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NF2
Final classification
Pathogenic
NF2 c.604G>T · p.Glu202Ter
NF2

NM_000268.3:c.604G>T (p.Glu202Ter) is a nonsense variant in exon 7 of NF2, creating a premature termination codon predicted to trigger nonsense-mediated decay or produce a severely truncated merlin protein lacking the FERM domain F3 lobe and all downstream domains.

Gene
NF2
Transcript
NM_000268.3
HGVS · transcript:coding
NM_000268.3:c.604G>T
Consequence
N/A
GRCh38
chr22:29658193 G>T
GRCh37
chr22:30054182 G>T
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 very strong, PM1 moderate, PM2 moderate; combination = 1 very strong + 2 moderate, which maps to Pathogenic.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 very strong, PM1 moderate, PM2 moderate; combination = 1 very strong + 2 moderate, which maps to Pathogenic.
Classification rationale
PVS1PM1PM2 Pathogenic
NF2 c.604G>T

NM_000268.3:c.604G>T (p.Glu202Ter) is a nonsense variant in exon 7 of NF2, creating a premature termination codon predicted to trigger nonsense-mediated decay or produce a severely truncated merlin protein lacking the FERM domain F3 lobe and all downstream domains.1 NF2 is a well-established tumor suppressor gene where germline loss-of-function variants cause NF2-related schwannomatosis, an autosomal dominant tumor predisposition syndrome characterized by bilateral vestibular schwannomas, meningiomas, and other nervous system tumors.2 Truncating NF2 mutations, including nonsense variants, are associated with a more severe disease phenotype with earlier age of onset compared to missense or splice site mutations, as demonstrated in the largest genotype-phenotype study of 125 NF2 families.3 The variant is absent from gnomAD v2.1 (~141,456 individuals) and gnomAD v4.1 (~807,162 individuals), consistent with a rare disease-causing variant not tolerated in the general population.4 The premature stop at codon 202 occurs within the FERM domain, a critical functional domain required for merlin membrane association and tumor suppressor activity; the truncation removes the F3 subdomain and all C-terminal domains essential for merlin-mediated growth regulation.5 Combined evidence satisfies ACMG/AMP Pathogenic classification: PVS1 (Very Strong) + PM2 (Moderate) + PM1 (Moderate).6

PVS1 + PM1 + PM2 Pathogenic
Gene diagram · NM_000268.3 · variants mapped to exon structure
NF2 NM_000268.3
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 15 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PVS1 very strong Pathogenic
NM_000268.3:c.604G>T is a nonsense variant (p.Glu202Ter) in exon 7 of 16 coding exons in NF2, a tumor suppressor gene where loss-of-function is an established germline disease mechanism for NF2-related schwannomatosis. Under the ClinGen SVI PVS1 framework (PMC6185798), nonsense variants in genes with confirmed LoF disease mechanism are assigned PVS1 at very strong strength. NMD is predicted as the premature termination codon (position 202 of 596) occurs more than 50 nucleotides upstream of the last exon junction.
Nonsense variant p.(Glu202Ter) creates a premature termination codon at amino acid 202 of 596NF2 loss-of-function is an established mechanism for NF2-related schwannomatosissupported by multiple germline disease publications
PM1 moderate Pathogenic
The nonsense variant p.Glu202Ter truncates merlin within the FERM domain (residues ~1-300), a well-characterized functional domain essential for membrane association and tumor suppressor activity. The premature stop at codon 202 removes the F3 lobe of the FERM domain and all downstream domains, including the alpha-helical and C-terminal regions. The FERM domain is established as critical for merlin function through extensive literature on NF2 pathogenesis.
Merlin FERM domain (residues ~1-300) is critical for membrane localization and tumor suppressor functionTruncation at codon 202 removes the FERM F3 lobe and all downstream domainsPMID:9643284 demonstrates truncating NF2 mutations are associated with severe disease phenotype
PM2 moderate Pathogenic
NM_000268.3:c.604G>T is absent from gnomAD v2.1 (~141,456 individuals), gnomAD v4.1 (~807,162 individuals), and gnomAD-Canada v1.0. Under generic ACMG, PM2 applies for variants with population frequency <0.1% that are absent from large population databases.
Absent from gnomAD v2.1 (0 alleles observed)Absent from gnomAD v4.1 (0 alleles observed)Absent from gnomAD-Canada v1.0 (0 alleles observed)
Assessed · not applied
Pathogenic
PS2 No de novo data is available in the case materials for this variant.
PS3 No variant-specific functional studies were identified for p.Glu202Ter or for a systematically characterized range that includes codon 202.
PS4 The variant is absent from gnomAD population databases, but no clinical cohort or case series reporting this specific variant in affected individuals was identified.
PM6 No de novo data is available for this variant in the case materials.
PP1 No family segregation data is available for this variant.
PP4 No patient phenotype data is available in the case materials to assess whether the clinical presentation is specific for NF2-related schwannomatosis.
PP5 ClinVar VariationID 3231107 is associated with NM_000268.4:c.718G>T (p.Gly240Trp), NOT NM_000268.3:c.604G>T (p.Glu202Ter).
Benign
BA1 The variant is absent from gnomAD v2.1 and v4.1.
BS1 The variant is absent from gnomAD v2.1 and v4.1.
BS2 No data available on observation of this variant in healthy adults.
BS3 No well-established functional studies demonstrating no deleterious effect were identified for p.Glu202Ter.
BS4 No cosegregation data is available.
BP2 No data on in trans observation with a known pathogenic variant is available.
BP5 No data available on this variant being observed in a case with an alternate molecular basis for disease.
BP6 ClinVar VariationID 3231107 is associated with NM_000268.4:c.718G>T (p.Gly240Trp), NOT this variant.
N/A · 8 PS1 · PM5 · PP2 · PP3 · BP1 · BP3 · BP4 · BP7
Research & evidence
Population frequency · supports pathogenic
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
Error retrieving ClinVar entry.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.14). BayesDel score = 0.66.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
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 previously been reported in somatic cancers (COSMIC; COSV58526910, n = 2 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Literature · how each cited paper was used
1papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 4 further PMIDs triaged but not cited — see Sources & References.
Genotype/phenotype correlations in type 2 neurofibromatosis (NF2): evidence for more severe disease associated with truncating mutations.
Searched
c.604G>Tp.Glu202Terp.E202*604G>TE202Glu202
Found
Genotype-phenotype study of 125 NF2 families demonstrating that truncating mutations (nonsense, frameshift) are associated with significantly earlier age of onset (mean 19 years) and more severe disease compared to missense, splice site, and large deletion mutations. Table 2 catalogues 60 NF2 mutations including nonsense mutations in nearby codons (e.g., Arg196Ter, Arg198Ter) but does not include p.Glu202Ter (c.604G>T). The variant p.Glu202Ter was not identified among the listed mutations.
Variant
◇ Residue / gene-level — variant not named
Applied to
PM1 supports · met
Why
Variant not specifically listed but paper confirms truncating NF2 mutations cause severe disease; general genotype-phenotype principle supports pathogenic interpretation of truncating variants but does not provide variant-specific evidence for PS3 or PS4.
Subjects with truncating mutations were significantly more likely to have symptoms before 20 years of age (p<0.001) and to develop at least two symptomatic CNS tumours in addition to vestibular schwannoma before 30 years (p<0.001).
Location Table 2 (complete mutation listing) — variant not present  ·  full text
Sources & reference links
8Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 4 PMIDs not cited in assessment
19545378 ↗ Neurofibromatosis type 2 (NF2): a clinical and molecular review. ONCOKB
22825583 ↗ New strategies in pleural mesothelioma: BAP1 and NF2 as novel targets for therapeutic development and risk assessment. ONCOKB
8755919 ↗ Type of mutation in the neurofibromatosis type 2 gene (NF2) frequently determines severity of disease. ONCOKB
25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR