NM_002524.5:c.149C>T

Variant names:

• chr1-114713941-G-A
• rs267606921
• NM_002524.5:c.149C>T

Variant summary

Our verdict is Pathogenic. The variant received 9 ACMG points: 9P and 0B. PM2_Supporting PS3_Moderate PS4 PM6

This summary comes from the ClinGen Evidence Repository: 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) LINK:https://erepo.genome.network/evrepo/ui/classification/CA257019/MONDO:0021060/039

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.3e-7 (0 hom.)
• Consequence: NRAS NM_002524.5 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:7 O:1
• Conservation: PhyloP100: 9.87
• Publications: 36 publications found

Genes affected

NRAS (HGNC:7989): (NRAS proto-oncogene, GTPase) This is an N-ras oncogene encoding a membrane protein that shuttles between the Golgi apparatus and the plasma membrane. This shuttling is regulated through palmitoylation and depalmitoylation by the ZDHHC9-GOLGA7 complex. The encoded protein, which has intrinsic GTPase activity, is activated by a guanine nucleotide-exchange factor and inactivated by a GTPase activating protein. Mutations in this gene have been associated with somatic rectal cancer, follicular thyroid cancer, autoimmune lymphoproliferative syndrome, Noonan syndrome, and juvenile myelomonocytic leukemia. [provided by RefSeq, Jun 2011]

NRAS Gene-Disease associations (from GenCC):

• Noonan syndrome

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
• Noonan syndrome 6

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), G2P, PanelApp Australia
• cardiofaciocutaneous syndrome

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: Genomics England PanelApp, ClinGen
• Costello syndrome

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• Noonan syndrome with multiple lentigines

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Pathogenic. The variant received 9 ACMG points.

• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PS4: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PM6: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NRAS	NM_002524.5	c.149C>T	p.Thr50Ile	missense_variant	Exon 3 of 7	ENST00000369535.5	NP_002515.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NRAS	ENST00000369535.5	c.149C>T	p.Thr50Ile	missense_variant	Exon 3 of 7	1	NM_002524.5	ENSP00000358548.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.33e-7 AC: 1 AN: 1364650 Hom.: 0 Cov.: 31 AF XY: 0.00000148 AC XY: 1 AN XY: 676466

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 30718

American (AMR) AF: 0.00 AC: 0 AN: 41644

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 22826

East Asian (EAS) AF: 0.00 AC: 0 AN: 33106

South Asian (SAS) AF: 0.00 AC: 0 AN: 84926

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44208

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5300

European-Non Finnish (NFE) AF: 9.54e-7 AC: 1 AN: 1047906

Other (OTH) AF: 0.00 AC: 0 AN: 54016

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:7 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Noonan syndrome 6 Pathogenic:3

Jan 01, 2010

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

Juno Genomics, Hangzhou Juno Genomics, Inc

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Absent from controls (or at extremely low frequency if recessive) in Genome Aggregation Database, Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium.;The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls.;Assumed de novo, but without confirmation of paternity and maternity.;Patient's phenotype or family history is highly specific for a disease with a single genetic etiology.;Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.

Oct 30, 2024

3billion

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The variant is observed at an extremely low frequency in the gnomAD v4.1.0 dataset (total allele frequency: <0.001%). Predicted Consequence/Location: Missense variant. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product [REVEL: 0.69 (>=0.6, sensitivity 0.68 and specificity 0.92); 3Cnet: 0.99 (>=0.6, sensitivity 0.72 and precision 0.9)]. The same nucleotide change resulting in the same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000013902 /PMID: 19966803). The variant has been observed in multiple (>3) similarly affected unrelated individuals (PMID: 19966803, 22855653, 28594414, 31219622). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

RASopathy Pathogenic:3

Jan 17, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects NRAS function (PMID: 19966803, 21263000). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 13902). This missense change has been observed in individual(s) with Noonan Syndrome (PMID: 19966803, 22855653). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 50 of the NRAS protein (p.Thr50Ile).

Sep 17, 2024

ClinGen RASopathy Variant Curation Expert Panel

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

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)

Jul 11, 2022

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: NRAS c.149C>T (p.Thr50Ile) results in a non-conservative amino acid change located in the Small GTP-binding protein domain (IPR005225) of the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant was absent in 251196 control chromosomes (gnomAD). c.149C>T has been reported in the literature in individuals affected with Noonan Syndrome and Related Conditions (Cirstea_2010, Denayer_2012, Altmuller_2017, Rodriguez_2018, Li_2019), including at least one confirmed de novo occurrence (Rodriguez_2018). These data indicate that the variant is very likely to be associated with disease. In zebrafish embryos the variant resulted in severe developmental defects during epiboly and gastrulation that resembled the defects observed with known Noonan-associated genes (Runtuwene_2011). Three ClinVar submitters have assessed the variant since 2014: all three classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

Noonan syndrome Pathogenic:1

Mar 06, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The Thr50Ile variant has been reported in 2 individuals with clinical features o f Noonan syndrome (Cirstea 2010). This variant was reported to have occurred de novo in these individuals. Studies have shown that the Thr50Ile variant may impa ct protein function (Cirstea 2010, Runtuwene 2011). However, this in vitro assay may not accurately represent biological function. Computational analyses (bioch emical amino acid properties, conservation, AlignGVGD, PolyPhen2, and SIFT) also suggest that the Thr50Ile variant may impact the protein, though this informati on is not predictive enough to determine pathogenicity. In summary, this varian t meets our criteria to be classified as pathogenic (http://pcpgm.partners.org/L MM).

Noonan syndrome 1 Other:1

GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.50
BayesDel_addAF	Pathogenic	0.31	D
BayesDel_noAF	Pathogenic	0.21
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.63	D
Eigen	Benign	0.073
Eigen_PC	Uncertain	0.24
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.94	D
M_CAP	Benign	0.019	T
MetaRNN	Pathogenic	0.86	D
MetaSVM	Benign	-0.74	T
MutationAssessor	Benign	0.67	N
PhyloP100		9.9
PrimateAI	Pathogenic	0.84	D
PROVEAN	Uncertain	-3.7	D
REVEL	Pathogenic	0.69
Sift	Benign	0.054	T
Sift4G	Benign	0.22	T
Vest4		0.90
ClinPred		0.97	D
GERP RS		4.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.83
gMVP		0.65
Mutation Taster		=15/85	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs267606921; hg19: chr1-115256562; COSMIC: COSV54755793; COSMIC: COSV54755793;