The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_004958.4(MTOR):c.7280T>C (p.Leu2427Pro)

CA338380762

417723 (ClinVar)

Gene: MTOR
Condition: overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes
Inheritance Mode: Autosomal dominant inheritance (mosaic)
UUID: d9f52cde-a2d2-4580-9f3d-af90946ce1f9

HGVS expressions

NM_004958.4:c.7280T>C
NM_004958.4(MTOR):c.7280T>C (p.Leu2427Pro)
NC_000001.11:g.11114338A>G
CM000663.2:g.11114338A>G
NC_000001.10:g.11174395A>G
CM000663.1:g.11174395A>G
NC_000001.9:g.11096982A>G
NG_033239.1:g.153214T>C
ENST00000361445.9:c.7280T>C
ENST00000361445.8:c.7280T>C
ENST00000376838.5:c.1895T>C
ENST00000455339.1:c.248T>C
ENST00000473471.5:n.292T>C
ENST00000490931.1:n.323T>C
NM_004958.3:c.7280T>C
NM_001386500.1:c.7280T>C
NM_001386501.1:c.6032T>C

Pathogenic

Met criteria codes 5
PS2_Moderate PS3 PS4_Moderate PM2_Supporting PP2
Not Met criteria codes 11
BS3 PS1 PP1 PP3 PP4 PM1 PM3 PM4 PM5 PM6 PVS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Brain Malformations VCEP
The c.7280T>C (NM_004958.4) variant in MTOR is a missense variant predicted to cause substitution of (p.Leu2427Pro). The prevalence of the variant in affected individuals is significantly increased compared with the prevalence in controls (PS4_M; PMIDs: 25799227, 25159823; identified in 2 individuals with neuropathology confirmatory of a malformation of cortical development, 1 tumor sample in the literature and COSMIC). An animal model generated with this variant shows a seizure phenotype which responded to treatment with rapamycin indicating that this variant impacts protein function (PMID: 29937275) (PS3_Strong). Testing of unaffected and affected tissue show variable allelic fractions consistent with a post-zygotic event (PS2_Moderate; PMID: 25799227). 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). 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: PS4_M, PS3, PS2_M, PM2_P, PP2; 10 points (VCEP specifications version 1; Approved: 1/31/2021)
Met criteria codes
PS2_Moderate
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
Mouse model electroporated with this variant developed seizures, which stopped upon treatment with rapamycin
PS4_Moderate
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2_Supporting
The variant is absent from gnomAD with adequate coverage.
PP2
The Z score for MTOR is 7.02
Not Met criteria codes
BS3
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
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
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
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
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
Approved on: 2022-02-12
Published on: 2022-02-12
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