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.71T>A (p.Ile24Asn)

CA356968

222971 (ClinVar)

Gene: NRAS
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 5c6b49f5-c2de-4cdd-b6e9-2e0480dc9267
Approved on: 2024-09-17
Published on: 2024-10-01

HGVS expressions

NM_002524.5:c.71T>A
NM_002524.5(NRAS):c.71T>A (p.Ile24Asn)
NC_000001.11:g.114716090A>T
CM000663.2:g.114716090A>T
NC_000001.10:g.115258711A>T
CM000663.1:g.115258711A>T
NC_000001.9:g.115060234A>T
NG_007572.1:g.5805T>A
ENST00000369535.5:c.71T>A
ENST00000369535.4:c.71T>A
NM_002524.4:c.71T>A
More

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PM6_Strong PP3 PS3_Supporting PS4_Moderate
Not Met criteria codes 4
BP4 PM1 PP1 PP2

Evidence Links 0

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.71T>A (p.Ile24Asn) variant in NRAS is a missense variant predicted to cause substitution of isoleucine by asparagine at amino acid 24. This variant is absent from gnomAD v2.1.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.863, which is above the threshold of 0.7, evidence that correlates with impact to NRAS function (PP3). This variant has been reported in 4 probands with features of RASopathy (PS4_Moderate; PMIDs:21263000, 22855653, 28594414, GeneDx). This variant has been identified as a de novo occurrence with unconfirmed parental relationships in 2 individuals with features of RASopathy (PM6_Strong; PMIDs: 21263000, 22855653). RAS activation assays in 293T cells showed a mild increase in GTP-bound RAS and enhanced MAPK phosphorylation indicating that this variant impacts protein function. A zebrafish model using injected RNA showed developmental and craniofacial defects. The phenotype was completely rescued by MEK inhibition (PMID:21263000)(PS3_Supporting). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal dominant RASopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen RASopathy VCEP: PM6_Strong, PS4_Moderate, PS3_Supporting, PM2_Supporting, PP3. (RASopathy VCEP specifications version 2.1; 9/17/2024)
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PM6_Strong
This variant has been identified as a de novo occurrence with unconfirmed parental relationships in 2 individuals with features of RASopathy (PM6_Strong; PMIDs: 21263000, 22855653).
PP3
The computational predictor REVEL gives a score of 0.863, which is above the threshold of 0.7, evidence that correlates with impact to NRAS function (PP3).
PS3_Supporting
RAS activation assays in 293T cells showed a mild increase in GTP-bound RAS and enhanced MAPK phosphorylation indicating that this variant impacts protein function. A zebrafish model using injected RNA showed developmental and craniofacial defects. The phenotype was completely rescued by MEK inhibition (PMID:21263000)(PS3_Supporting).
PS4_Moderate
This variant has been reported in 4 probands with features of RASopathy (PS4_Moderate; PMIDs:21263000, 22855653, 28594414, GeneDx).
Not Met criteria codes
BP4
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
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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