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MTOR
Final classification
VUS
MTOR c.3610A>G · p.Ile1204Val
MTOR

NM_004958.4:c.3610A>G (p.Ile1204Val) is a missense variant in the MTOR gene, which is associated with cerebral malformation via a gain-of-function mechanism (Brain Malformations CSPEC v1.1).

Gene
MTOR
Transcript
NM_004958.4
HGVS · transcript:coding
NM_004958.4:c.3610A>G
Consequence
N/A
GRCh38
chr1:11210858 T>C
GRCh37
chr1:11270915 T>C
Basis ClinGen Brain Malformations Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1.1 v1.1 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
ClinGen Brain Malformations Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1.1 v1.1 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
MTOR c.3610A>G

NM_004958.4:c.3610A>G (p.Ile1204Val) is a missense variant in the MTOR gene, which is associated with cerebral malformation via a gain-of-function mechanism (Brain Malformations CSPEC v1.1).1 This variant is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2 at supporting strength under the Brain Malformations CSPEC.2 No pathogenic or benign classifications exist in ClinVar; the variant has not been reported in any clinical or research database.3 No functional studies, case reports, de novo observations, or segregation data are available for this variant. OncoKB classifies the variant as Unknown Oncogenic Effect.4 The CSPEC framework marks 13 criteria as not applicable for MTOR variant assessment: PVS1 (GOF mechanism), PM6 (addressed under PS2), PP1 (mosaic/de novo), PP3 (LOF-focused algorithms), PP4 (accounted under PS4), PP5 (SVI recommendation), BS4 (de novo/mosaic), BP1 (LOF not mechanism), BP4 and BP7 (not applicable to missense), BP6 (SVI recommendation).5 With only one supporting-level pathogenic criterion (PM2_supporting) met and no benign criteria met, this variant is classified as a Variant of Uncertain Significance (VUS) under ACMG/AMP 2015 combination rules.6

PM2 VUS
Gene diagram · NM_004958.4 · variants mapped to exon structure
MTOR NM_004958.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 13 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_004958.4:c.3610A>G is absent from all population databases (gnomAD v2.1, gnomAD v4.1, gnomAD-Canada v1.0). Under the Brain Malformations CSPEC v1.1, PM2 is applied at supporting strength for variants absent/rare from controls in an ethnically-matched cohort population sample.
Absent from gnomAD v2.1 (exomes).Absent from gnomAD v4.1 (exomes).Absent from gnomAD-Canada v1.0 (genomes).
Assessed · not applied
Pathogenic
PS1 No different nucleotide change at codon 1204 that produces the same p.Ile1204Val amino acid change has been established as pathogenic.
PS2 No de novo observation has been reported for NM_004958.4:c.3610A>G.
PS3 No well-established in vitro or in vivo functional studies have been identified for p.Ile1204Val.
PS4 No affected individuals harboring NM_004958.4:c.3610A>G have been reported in the literature or clinical databases (ClinVar, COSMIC).
PM1 The CSPEC restricts PM1 to supporting-strength for residues affecting critical functional domains as specified in Table 4.
PM5 No pathogenic missense variant at amino acid residue 1204 of MTOR has been identified in ClinVar or the literature.
PP2 The CSPEC awards PP2 at supporting strength when the gnomAD missense constraint z-score exceeds 3.09 for MTOR.
Benign
BA1 Under the Brain Malformations CSPEC v1.1, BA1 requires an allele frequency greater than 0.0926%.
BS1 Under the Brain Malformations CSPEC v1.1, BS1 requires an allele frequency greater than 0.0185%.
BS2 The CSPEC awards BS2 if ≥3 homozygotes are present in gnomAD or ≥3 heterozygous individuals are observed in well-phenotyped family members.
BS3 No well-established in vitro or in vivo functional studies demonstrating no damaging effect on MTOR protein function have been identified for p.Ile1204Val.
BP2 No evidence that NM_004958.4:c.3610A>G has been observed in cis or trans with a known pathogenic variant in MTOR.
BP5 No evidence exists that NM_004958.4:c.3610A>G has been observed in a case with an alternate molecular basis for disease.
N/A · 11 PVS1 · PM6 · PP1 · PP3 · PP4 · PP5 · BS4 · BP1 · BP4 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.186. BayesDel score = -0.200856.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. MTOR, an intracellular kinase that regulates cell growth and metabolism, is infrequently mutated in various cancer types.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots