NRAS
protein-codingNRAS proto-oncogene, GTPase, the group of RAS type GTPase family
Gene summary
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]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0007893
Submitter: ClinGen
There have been three studies published implicating NRAS with Noonan syndrome with multiple lentigines (NSML), however only one unique variant has been identified. The p.Gly60Glu variant has been identified in de novo cases, segregated in one family with disease, and individuals with unknown origin who possess clinical features of NSML (Ekvall et al., 2015; Kraoua et al., 2012). This variant has also been found in individuals without multiple lentigines with clinical features of NS (Cirstea et al., 2010). Of note, one individual with the p.Gly13Asp variant possessed the juvenile myelomonocytic leukemia phenotype in addition to clinical features of NSML (De Filippi et al., 2009). This case was not scored, but should be noted as a possible additional phenotype. The NRAS gene is also located in the Ras/MAPK pathway, which is associated with the NSML phenotype (Aoki et al., 2016; Rauen, 2013). In summary, the evidence supporting NRAS’s association with NSML is Limited, however the presence of multiple lentigines makes this evidence distinct from the other Noonan cases. Of note, NRAS has also been classified as Definitive in association with NS and as Limited in association with Costello syndrome and cardiofaciocutaneous syndrome. The ClinGen RASopathy Expert Panel found no evidence associating NRAS with NS-like disorder with loose anagen hair. This curation was approved by the ClinGen RASopathy Gene Curation Expert Panel on 5/30/18 (SOP Version 5).
Inheritance Pattern: AD
Disease ID:MONDO:0013186
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0018997
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0013186
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0015280
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0015280
Submitter: ClinGen
Only two patients to date have been identified to have a cardiofaciocutaneous syndrome (CFC) diagnosis with NRAS variants (Altmuller et al., 2017). Of note, one patient had a complex phenotype that may be due to modifications from a 22q11.23 rearrangement, and the other patient presented with a p.T50I variant which has also been identified in patients with Noonan syndrome (NS) and no or mild developmental problems. This 11-year-old individual was noted to have mildly delayed motor and intellectual development with CFC facial features; however, variable expressivity, age of ascertainment, and outdated clinical assessments of affected individuals may complicate the clinical diagnosis of NS versus CFC. The NRAS gene is also located in the Ras/MAPK pathway, which is associated with the CFC phenotype (Aoki et al., 2016; Rauen, 2013). In summary, the evidence supporting the association between NRAS and CFC is Limited at this time. Of note, NRAS has also been classified as Definitive in association with NS and as Limited in association with NS with multiple lentigines and Costello syndrome. The ClinGen RASopathy Expert Panel found no evidence associating NRAS with NS-like disorder with loose anagen hair. This curation was approved by the ClinGen RASopathy Gene Curation Expert Panel on 7/24/18 (SOP Version 5).
Inheritance Pattern: AD
Disease ID:MONDO:0013186
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0018997
Submitter: ClinGen
There is a definitive association between alteration of the NRAS gene and Noonan syndrome (NS). The maximum amount of scorable genetic evidence has been published showing de novo as well as non-de novo variants occur in NRAS in patients with NS (Altmuller et al., 2017; Cirstea et al., 2010; Denayer et al., 2012; Runtuwene et al., 2011). The NRAS gene is also located in the Ras/MAPK pathway, which is associated with the NS phenotype and variants found in NS patients in this gene disrupt the RAS pathway function as demonstrated by zebrafish models (Aoki et al., 2016; Rauen, 2013; Runtuwene et al., 2011). Of note, NRAS has also been classified as Limited in association with Costello syndrome, cardiofaciocutaneous syndrome, and NS with multiple lentigines. The ClinGen RASopathy Expert Panel found no evidence associating NRAS with NS-like disorder with loose anagen hair. This curation was approved by the ClinGen RASopathy Gene Curation Expert Panel on 5/30/18 (SOP Version 5).
Inheritance Pattern: AD
Disease ID:MONDO:0009026
Submitter: ClinGen
One patient with clinical features of Costello syndrome (CS) has been identified in the literature to date (Altmuller et al., 2017). This patient carries a de novo p.Gly12Arg variant in NRAS and was assessed via WES. However, the age of evaluation may be a potential confounding factor of this diagnosis. The NRAS gene is also located in the Ras/MAPK pathway, which is associated with the CS phenotype (Aoki et al., 2016; Rauen, 2013). For now, the association remains as Limited, but will likely move to Disputed with time. Of note, NRAS has also been classified as Definitive in association with Noonan syndrome (NS) and as Limited in association with NS with multiple lentigines and cardiofaciocutaneous syndrome. The ClinGen RASopathy Expert Panel found no evidence associating NRAS with NS-like disorder with loose anagen hair. This curation was approved by the ClinGen RASopathy Gene Curation Expert Panel on 7/24/18 (SOP Version 5).
