ClinVar Miner

Submissions for variant NM_004958.4(MTOR):c.4447T>C (p.Cys1483Arg)

dbSNP: rs1057519914
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Brain Malformations Variant Curation Expert Panel RCV001836813 SCV001949983 pathogenic Overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes 2022-02-11 reviewed by expert panel curation 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)
Heinzen Lab, Columbia University RCV000494705 SCV000485071 pathogenic Hemimegalencephaly no assertion criteria provided research
Database of Curated Mutations (DoCM) RCV000442035 SCV000506728 likely pathogenic Glioblastoma 2016-05-31 no assertion criteria provided literature only
Database of Curated Mutations (DoCM) RCV000426008 SCV000506729 likely pathogenic Breast neoplasm 2016-05-31 no assertion criteria provided literature only
Database of Curated Mutations (DoCM) RCV000431432 SCV000506730 likely pathogenic Papillary renal cell carcinoma type 1 2016-05-31 no assertion criteria provided literature only

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