NM_002524.5:c.101C>T (p.Pro34Leu) in NRAS is a missense variant located in the Switch I functional domain, a VCEP-approved critical domain per the RASopathy Expert Panel supplemental material.1 This variant is completely absent from gnomAD v2.1, v4.1, and gnomAD-Canada, satisfying the RASopathy VCEP PM2 requirement of complete absence from all population databases.2 PP2 applies by VCEP rule, as missense variants in RASopathy genes have a low rate of benign missense variation.3 PVS1, PP4, PP5, and BP6 are not applicable per explicit RASopathy VCEP specification.4 No PS3 functional data from VCEP-approved assays are available for this specific variant; OncoKB reports Unknown Oncogenic Effect. The somatic observation in keratinocytic epidermal nevi (PMID:22499344) does not meet VCEP functional study requirements.5 No germline RASopathy probands, de novo events, or segregation data have been identified for this variant in the literature reviewed; PS4, PS2, PM6, and PP1 are not met.6 REVEL score of 0.845 supports a deleterious effect, but BayesDel (0.347) and SpliceAI (0.00) do not provide additional independent lines, so PP3 is not met.7 Applying the generic ACMG/AMP 2015 classification framework (PMID:25741868) as a fallback due to the absence of RASopathy VCEP-specific final combination rules: two moderate criteria (PM1, PM2) and one supporting criterion (PP2) do not reach the threshold for Likely Pathogenic classification (requires e.g., 3 moderate, or 2 moderate + 2 supporting, or 1 strong + 1-2 moderate). This variant is classified as a Variant of Uncertain Significance (VUS).8
NRAS
Final classification
VUS
NRAS c.101C>T · p.Pro34Leu
NRAS
NM_002524.5:c.101C>T (p.Pro34Leu) in NRAS is a missense variant located in the Switch I functional domain, a VCEP-approved critical domain per the RASopathy Expert Panel supplemental material.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1.0 v1.0 lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate, PP2 supporting; combination = 2 moderate + 1 supporting, which maps to VUS.
Classification rationale
PM1PM2PP2
VUS
NRAS c.101C>T
PM1 + PM2 + PP2
→
VUS
1
cspec ↗vcep_alignment_with_pm1_domains_pptx
3
cspec ↗
4
cspec ↗
7
revelbayesdelspliceai ↗
8
generic_acmg_combination_rules
Gene diagram
· NM_002524.5 · variants mapped to exon structure
NRAS
NM_002524.5
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 16 assessed
Applied · 3
Strength
Supporting
Moderate
Strong
Very strong
✓
PM1
moderate
Pathogenic
Residue Pro34 is located within the Switch I domain of NRAS (analogous to HRAS aa 25-40), which is a VCEP-approved critical functional domain per the supplemental material (Alignment-with-PM1-domains.pptx). Switch I is essential for GTP binding and effector interactions in RAS proteins. The VCEP explicitly permits PM1 application across analogous residues in Group 1 genes (HRAS, NRAS, KRAS). The variant substitutes proline with leucine, altering a residue within this well-established functional domain.
Switch I domain (HRAS 25-40analogous to NRAS) is a VCEP-approved critical functional domain.NRAS P34 is within Switch I.
✓
PM2
moderate
Pathogenic
NM_002524.5:c.101C>T is completely absent from all population databases queried (gnomAD v2.1, gnomAD v4.1, gnomAD-Canada v1.0), satisfying the RASopathy VCEP requirement that the variant must be completely absent from all population databases.
Variant absent from gnomAD v2.1gnomAD v4.1and gnomAD-Canada v1.0.
✓
PP2
supporting
Pathogenic
The RASopathy VCEP explicitly states that PP2 is applicable to all RASopathy genes described and curated in its scope, including NRAS. This is a missense variant in a gene with a low rate of benign missense variation where missense variants are a common mechanism of disease.
VCEP RASopathy Expert Panel v1.0: PP2 is applicable to all RASopathy genes described and curated herein.
Assessed · not applied
Pathogenic
PS1
No previously established pathogenic variant resulting in the same amino acid change (p.Pro34Leu) at this residue in NRAS or in analogous Group 1 genes (HRAS, KRAS) has been identified.
PS2
No de novo occurrence with confirmed paternity identified in the literature reviewed for this case.
PS3
The RASopathy VCEP limits PS3 to approved functional studies listed in the supplemental material.
PS4
The only report of this variant is in a somatic mosaic context (keratinocytic epidermal nevus, PMID:22499344), which does not meet the VCEP definition of an independent occurrence in a germline RASopathy proband.
PM5
NM_002524.5:c.101C>T (p.Pro34Leu) is a missense variant eligible for PM5 consideration under the VCEP rule, which requires a previously established pathogenic missense variant at the same residue (or analogous residue in Group 1 genes HRAS, NRAS, KRAS).
PM6
No de novo report for this variant, with or without confirmation of paternity/maternity, was identified in the literature reviewed.
PP1
No segregation data are available for this variant.
PP3
The RASopathy VCEP requires multiple lines of computational evidence supporting a deleterious effect.
Benign
BA1
The variant is absent from all population databases queried, with an allele frequency of 0, well below the RASopathy VCEP BA1 threshold of ≥0.05% (5e-4).
BS1
The variant is absent from all population databases queried, well below the RASopathy VCEP BS1 threshold of ≥0.025%.
BS2
The RASopathy VCEP instructs that general population data should not be used for BS2 due to variable expressivity and severity.
BS3
No VCEP-approved functional study demonstrates a benign effect for this variant.
BS4
No segregation data available to assess lack of segregation in affected family members.
BP2
No evidence that this variant has been observed in trans with a pathogenic variant for a fully penetrant dominant disorder, or in cis with a pathogenic variant in any inheritance pattern.
BP4
The RASopathy VCEP requires multiple lines of computational evidence suggesting no impact.
BP5
No evidence that this variant has been found in a case with an alternate molecular basis for disease.
N/A · 9
PVS1 · PM3 · PM4 · PP4 · PP5 · BP1 · BP3 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1
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
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
ClinVar
This variant has been reported in ClinVar but submission details could not be extracted. (ClinVarID = 39647)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.845. BayesDel score = 0.347316.
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. NRAS, a GTPase, is mutated in a diverse range of cancers, most frequently in melanoma and thyroid cancer.
COSMIC
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; COSV54738538, n = 1 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
Triaged references · 6 PMIDs not cited in assessment
23970018 ↗
Acute myeloblastic leukaemias in adult patients: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up.
CLINVAR
25173338 ↗
2014 ESC Guidelines on diagnosis and management of hypertrophic cardiomyopathy: the Task Force for the Diagnosis and Management of Hypertrophic Cardiomyopathy of the European Society of Cardiology (ESC).
CLINVAR