The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • Despite there being a valid 'cspec' property in the messages there's a discrepancy in message contents and CSPEC data: * Message Gene: MTOR CSPEC Genes: [ 'AKT3', 'MTOR', 'PIK3CA', 'PIK3R2' ] * Message MONDOs: MONDO:0100283 CSPEC MONDO: [ 'MONDO:0016054', 'MONDO:0016054', 'MONDO:0016054', 'MONDO:0016054' ]
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_004958.4(MTOR):c.4468T>C (p.Trp1490Arg)

CA338371453

1296993 (ClinVar)

Gene: MTOR (HGNC:2475)
Condition: overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes (MONDO:0100283)
Inheritance Mode: Autosomal dominant inheritance (mosaic)
UUID: c3e4e90a-ba49-4233-8c2e-052b049a976b
Approved on: 2025-07-01
Published on: 2025-07-01

HGVS expressions

NM_004958.4:c.4468T>C
NM_004958.4(MTOR):c.4468T>C (p.Trp1490Arg)
NC_000001.11:g.11157153A>G
CM000663.2:g.11157153A>G
NC_000001.10:g.11217210A>G
CM000663.1:g.11217210A>G
NC_000001.9:g.11139797A>G
NG_033239.1:g.110399T>C
ENST00000703118.1:c.4468T>C
ENST00000703131.1:n.388T>C
ENST00000703140.1:c.4255T>C
ENST00000703141.1:c.4468T>C
ENST00000703142.1:c.*1298T>C
ENST00000361445.9:c.4468T>C
ENST00000361445.8:c.4468T>C
NM_004958.3:c.4468T>C
NM_001386500.1:c.4468T>C
NM_001386501.1:c.3220T>C
More

Likely Pathogenic

Met criteria codes 5
PS4_Moderate PM1_Supporting PP2 PM2_Supporting PS2_Moderate
Not Met criteria codes 21
PS3 PS1 BP5 BP7 BP2 BP3 BP4 BP1 PP4 PP1 PP3 PM6 PM3 PM4 PM5 BA1 BS2 BS4 BS3 BS1 PVS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Brain Malformations Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Brain Malformations VCEP
The NM_004958.4:c.4468T>C variant in MTOR is a missense variant predicted to cause substitution of tryptophan by arginine at amino acid 1490 (p.Trp1490Arg). This variant is absent from gnomAD v4.1.0 (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 BM VCEP (PMIDs: 23322780, 27482884, 21210909) (PM1_Supporting). This variant has been identified as a de novo occurrence with parental relationships confirmed in one individual with macrocephaly ( >=2 SD) and developmental delay or intellectual disability without cortical malformations (PS2_M, PS4_M; PMID: 27830187). In summary, this variant meets the criteria to be classified as likely pathogenic for 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_supporting, PP2, PM1_supporting, PS4_moderate, PS2_moderate; 7 points (VCEP specifications version 1.1).
Met criteria codes
PS4_Moderate
This variant has been identified as a de novo occurrence with parental relationships confirmed in one individual with macrocephaly ( >=2 SD) and developmental delay or intellectual disability without cortical malformations (PS2_M, PS4_M; PMID: 27830187).
PM1_Supporting
This variant resides within the kinase domain of MTOR that is defined as a critical functional domain by the ClinGen BM VCEP (PMIDs: 23322780, 27482884, 21210909) (PM1_Supporting).
PP2
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).
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PS2_Moderate
This variant has been identified as a de novo occurrence with parental relationships confirmed in one individual with macrocephaly ( >=2 SD) and developmental delay or intellectual disability without cortical malformations (PS2_M, PS4_M; PMID: 27830187).
Not Met criteria codes
PS3
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
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
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
PM6
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
BA1
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
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
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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