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NRAS
Final classification
Pathogenic
NRAS c.182A>G · p.Gln61Arg
NRAS

NM_002524.5:c.182A>G (p.Gln61Arg) is a missense variant in exon 3 of NRAS affecting the critical Switch II domain (codon 61). This variant is absent from population databases (gnomAD v2.1, v4.1, gnomAD-Canada).

Gene
NRAS
Transcript
NM_002524.5
HGVS · transcript:coding
NM_002524.5:c.182A>G
Consequence
N/A
GRCh38
chr1:114713908 T>C
GRCh37
chr1:115256529 T>C
Basis ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for NRAS Version 2.3.0 v2.3.0 criteria-combination framework: matched Rule7 (1 Pathogenic.Strong + 2 Pathogenic.Moderate + Pathogenic.Supporting >=2) with applied criteria: PS1 strong, PS3 moderate, PM1 moderate, PM2 supporting, PM5 moderate, PP3 supporting; maps to Pathogenic.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for NRAS Version 2.3.0 v2.3.0 criteria-combination framework: matched Rule7 (1 Pathogenic.Strong + 2 Pathogenic.Moderate + Pathogenic.Supporting >=2) with applied criteria: PS1 strong, PS3 moderate, PM1 moderate, PM2 supporting, PM5 moderate, PP3 supporting; maps to Pathogenic.
Classification rationale
PS1PS3PM1PM2PM5PP3 Pathogenic
NRAS c.182A>G

NM_002524.5:c.182A>G (p.Gln61Arg) is a missense variant in exon 3 of NRAS affecting the critical Switch II domain (codon 61). This variant is absent from population databases (gnomAD v2.1, v4.1, gnomAD-Canada).1 The p.Gln61Arg amino acid change is an established pathogenic variant at the analogous residue in HRAS and KRAS, satisfying PS1 at Strong strength per the RASopathy VCEP.2 Functional studies approved by the RASopathy VCEP have characterized this variant across at least two independent assay platforms (RAS Activation, MEK Activation, ERK Activation, AKT Phosphorylation), supporting a gain-of-function mechanism consistent with RASopathy pathogenesis (PS3_Moderate).3 The variant lies within the Switch II domain (AA 57-64), a VCEP-approved critical functional domain, satisfying PM1 at Moderate strength. Residue Q61 is the key catalytic glutamine that positions the water molecule for GTP hydrolysis.4 Multiple alternative pathogenic residue changes at NRAS codon 61 (Q61K, Q61L, Q61H) are established in the literature, satisfying PM5 at Moderate strength per VCEP rules.5 The variant is absent from gnomAD population databases, meeting PM2 at Supporting strength (VCEP-downgraded).6 REVEL in silico prediction score of 0.888 exceeds the VCEP threshold of 0.7, supporting a deleterious effect (PP3).7 Applying the RASopathy VCEP combination rules: one Strong criterion (PS1) and at least two Moderate criteria (PS3 + PM1 + PM5) satisfy Rule 7 or Rule 6 for Pathogenic classification. Alternatively, one Strong plus one Moderate plus two Supporting criteria may satisfy other rules. The evidence combination is consistent with a Pathogenic classification.8

PS1 + PS3 + PM1 + PM2 + PM5 + PP3 Pathogenic
Gene diagram · NM_002524.5 · variants mapped to exon structure
NRAS NM_002524.5
Fetching transcript structure from UCSC…
Applied criteria · 6 applied · 11 assessed
Applied · 6
Strength Supporting Moderate Strong Very strong
PS1 strong Pathogenic
The p.Gln61Arg (Q61R) amino acid change is an established pathogenic variant at the analogous residue in HRAS and KRAS. The RASopathy VCEP explicitly allows PS1 at Strong strength for the same amino acid change as a previously established pathogenic variant in HRAS, KRAS, MRAS, NRAS, RIT1, or RRAS2.
VCEP PS1 rule: same amino acid change at analogous pathogenic residue positions across RAS gene family applies at StrongQ61R is an established pathogenic variant in HRAS and KRAS (ClinVar Pathogenic)N-RAS Q61R (CAA→CGA) is the most common N-RAS codon 61 mutation in thyroid follicular carcinomas (PMID:12727991)
PS3 moderate review Pathogenic
The RASopathy VCEP has approved four functional assay types for NRAS: RAS Activation, MEK Activation, ERK Activation, and AKT Phosphorylation assays. The variant p.Gln61Arg has been characterized in at least two different approved assay platforms across VCEP-vetted publications (PMIDs: 19966803, 28594414, 21263000), satisfying the VCEP PS3 Moderate requirement of two or more unique assay types.
VCEP-approved NRAS functional assays: RAS ActivationMEK ActivationERK Activation
PM1 moderate Pathogenic
The variant p.Gln61Arg (residue 61) lies within the Switch II (SW2) domain (amino acids 57-64), which is one of the four critical functional domains explicitly listed in the RASopathy VCEP supplementary table for PM1 application. SW2 is a well-established functional domain critical for GTP hydrolysis and effector interaction.
VCEP PM1 rule: SW2 domain (AA 57-64) is an approved critical functional domain for PM1 at ModerateResidue Q61 is the key catalytic residue within SW2directly involved in GTP hydrolysis
PM2 supporting Pathogenic
The variant is absent from gnomAD population databases (v2.1, v4.1, and gnomAD-Canada), meeting the RASopathy VCEP requirement for PM2 at Supporting strength. The VCEP downgrades PM2 from its default Moderate to Supporting for NRAS.
Absent from gnomAD v2.1 (exomes)Absent from gnomAD v4.1 (exomes)Absent from gnomAD-Canada v1.0
PM5 moderate review Pathogenic
Multiple alternative pathogenic residue changes at NRAS codon 61 have been established as pathogenic. N-RAS Q61K (c.181C>A) is a well-established pathogenic variant reported in Noonan syndrome (PMID:19966803) and somatic cancers. N-RAS Q61L (c.182A>T) is also pathogenic. This satisfies the VCEP PM5 Moderate requirement of at least one [likely] pathogenic residue change at the same codon.
NRAS codon 61 is a well-established mutational hotspot with multiple pathogenic residue changes (Q61KQ61LQ61H
PP3 supporting Pathogenic
The REVEL score for this variant is 0.888, which is ≥0.7, meeting the RASopathy VCEP PP3 threshold for pathogenic in silico prediction at Supporting strength. SpliceAI predicts no significant splice impact (max delta = 0.01), which is consistent with a missense effect rather than splicing.
REVEL score: 0.888 (≥0.7 threshold met)SpliceAI max delta: 0.01 (no splicing impact)
Assessed · not applied
Pathogenic
PS2 No de novo occurrence data with confirmed maternity and paternity is available for this variant in the case materials.
PS4 The RASopathy VCEP uses point-based scoring for PS4 requiring specific proband counts with RASopathy phenotypes.
PM6 No assumed de novo observations (without confirmed parentage) were identified in the case materials.
PP1 No co-segregation data in affected family members is available.
Benign
BA1 The RASopathy VCEP BA1 threshold is gnomAD filtering allele frequency ≥0.05%.
BS1 The RASopathy VCEP BS1 threshold is gnomAD filtering allele frequency ≥0.025%.
BS2 No observation of this variant in healthy adult individuals.
BS4 No lack-of-segregation data are available.
BP2 No evidence of an alternative molecular cause of RASopathy in the same gene, and no phenotype data inconsistent with RASopathy explained by a different variant.
BP4 The RASopathy VCEP BP4 threshold for missense variants is REVEL ≤0.3.
BP5 No evidence of an alternative molecular cause of RASopathy in a different gene, and no phenotype data inconsistent with RASopathy explained by a different causative variant.
N/A · 11 PVS1 · PM3 · PM4 · PP2 · PP4 · PP5 · BS3 · BP1 · BP3 · BP6 · 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
This variant has been reported in ClinVar as Pathogenic (9 clinical laboratories). (ClinVarID = 13900)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.888. BayesDel score = 0.378634.
Functional / OncoKB screenshot
Functional Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Oncogenic.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Hotspot
COSMIC
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV54736340, n = 2170 times).
Hotspots
This variant lies in a statistically significant hotspot.
Literature · how each cited paper was used
2papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 6 further PMIDs triaged but not cited — see Sources & References.
RAS point mutations and PAX8-PPAR gamma rearrangement in thyroid tumors: evidence for distinct molecular pathways in thyroid follicular carcinoma.
Searched
c.182A>GCAA>CGAQ61RGln61Argcodon 61
Found
N-RAS codon 61 CAA→CGA (p.Gln61Arg) was the most common RAS mutation detected in conventional follicular thyroid carcinomas and adenomas, found in 12 of 17 (70%) follicular carcinomas with RAS mutations. RAS mutations and PAX8-PPARγ rearrangements defined distinct, nearly non-overlapping molecular pathways in follicular thyroid carcinoma.
Variant
✓ Names this variant — characterised directly
Applied to
PM5 supports · met PS1 supports · met
Why
Confirms N-RAS Q61R is the most prevalent N-RAS codon 61 mutation in thyroid follicular tumors. Supports PS1 (same amino acid change at analogous residue) and PM5 (multiple pathogenic changes at same codon). Somatic context — does not provide germline proband data.
In follicular carcinomas and adenomas, the CAA→CGA mutation of N-RAS codon 61 was the most common.
Location Results (Table 3); Discussion  ·  Context LightCycler FMCA and direct sequencing of 88 follicular and Hürthle cell thyroid tumors  ·  full text
Allosteric modulation of Ras positions Q61 for a direct role in catalysis.
Searched
c.182A>GQ61RGln61ArgNRASN-RAS
Found
Structural study of H-Ras demonstrating that Q61 is positioned for a direct catalytic role in GTP hydrolysis via an allosteric switch mechanism involving helix 3/loop 7. Switch II (residues 60-76) ordering places Q61 in the active site near the bridging water molecule. Q61 mutants impair GTPase activity and are found prominently in human cancers.
Variant
◇ Residue / gene-level — variant not named
Applied to
PM1 supports · met
Why
Does not mention NM_002524.5:c.182A>G or NRAS specifically. Provides domain-level functional evidence that Q61 is a critical catalytic residue in the Switch II domain. Supports PM1 domain-level applicability.
Mutants of residue Q61 impair the GTPase activity of Ras and are found prominently in human cancers.
Location Abstract; Results; Discussion  ·  Context X-ray crystallography of H-Ras (residues 1-166) with GppNHp; calcium acetate allosteric modulation  ·  full text
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 6 PMIDs not cited in assessment
10574788 ↗ The pre-hydrolysis state of p21(ras) in complex with GTP: new insights into the role of water molecules in the GTP hydrolysis reaction of ras-like proteins. ONCOKB
23515407 ↗ Characteristics of lung cancers harboring NRAS mutations. ONCOKB
26619011 ↗ Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity. ONCOKB
30552700 ↗ NRAS Q61R and BRAF G466A mutations in atypical melanocytic lesions newly arising in advanced melanoma patients treated with vemurafenib. ONCOKB
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
39434542 ↗ Modified Rules for Classification of Variants Associated With Disorders of Somatic Mosaicism. CLINVAR