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
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_002524.5(NRAS):c.149C>T (p.Thr50Ile)

CA257019

13902 (ClinVar)

Gene: NRAS
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 178ae908-8176-427c-9164-1d0e74b7cc79
Approved on: 2024-09-17
Published on: 2024-10-01

HGVS expressions

NM_002524.5:c.149C>T
NM_002524.5(NRAS):c.149C>T (p.Thr50Ile)
NC_000001.11:g.114713941G>A
CM000663.2:g.114713941G>A
NC_000001.10:g.115256562G>A
CM000663.1:g.115256562G>A
NC_000001.9:g.115058085G>A
NG_007572.1:g.7954C>T
ENST00000369535.5:c.149C>T
ENST00000369535.4:c.149C>T
NM_002524.4:c.149C>T
More

Pathogenic

Met criteria codes 4
PS4 PS3_Moderate PM6_Very Strong PM2_Supporting
Not Met criteria codes 9
PS1 BP4 BA1 PP1 PP3 PP2 PM1 PM5 BS1

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for NRAS Version 2.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.149C>T (p.Thr50Ile) variant in NRAS is a missense variant predicted to cause substitution of threonine by isoleucine at amino acid 50. This variant is absent from gnomAD v2.1.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.693, which is neither above nor below the thresholds predicting a damaging or benign impact on NRAS function. This variant has been reported in over 6 probands with features of RASopathy (PS4; PMIDs: 22855653, 28594414, 31219622, GeneDx). This variant has been identified as a de novo occurrence with unconfirmed parental relationships in 4 individuals with autosomal dominant RASopathy (PM6_VeryStrong; PMIDs: 19966803, 29752777, APHP-Robert Debré). MEK and ERK activation assays in COS-7 cells showed enhanced phosphorylation of MEK and ERK in the presence of serum or after EGF stimulation indicating that this variant impacts protein function (PMID: 19966803)(PS3_Moderate). In summary, this variant meets the criteria to be classified as pathogenic for autosomal dominant RASopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen RASopathy VCEP: PM6_VeryStrong, PS4, PS3_Moderate, PM2_Supporting. (RASopathy VCEP specifications version 2.1; 9/17/2024)
Met criteria codes
PS4
This variant has been reported in over 6 probands with features of RASopathy (PS4; PMIDs: 22855653, 28594414, 31219622, GeneDx).
PS3_Moderate
MEK and ERK activation assays in COS-7 cells showed enhanced phosphorylation of MEK and ERK in the presence of serum or after EGF stimulation indicating that this variant impacts protein function (PMID: 19966803)(PS3_M).

PM6_Very Strong
This variant has been identified as a de novo occurrence with unconfirmed parental relationships in 4 individuals with autosomal dominant RASopathy (PM6_VS; PMIDs: 19966803, 29752777, APHP-Robert Debré).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
Not Met criteria codes
PS1
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
BA1
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
The computational predictor REVEL gives a score of 0.693, which is neither above nor below the thresholds predicting a damaging or benign impact on NRAS function.
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
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
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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