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NM_002524.5(NRAS):c.38G>A (p.Gly13Asp) AND Noonan syndrome 6

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Jul 17, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000022690.28

Allele description [Variation Report for NM_002524.5(NRAS):c.38G>A (p.Gly13Asp)]

NM_002524.5(NRAS):c.38G>A (p.Gly13Asp)

Gene:
NRAS:NRAS proto-oncogene, GTPase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p13.2
Genomic location:
Preferred name:
NM_002524.5(NRAS):c.38G>A (p.Gly13Asp)
HGVS:
  • NC_000001.11:g.114716123C>T
  • NG_007572.1:g.5772G>A
  • NM_002524.5:c.38G>AMANE SELECT
  • NP_002515.1:p.Gly13Asp
  • LRG_92t1:c.38G>A
  • LRG_92:g.5772G>A
  • LRG_92p1:p.Gly13Asp
  • NC_000001.10:g.115258744C>T
  • NM_002524.2:c.38G>A
  • NM_002524.3:c.38G>A
  • NM_002524.4:c.38G>A
  • P01111:p.Gly13Asp
Protein change:
G13D; GLY13ASP
Links:
UniProtKB: P01111#VAR_063084; OMIM: 164790.0003; dbSNP: rs121434596
NCBI 1000 Genomes Browser:
rs121434596
Molecular consequence:
  • NM_002524.5:c.38G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Noonan syndrome 6 (NS6)
Synonyms:
NRAS gene related Noonan syndrome
Identifiers:
MONDO: MONDO:0013186; MedGen: C2750732; Orphanet: 648; OMIM: 613224

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000043979OMIM
no assertion criteria provided
Pathogenic
(Mar 10, 2011)
unknownliterature only

PubMed (6)
[See all records that cite these PMIDs]

SCV005086264Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 17, 2023)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownnot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Amino-acid substitutions at codon 13 of the N-ras oncogene in human acute myeloid leukaemia.

Bos JL, Toksoz D, Marshall CJ, Verlaan-de Vries M, Veeneman GH, van der Eb AJ, van Boom JH, Janssen JW, Steenvoorden AC.

Nature. 1985 Jun 27-Jul 3;315(6022):726-30.

PubMed [citation]
PMID:
2989702

N-ras gene point mutations in childhood acute lymphocytic leukemia correlate with a poor prognosis.

Lübbert M, Mirro J Jr, Miller CW, Kahan J, Isaac G, Kitchingman G, Mertelsmann R, Herrmann F, McCormick F, Koeffler HP.

Blood. 1990 Mar 1;75(5):1163-9.

PubMed [citation]
PMID:
2407301
See all PubMed Citations (9)

Details of each submission

From OMIM, SCV000043979.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (6)

Description

In white blood cells derived from 2 unrelated children with juvenile myelomonocytic leukemia (JMML; 607785), Matsuda et al. (2007) identified a somatic heterozygous G-to-A transition in the NRAS gene, resulting in a gly13-to-asp (G13D) substitution.

Oliveira et al. (2007) identified a heterozygous G-to-A transition in the NRAS gene, resulting in a gly13-to-asp (G13D) substitution, in a 49-year-old patient with RAS-associated autoimmune leukoproliferative disorder (RALD; 614470). The patient had a lifelong overexpansion of lymphocytes and a history of childhood leukemia, and early adulthood lymphoma, both successfully treated. There were no developmental defects. Laboratory studies showed increased serum alpha/beta CD4-/CD8- T cells and lymph node follicular hyperplasia. There was no evidence of CD95 (134637)-mediated apoptosis, but the patient's lymphocytes resisted death by IL2 (147680) withdrawal, indicating a specific defect in lymphocyte apoptosis. Further studies of the patient's cells indicated a decrease of the proapoptotic protein BIM (BCL2L11; 603827), which is critical for withdrawal-induced mitochondrial apoptosis. The mutation was found in the patient's lymphoblasts, peripheral blood mononuclear cells, monocytes, EBV-transformed B cells, and buccal epithelial cells. It was not present in the patient's unaffected relatives, suggesting de novo occurrence. The patient had no developmental abnormalities or features of Noonan syndrome. Oliveira et al. (2007) noted that the same mutation had been identified somatically in myeloid and lymphoid malignancies (Bos et al., 1985; Lubbert et al., 1990). Niemela et al. (2010) stated that the NRAS mutation found by Oliveira et al. (2007) was a somatic mutation.

De Filippi et al. (2009) identified a de novo germline heterozygous G13D substitution in the NRAS gene in a male infant who presented at age 2 months with juvenile myelomonocytic leukemia (JMML; 607785) and was later noted to have dysmorphic features suggestive of, but not diagnostic of, Noonan syndrome (NS6; 613224). Features included short stature, relative macrocephaly, high forehead, epicanthal folds, long eyebrows, low nasal bridge, low-set ears, 2 cafe-au-lait spots, and low scores on performance tasks. Cardiac studies were normal. There were no hematologic abnormalities related to RALD in this patient.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownnot providednot providednot providednot providednot providednot providednot providednot provided

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV005086264.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0101 - Gain of function is a known mechanism of disease in this gene and is associated with NRAS-related conditions (OMIM). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0115 - Variants in this gene are known to have variable expressivity. Noonan syndrome, caused by germline variants in the NRAS gene, have variable expressivity (GeneReviews). (I) 0200 - Variant is predicted to result in a missense amino acid change from glycine to aspartic acid. (I) 0254 - This variant is low level mosaic in DNA extracted from snap frozen skin biopsy. (I) 0302 - Variant is present in gnomAD <0.001 for a dominant condition (v2: 1 heterozygote, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2: 1 heterozygote, 0 homozygotes). (I) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants (DECIPHER). (SP) 0801 - This variant has very strong previous evidence of pathogenicity in unrelated individuals. It is one of the variants in this gene most commonly associated with juvenile myelomonocytic leukaemia (JMML) and it has also been reported in somatic tissue associated with other cancers (ClinVar, PMIDs: 17332249, 18375819, 36130886). In addition, it has been regarded as pathogenic in germline tissue (ClinVar) and has been reported de novo in one individual with JMML and features of Noonan syndrome (PMID: 19775298) and in another individual with autoimmune lymphoproliferative syndrome without features of Noonan syndrome (PMID: 17517660). 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Aug 4, 2024