Inheritance Pattern: AD
Disease ID:MONDO:0013186
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Craniofacial; Dermatologic; Genitourinary; Musculoskeletal; Neurologic; Oncologic
Intervention: Cardiovascular; Oncologic
Rationale: Individuals with RAS-associated autoimmune lymphoproliferative disorder may be at risk of hematologic malignancies, and individuals with Noonan syndrome 6 have been described with juvenile myelomonocytic leukemia such that surveillance/early treatment may reduce morbidity; Noonan syndrome may also include cardiac anomalies and dysrhythmias, and appropriate care may be beneficial;
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NRAS variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002524.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 48 | 2 | 51 | ||
| missense | 8 | 22 | 113 | 4 | 147 | |
| nonsense | 4 | 4 | ||||
| start loss | 0 | |||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 8 | 22 | 124 | 52 | 2 | 208 |
Highest pathogenic variant AF is 0.000010533125
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002515.1 | 4 | MANE Select | |
| Ensembl | ENSP00000358548.4 | 4 | MANE Select | |
| Ensembl | ENSP00000569489.1 | 5 | Standard | |
| Ensembl | ENSP00000569489.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- PI3K-Akt signaling pathway - Homo sapiens (human)
- Non-small cell lung cancer - Homo sapiens (human)
- Chronic myeloid leukemia - Homo sapiens (human)
- Gastric cancer - Homo sapiens (human)
- mTOR signaling pathway - Homo sapiens (human)
Biological Process
- MAPK cascade
- positive regulation of endothelial cell proliferation
- stimulatory C-type lectin receptor signaling pathway
- Ras protein signal transduction
- neutrophil degranulation
Molecular Function
- GTPase activity
- protein binding
- GTP binding
- protein-containing complex binding
Cellular Component
- Golgi membrane
- Golgi apparatus
- plasma membrane
- membrane
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000369535
- Coding exons
- 4
- Length
- 12426
- Individuals with no LoFs
- 125744
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 4
- Defined
- 125748
- p
- 0.0000159
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.71 | 55 | 104 | 0.528 | 0.00000520 | 1247 |
| Missense (PolyPhen) | 8 | 28.786 | 0.27791 | 385 | ||
| Synonymous | 0.0111 | 39 | 39.1 | 0.998 | 0.00000219 | 355 |
| Loss of Function | 2.39 | 2 | 10.3 | 0.194 | 6.06e-7 | 112 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000026 | 0.000026 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Ras proteins bind GDP/GTP and possess intrinsic GTPase activity.;
- Disease
- DISEASE: Leukemia, juvenile myelomonocytic (JMML) [MIM:607785]: An aggressive pediatric myelodysplastic syndrome/myeloproliferative disorder characterized by malignant transformation in the hematopoietic stem cell compartment with proliferation of differentiated progeny. Patients have splenomegaly, enlarged lymph nodes, rashes, and hemorrhages. {ECO:0000269|PubMed:17332249}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Noonan syndrome 6 (NS6) [MIM:613224]: A form of Noonan syndrome, a disease characterized by short stature, facial dysmorphic features such as hypertelorism, a downward eyeslant and low-set posteriorly rotated ears, and a high incidence of congenital heart defects and hypertrophic cardiomyopathy. Other features can include a short neck with webbing or redundancy of skin, deafness, motor delay, variable intellectual deficits, multiple skeletal defects, cryptorchidism, and bleeding diathesis. Individuals with Noonan syndrome are at risk of juvenile myelomonocytic leukemia, a myeloproliferative disorder characterized by excessive production of myelomonocytic cells. {ECO:0000269|PubMed:19966803}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: RAS-associated autoimmune leukoproliferative disorder (RALD) [MIM:614470]: A disorder of apoptosis, characterized by chronic accumulation of non-malignant lymphocytes, defective lymphocyte apoptosis, and an increased risk for the development of hematologic malignancies. {ECO:0000269|PubMed:17517660}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Melanocytic nevus syndrome, congenital (CMNS) [MIM:137550]: A syndrome characterized by congenital pigmentary skin lesions which can occur at any site and can cover most of the body surface. These lesions may or may not be hairy. Congenital melanocytic nevi are associated with neuromelanosis (the presence of melanin-producing cells within the brain parenchyma or leptomeninges). Less commonly they are associated with malignant melanoma in childhood, both in the skin and the central nervous system. CMNS patients also tend to have a characteristic facial appearance, including wide or prominent forehead, periorbital fullness, small short nose with narrow nasal bridge, round face, full cheeks, prominent premaxilla, and everted lower lip. {ECO:0000269|PubMed:18633438, ECO:0000269|PubMed:23392294}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Melanosis, neurocutaneous (NCMS) [MIM:249400]: A rare congenital disease characterized by the presence of giant or multiple melanocytic nevi on the skin, foci of melanin-producing cells within the brain parenchyma, and infiltration of leptomeninges by abnormal melanin deposits. Neurologic abnormalities include seizures, hydrocephalus, arachnoid cysts, tumors, and syringomyelia. Some patients may develop malignant melanoma. {ECO:0000269|PubMed:23392294}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Keratinocytic non-epidermolytic nevus (KNEN) [MIM:162900]: Epidermal nevi of the common, non-organoid and non- epidermolytic type are benign skin lesions and may vary in their extent from a single (usually linear) lesion to widespread and systematized involvement. They may be present at birth or develop early during childhood. {ECO:0000269|PubMed:22499344}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Thyroid cancer, non-medullary, 2 (NMTC2) [MIM:188470]: A form of non-medullary thyroid cancer (NMTC), a cancer characterized by tumors originating from the thyroid follicular cells. NMTCs represent approximately 95% of all cases of thyroid cancer and are classified into papillary, follicular, Hurthle cell, and anaplastic neoplasms. {ECO:0000269|PubMed:12727991}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.124
Intolerance Scores
- RVIS EVS
- 0.01
- RVIS percentile EVS
- 54.63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |