive regulation of nitric oxide biosynthetic process;regulation of osteoclast differentiation;positive regulation of translation;negative regulation of cell size;positive regulation of transcription by RNA polymerase III;protein autophosphorylation;positive regulation of lipid biosynthetic process;mRNA stabilization;positive regulation of smooth muscle cell proliferation;positive regulation of oligodendrocyte differentiation;positive regulation of peptidyl-tyrosine phosphorylation;voluntary musculoskeletal movement;positive regulation of stress fiber assembly;positive regulation of keratinocyte migration;positive regulation of protein kinase B signaling;cardiac muscle cell development;cardiac muscle contraction;maternal process involved in female pregnancy;positive regulation of glial cell proliferation;positive regulation of dendritic spine development;positive regulation of cell growth involved in cardiac muscle cell development;negative regulation of calcineurin-NFAT signaling cascade;cellular response to amino acid stimulus;cellular response to leucine;cellular response to hypoxia;regulation of brown fat cell differentiation;regulation of membrane permeability;regulation of translation at synapse, modulating synaptic transmission;regulation of cellular response to heat;positive regulation of neuron death;positive regulation of transcription of nucleolar large rRNA by RNA polymerase I;positive regulation of wound healing, spreading of epidermal cells;positive regulation of eating behavior;positive regulation of cholangiocyte proliferation;positive regulation of sensory perception of pain;negative regulation of cholangiocyte apoptotic process;positive regulation of granulosa cell proliferation;positive regulation of skeletal muscle hypertrophy;negative regulation of iodide transmembrane transport;positive regulation of cytoplasmic translational initiation;cellular response to leucine starvation
Cellular component
Golgi membrane;nucleus;nucleoplasm;cytoplasm;mitochondrial outer membrane;lysosome;lysosomal membrane;endoplasmic reticulum membrane;cytosol;endomembrane system;membrane;PML body;dendrite;TORC1 complex;TORC2 complex;neuronal cell body;glutamatergic synapse;postsynaptic cytosol
Molecular function
RNA polymerase III type 1 promoter DNA binding;RNA polymerase III type 2 promoter DNA binding;RNA polymerase III type 3 promoter DNA binding;TFIIIC-class transcription factor complex binding;protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding;kinase activity;protein kinase binding;protein domain specific binding;identical protein binding;ribosome binding;translation regulator activity;phosphoprotein binding