ClinVar Genomic variation as it relates to human health
NM_004958.4(MTOR):c.5395G>A (p.Glu1799Lys)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_004958.4(MTOR):c.5395G>A (p.Glu1799Lys)
Variation ID: 217823 Accession: VCV000217823.54
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 1p36.22 1: 11130747 (GRCh38) [ NCBI UCSC ] 1: 11190804 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Mar 8, 2017 Oct 20, 2024 Dec 13, 2023 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_004958.4:c.5395G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_004949.1:p.Glu1799Lys missense NC_000001.11:g.11130747C>T NC_000001.10:g.11190804C>T NG_033239.1:g.136805G>A LRG_734:g.136805G>A LRG_734t1:c.5395G>A P42345:p.Glu1799Lys - Protein change
- E1799K
- Other names
- -
- Canonical SPDI
- NC_000001.11:11130746:C:T
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
- -
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
---|---|---|---|---|---|---|
HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
MTOR | - | - |
GRCh38 GRCh37 |
2419 | 2608 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
---|---|---|---|---|
Pathogenic (6) |
criteria provided, multiple submitters, no conflicts
|
Sep 30, 2022 | RCV000201885.13 | |
Pathogenic (4) |
criteria provided, multiple submitters, no conflicts
|
Dec 13, 2023 | RCV000255268.38 | |
Pathogenic (1) |
criteria provided, single submitter
|
Apr 27, 2016 | RCV000624365.5 | |
Pathogenic (1) |
criteria provided, single submitter
|
Jul 10, 2019 | RCV001329983.3 | |
Pathogenic (1) |
criteria provided, single submitter
|
Sep 1, 2020 | RCV001260508.4 | |
Pathogenic (1) |
no assertion criteria provided
|
- | RCV001003568.3 | |
Pathogenic (1) |
no assertion criteria provided
|
- | RCV001256976.4 | |
Pathogenic (1) |
criteria provided, single submitter
|
Aug 2, 2021 | RCV001544505.4 | |
Pathogenic (1) |
criteria provided, single submitter
|
- | RCV003883143.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
---|---|---|---|---|---|
Pathogenic
(Jan 01, 2019)
|
criteria provided, single submitter
Method: clinical testing
|
Macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome
Affected status: yes
Allele origin:
de novo
|
Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV001439961.1
First in ClinVar: Oct 31, 2020 Last updated: Oct 31, 2020 |
Comment:
This variant was identified as de novo.
|
|
Pathogenic
(Sep 01, 2020)
|
criteria provided, single submitter
Method: clinical testing
|
MTOR-related hypomelanosis of Ito with neurodevelopmental abnormalities
Affected status: yes
Allele origin:
somatic
|
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
Accession: SCV001437529.1
First in ClinVar: Oct 10, 2020 Last updated: Oct 10, 2020 |
Observation 1: Observation 2: |
|
Pathogenic
(Jul 10, 2019)
|
criteria provided, single submitter
Method: clinical testing
|
Isolated focal cortical dysplasia type II
Affected status: yes
Allele origin:
unknown
|
Baylor Genetics
Accession: SCV001521562.1
First in ClinVar: Mar 22, 2021 Last updated: Mar 22, 2021 |
Comment:
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
|
|
Pathogenic
(Dec 30, 2020)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center
Accession: SCV002051550.2
First in ClinVar: Jan 08, 2022 Last updated: Feb 11, 2022 |
Comment:
PS4, PS3, PM6
|
|
Pathogenic
(Dec 13, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000965481.6
First in ClinVar: Aug 14, 2019 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 1799 of the MTOR protein … (more)
This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 1799 of the MTOR protein (p.Glu1799Lys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Smith–Kingsmore syndrome or MTOR-related megalencephaly and intellectual disability (PMID: 25851998, 26542245, 27159400, 27513193, 27753196, 28475857). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 217823). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt MTOR protein function with a negative predictive value of 95%. Experimental studies have shown that this missense change affects MTOR function (PMID: 24631838, 25851998). For these reasons, this variant has been classified as Pathogenic. (less)
|
|
Pathogenic
(Nov 01, 2019)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
CeGaT Center for Human Genetics Tuebingen
Accession: SCV001247275.26
First in ClinVar: May 09, 2020 Last updated: Oct 20, 2024 |
Number of individuals with the variant: 1
|
|
Pathogenic
(Aug 02, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Intellectual disability
(Sporadic)
Affected status: yes
Allele origin:
de novo
|
Génétique des Maladies du Développement, Hospices Civils de Lyon
Accession: SCV001762520.1
First in ClinVar: Aug 05, 2021 Last updated: Aug 05, 2021 |
Comment:
de novo variant, absent from gnomAD. Smith-Kingsmore syndrome
|
|
Pathogenic
(Mar 22, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome
Affected status: unknown
Allele origin:
unknown
|
Illumina Laboratory Services, Illumina
Accession: SCV001786563.1
First in ClinVar: Aug 14, 2021 Last updated: Aug 14, 2021 |
Comment:
The MTOR c.5395G>A (p.Glu1799Lys) variant is a missense variant that has been described in a heterozygous state in at least 12 individuals from seven unrelated … (more)
The MTOR c.5395G>A (p.Glu1799Lys) variant is a missense variant that has been described in a heterozygous state in at least 12 individuals from seven unrelated families with features of Smith-Kingsmore syndrome (Baynam et al. 2015; Mroske et al. 2015; Mirzaa et al. 2016; Moosa et al. 2017; Gordo et al. 2018; Dobyns and Mirzaa 2019). An additional feature of multiple intestinal polyps was reported in one individual. In multiple cases, the variant was shown to occur de novo. In at least three families, the variant was found in multiple affected children despite not being detected in the parent's blood, suggesting gonadal mosaicism. The p.Glu1799Lys variant is not reported in the Genome Aggregation Database in a region of good sequence coverage, so the variant is presumed to be rare. Glu1799 is located in the FAT domain, which serves to regulate MTOR activity, and experiments in patient cells, human cell lines, and cultured rodent neurons have confirmed a gain-of-function effect of the p.Glu1799Lys variant (Grabiner et al. 2014; Baynam et al. 2015; Mirzaa et al. 2016). Based on the collective evidence, the p.Glu1799Lys variant is classified as pathogenic for Smith-Kingsmore syndrome. (less)
|
|
Pathogenic
(Jun 21, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome
Affected status: yes
Allele origin:
de novo
|
Centogene AG - the Rare Disease Company
Accession: SCV002059570.1
First in ClinVar: Jan 08, 2022 Last updated: Jan 08, 2022 |
|
|
Pathogenic
(Apr 27, 2016)
|
criteria provided, single submitter
Method: clinical testing
|
Inborn genetic diseases
Affected status: yes
Allele origin:
germline
|
Ambry Genetics
Accession: SCV000741517.3
First in ClinVar: Apr 15, 2018 Last updated: Jan 07, 2023 |
Observation 1:
Number of individuals with the variant: 1
Sex: male
Ethnicity/Population group: Unknown
Observation 2:
Number of individuals with the variant: 1
Clinical Features:
Global developmental delay (present) , Intellectual disability (present) , Hypoplasia of the corpus callosum (present) , Macrocephalus (present) , Autistic disorder of childhood onset (present) … (more)
Global developmental delay (present) , Intellectual disability (present) , Hypoplasia of the corpus callosum (present) , Macrocephalus (present) , Autistic disorder of childhood onset (present) , Overgrowth (present) , Vomiting (present) , Sleep disturbance (present) , Bruising susceptibility (present) , Depressed nasal bridge (present) , Prominent forehead (present) , Open mouth (present) , Attention deficit hyperactivity disorder (present) , Gastroesophageal reflux (present) , Episodic vomiting (present) , Multiple cafe-au-lait spots (present) , Absent speech (present) , Facial hypotonia (present) , Hyperhidrosis (present) , Polydipsia (present) (less)
Sex: male
Ethnicity/Population group: African American/Caucasian/German
Observation 3:
Number of individuals with the variant: 1
Sex: female
Ethnicity/Population group: African American/Caucasian
|
|
Pathogenic
(Dec 30, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV000321909.10
First in ClinVar: Oct 09, 2016 Last updated: Mar 04, 2023 |
Comment:
Functional studies indicate that E1799K results in an increase in mTOR pathway activity, suggesting a gain-of-function mechanism of disease (Baynam, et al., 2015); In silico … (more)
Functional studies indicate that E1799K results in an increase in mTOR pathway activity, suggesting a gain-of-function mechanism of disease (Baynam, et al., 2015); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 27739187, 27159400, 25851998, 26542245, 27513193, 27753196, 28892148, 28475857, 32581362, 33077954, 23636326, 24631838, 31441589, 31064327, 30764584, 30050716, 29296277, 27860216, 28007777, 24625776, 26432419) (less)
|
|
Pathogenic
(Sep 30, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome
Affected status: yes
Allele origin:
germline
|
Eurofins-Biomnis
Accession: SCV003935104.1
First in ClinVar: Jun 24, 2023 Last updated: Jun 24, 2023 |
|
|
pathogenic
(-)
|
criteria provided, single submitter
Method: clinical testing
|
Macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome
Isolated focal cortical dysplasia type II
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases.
Affected status: yes
Allele origin:
de novo
|
Molecular Genetics Lab, CHRU Brest
Accession: SCV004697599.1
First in ClinVar: Mar 05, 2024 Last updated: Mar 05, 2024 |
|
|
Pathogenic
(Jul 01, 2015)
|
no assertion criteria provided
Method: literature only
|
SMITH-KINGSMORE SYNDROME
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000256631.3
First in ClinVar: Nov 15, 2015 Last updated: Apr 21, 2018 |
Comment on evidence:
In 3 Aboriginal Australian sibs, aged 2, 3, and 7 years, with intellectual disability, macrocephaly, seizures, facial dysmorphism, and small thoraces (SKS; 616638), Baynam et … (more)
In 3 Aboriginal Australian sibs, aged 2, 3, and 7 years, with intellectual disability, macrocephaly, seizures, facial dysmorphism, and small thoraces (SKS; 616638), Baynam et al. (2015) identified a de novo c.5395G-A transition in exon 39 of the MTOR gene, resulting in a glu1799-to-lys (E1799K) substitution at a conserved residue. Peripheral blood cells derived from 1 of the patients showed increased mTOR activity when stimulated, and the increased response was inhibited by coincubation with rapamycin. The findings were consistent with a gain-of-function effect at the cellular level. Because the 3 sibs had different fathers and the mutation was not detected in the mother's peripheral blood, Baynam et al. (2015) suggested that the mother was gonadal mosaic for the mutation. Mroske et al. (2015) identified a de novo heterozygous E1799K mutation in 2 brothers with SKS. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not found in the peripheral blood of either parent, suggesting it orginated as a consequence of gonadal mosaicism. The mutation was not present in the dbSNP, 1000 Genomes Project, or ExAC databases. Based on molecular modeling, Mroske et al. (2015) noted that the E1799K mutation occurs in the FAT domain, which clamps onto the kinase domain and negatively regulates MTOR activity. Disruption of this residue may detabilize the protein and shift it to a more active state. Mirzaa et al. (2016) reported 4 children, including identical twins, with a mosaic MTOR mutation E1799K present at an alternative allele ratio of about 50% in saliva or white blood cells; no neurologic tissue was available for quantitation. All 4 children had symmetric megalencephaly and intellectual disability, but limited or no polymicrogyria. The twins had autism. In 2 sibs, born of unrelated German parents, with SKS, Moosa et al. (2017) identified a de novo heterozygous E1799K mutation in the MTOR gene. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not detected in the parents' peripheral blood. Additional sequencing indicated that the mutation was located on the paternal chromosome, which Moosa et al. (2017) suggested was consistent with paternal gonadal mosaicism. Functional studies of the variant and studies of patient cells were not performed. (less)
|
|
Pathogenic
(-)
|
no assertion criteria provided
Method: research
|
Intellectual disability, severe
Affected status: yes
Allele origin:
unknown
|
NIHR Bioresource Rare Diseases, University of Cambridge
Accession: SCV001161929.1
First in ClinVar: Feb 27, 2020 Last updated: Feb 27, 2020 |
Number of individuals with the variant: 1
Sex: male
|
|
Pathogenic
(Oct 19, 2020)
|
no assertion criteria provided
Method: literature only
|
Macrocephaly-intellectual disability-neurodevelopmental disorder-small thorax syndrome
Affected status: yes
Allele origin:
de novo
|
Yale Center for Mendelian Genomics, Yale University
Study: Yale Center for Mendelian Genomics
Accession: SCV002106928.1 First in ClinVar: Mar 23, 2022 Last updated: Mar 23, 2022 |
|
|
Pathogenic
(-)
|
no assertion criteria provided
Method: clinical testing
|
Rare genetic intellectual disability
Affected status: yes
Allele origin:
de novo
|
Service de Génétique Moléculaire, Hôpital Robert Debré
Accession: SCV001433522.1
First in ClinVar: Sep 27, 2020 Last updated: Sep 27, 2020 |
|
|
click to load more click to collapse |
Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
---|---|---|---|---|
Exome sequencing implicates genetic disruption of prenatal neuro-gliogenesis in sporadic congenital hydrocephalus. | Jin SC | Nature medicine | 2020 | PMID: 33077954 |
Whole-genome sequencing of patients with rare diseases in a national health system. | Turro E | Nature | 2020 | PMID: 32581362 |
Megalencephaly syndromes associated with mutations of core components of the PI3K-AKT-MTOR pathway: PIK3CA, PIK3R2, AKT3, and MTOR. | Dobyns WB | American journal of medical genetics. Part C, Seminars in medical genetics | 2019 | PMID: 31441589 |
mTOR mutations in Smith-Kingsmore syndrome: Four additional patients and a review. | Gordo G | Clinical genetics | 2018 | PMID: 28892148 |
Mutations in Epigenetic Regulation Genes Are a Major Cause of Overgrowth with Intellectual Disability. | Tatton-Brown K | American journal of human genetics | 2017 | PMID: 28475857 |
Smith-Kingsmore syndrome: A third family with the MTOR mutation c.5395G>A p.(Glu1799Lys) and evidence for paternal gonadal mosaicism. | Moosa S | American journal of medical genetics. Part A | 2017 | PMID: 27753196 |
Candidate-gene criteria for clinical reporting: diagnostic exome sequencing identifies altered candidate genes among 8% of patients with undiagnosed diseases. | Farwell Hagman KD | Genetics in medicine : official journal of the American College of Medical Genetics | 2017 | PMID: 27513193 |
Association of MTOR Mutations With Developmental Brain Disorders, Including Megalencephaly, Focal Cortical Dysplasia, and Pigmentary Mosaicism. | Mirzaa GM | JAMA neurology | 2016 | PMID: 27159400 |
Germline activating MTOR mutation arising through gonadal mosaicism in two brothers with megalencephaly and neurodevelopmental abnormalities. | Mroske C | BMC medical genetics | 2015 | PMID: 26542245 |
A germline MTOR mutation in Aboriginal Australian siblings with intellectual disability, dysmorphism, macrocephaly, and small thoraces. | Baynam G | American journal of medical genetics. Part A | 2015 | PMID: 25851998 |
A diverse array of cancer-associated MTOR mutations are hyperactivating and can predict rapamycin sensitivity. | Grabiner BC | Cancer discovery | 2014 | PMID: 24631838 |
mTOR kinase structure, mechanism and regulation. | Yang H | Nature | 2013 | PMID: 23636326 |
click to load more click to collapse |
Text-mined citations for rs863225264 ...
HelpRecord last updated Oct 20, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.