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  • See Evidence submitted by expert panel for details.

Variant: NM_004958.3(MTOR):c.4447T>C (p.Cys1483Arg)

CA16602264

374796 (ClinVar)

Gene: MTOR
Condition: overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
Inheritance Mode: Autosomal dominant inheritance (mosaic)
UUID: 6ed31c33-11e4-468c-82e0-419ec860d576
Approved on: 2022-02-11
Published on: 2022-02-11

HGVS expressions

NM_004958.3:c.4447T>C
NM_004958.3(MTOR):c.4447T>C (p.Cys1483Arg)
NC_000001.11:g.11157174A>G
CM000663.2:g.11157174A>G
NC_000001.10:g.11217231A>G
CM000663.1:g.11217231A>G
NC_000001.9:g.11139818A>G
NG_033239.1:g.110378T>C
ENST00000361445.9:c.4447T>C
ENST00000361445.8:c.4447T>C
NM_004958.4:c.4447T>C
NM_001386500.1:c.4447T>C
NM_001386501.1:c.3199T>C
NM_004958.4(MTOR):c.4447T>C (p.Cys1483Arg)
More

Pathogenic

Met criteria codes 6
PM2_Supporting PM1_Supporting PS3_Supporting PS4 PS2_Moderate PP2
Not Met criteria codes 20
BA1 PM3 PM4 PM5 PM6 BS4 BS3 BS1 BS2 PVS1 BP5 BP7 BP2 BP3 BP4 BP1 PS1 PP4 PP1 PP3

Evidence Links 4

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Brain Malformations VCEP
The c.4447T>C (NM_004958.4) variant in MTOR is a missense variant predicted to cause substitution of (p.Cys1483Arg). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). MTOR, in which the variant was identified, is defined by the ClinGen Brain Malformations Expert Panel as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). This variant resides within the kinase domain of MTOR that is defined as a critical functional domain by the ClinGen BMEP (PMIDs: 23322780, 27482884, 21210909) (PM1_Supporting). This variant has been shown to significantly increase phosphorylation levels in experiments with case and control cells of similar isogenic backgrounds indicating that this variant impacts protein function (PMIDs: 25799227, 24631838) (PS3_Supporting). The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls (PS4; PMIDs: 28864461, 25799227; identified in 2 individuals with neuropathology confirmatory of a malformation of cortical development, 1 individual with neuroimaging demonstrating at least one large cerebral hemisphere with cortical malformation(s), 3 tumor samples in the literature and COSMIC ). Testing of unaffected and affected tissue show variable allelic fractions consistent with a post-zygotic event (PS2_Moderate; PMID: 25799227). In summary, this variant meets the criteria to be classified as Pathogenic for mosaic autosomal dominant overgrowth with or without cerebral malformations due to abnormalities in MTOR-pathway genes based on the ACMG/AMP criteria applied, as specified by the ClinGen Brain Malformations Expert Panel: PM2_P, PP2, PM1_P, PS3_P, PS4, PS2_M; 10 points (VCEP specifications version 1; Approved: 1/31/2021)
Met criteria codes
PM2_Supporting
absent from gnomAD
PM1_Supporting
located in the kinase domain
PS3_Supporting
PS4
3 tumor samples in COSMIC

PS2_Moderate
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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