HRAS
protein-codingHRas proto-oncogene, GTPase, the group of RAS type GTPase family
Gene summary
This gene belongs to the Ras oncogene family, whose members are related to the transforming genes of mammalian sarcoma retroviruses. The products encoded by these genes function in signal transduction pathways. These proteins can bind GTP and GDP, and they have intrinsic GTPase activity. This protein undergoes a continuous cycle of de- and re-palmitoylation, which regulates its rapid exchange between the plasma membrane and the Golgi apparatus. Mutations in this gene cause Costello syndrome, a disease characterized by increased growth at the prenatal stage, growth deficiency at the postnatal stage, predisposition to tumor formation, cognitive disability, skin and musculoskeletal abnormalities, distinctive facial appearance and cardiovascular abnormalities. Defects in this gene are implicated in a variety of cancers, including bladder cancer, follicular thyroid cancer, and oral squamous cell carcinoma. Multiple transcript variants, which encode different isoforms, have been identified for this gene. [provided by RefSeq, Jul 2008]
- HRAS1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~5.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0009026
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0005212
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0011899
Submitter: ClinGen
There has only been one study suggesting that patients with variants in HRAS have features consistent with Noonan-like syndrome with loose anagen hair (NS/LAH) (Bertola et al. 2017). This study identified five patients with sparse, loose anagen hair and p.Gly13Asp/p.Gly13Cys variants in HRAS. The authors note that no malignant tumors have been identified in these patients, however only one patient was older than 15 yrs (28 yrs) at the time of report, and it remains to be determined if the alteration of p.Gly13 in HRAS increases risk of tumor development. These patients did develop papillomata and vascular proliferation lesions as well as other features more consistent with Costello syndrome (CS), which led to the authors concluding that these cases expand the phenotypic spectrum of CS rather than support that HRAS causes NS/LAH. Therefore, the evidence for this association is Disputed. Of note, HRAS has been definitively associated with Costello syndrome. The ClinGen RASopathy Expert Panel found no evidence associating HRAS with Noonan syndrome (NS), NS with multiple lentigines, or cardiofaciocutaneous syndrome. This curation was approved by the ClinGen RASopathy Gene Curation Expert Panel on 7/25/18 (SOP Version 5).
Inheritance Pattern: AD
Disease ID:MONDO:0009026
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0009026
Submitter: ClinGen
There is a definitive association between alteration of the HRAS gene and a Costello syndrome (CS) phenotype. The maximum amount of scorable genetic evidence has been published showing de novo as well as non-de novo variants occur in HRAS in patients with CS (Alfieri et al., 2015; Aoki et al., 2005; Burkitt-Wright et al., 2012; Gripp et al., 2015; Hiippala et al., 2016; Lorenz et al., 2013; Xu, Wang, Lin, & Yu, 2015). Furthermore, the HRAS gene is the only gene that is definitively associated with CS (Rauen, 2007). The HRAS gene is also located in the Ras/MAPK pathway which is associated with the Costello phenotype (Aoki et al., 2016; Rauen, 2013). Finally, a mouse model with the p.Gly12Val variant in HRAS was found to possess CS specific features (Goodwin et al., 2014; Oba et al., 2018). Of note, HRAS has also been classified as disputed in association with Noonan syndrome (NS) with loose anagen hair. The ClinGen RASopathy Expert Panel found no evidence associating HRAS with NS, NS with multiple lentigines, or cardiofaciocutaneous syndrome. 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:0009026
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0009026
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0009026
Submitter: Genomics England PanelApp
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Craniofacial; Dental; Dermatologic; Musculoskeletal; Neurologic; Oncologic
Intervention: Cardiovascular; Oncologic
Rationale: The condition may be frequently clinically recognizable, but often includes cardiovascular manifestations, including structural anomalies, hypertrophic cardiomyopathy, and arrhythmias, as well as an elevated risk for malignancy, and surveillance and appropriate care may be beneficial
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to HRAS variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005343.4. 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 | 3 | 174 | 5 | 182 | ||
| missense | 18 | 22 | 231 | 16 | 2 | 289 |
| nonsense | 1 | 12 | 1 | 14 | ||
| start loss | 0 | |||||
| frameshift | 21 | 1 | 22 | |||
| splice donor/acceptor (+/-2bp) | 1 | 5 | 1 | 7 | ||
| Total | 19 | 23 | 272 | 193 | 7 | 514 |
Highest pathogenic variant AF is 0.0000047909766
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005334.1 | 4 | MANE Select | |
| Ensembl | ENSP00000309845.7 | 4 | MANE Select | |
| RefSeq | NP_001123914.1 | 4 | Standard | |
| RefSeq | NP_001304983.1 | 3 | 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)
- Focal adhesion - Homo sapiens (human)
Biological Process
- MAPK cascade
- positive regulation of protein phosphorylation
- stimulatory C-type lectin receptor signaling pathway
- endocytosis
- chemotaxis
Molecular Function
- GTPase activity
- protein binding
- GTP binding
- protein C-terminus binding
- GDP binding
Cellular Component
- Golgi membrane
- nucleus
- cytoplasm
- Golgi apparatus
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000451590
- Coding exons
- 4
- Length
- 5046
- Individuals with no LoFs
- 125711
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 10
- Defined
- 125721
- p
- 0.0000398
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.51 | 75 | 122 | 0.615 | 0.00000891 | 1232 |
| Missense (PolyPhen) | 18 | 40.167 | 0.44813 | 409 | ||
| Synonymous | -2.27 | 74 | 53.0 | 1.40 | 0.00000405 | 372 |
| Loss of Function | 1.72 | 3 | 8.37 | 0.358 | 4.54e-7 | 90 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| 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) | 0.000088 | 0.000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in the activation of Ras protein signal transduction (PubMed:22821884). Ras proteins bind GDP/GTP and possess intrinsic GTPase activity (PubMed:12740440, PubMed:14500341, PubMed:9020151). {ECO:0000269|PubMed:12740440, ECO:0000269|PubMed:14500341, ECO:0000269|PubMed:22821884, ECO:0000269|PubMed:9020151}.;
- Disease
- DISEASE: Costello syndrome (CSTLO) [MIM:218040]: A rare condition characterized by prenatally increased growth, postnatal growth deficiency, mental retardation, distinctive facial appearance, cardiovascular abnormalities (typically pulmonic stenosis, hypertrophic cardiomyopathy and/or atrial tachycardia), tumor predisposition, skin and musculoskeletal abnormalities. {ECO:0000269|PubMed:16170316, ECO:0000269|PubMed:16329078, ECO:0000269|PubMed:16443854, ECO:0000269|PubMed:17054105, ECO:0000269|PubMed:18039947, ECO:0000269|PubMed:18247425, ECO:0000269|PubMed:19995790}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Congenital myopathy with excess of muscle spindles (CMEMS) [MIM:218040]: Variant of Costello syndrome. {ECO:0000269|PubMed:17412879}. 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.; DISEASE: Note=Mutations which change positions 12, 13 or 61 activate the potential of HRAS to transform cultured cells and are implicated in a variety of human tumors. {ECO:0000269|PubMed:3670300}.; DISEASE: Bladder cancer (BLC) [MIM:109800]: A malignancy originating in tissues of the urinary bladder. It often presents with multiple tumors appearing at different times and at different sites in the bladder. Most bladder cancers are transitional cell carcinomas that begin in cells that normally make up the inner lining of the bladder. Other types of bladder cancer include squamous cell carcinoma (cancer that begins in thin, flat cells) and adenocarcinoma (cancer that begins in cells that make and release mucus and other fluids). Bladder cancer is a complex disorder with both genetic and environmental influences. {ECO:0000269|PubMed:6298635, ECO:0000269|PubMed:6844927}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Schimmelpenning-Feuerstein-Mims syndrome (SFM) [MIM:163200]: A disease characterized by sebaceous nevi, often on the face, associated with variable ipsilateral abnormalities of the central nervous system, ocular anomalies, and skeletal defects. Many oral manifestations have been reported, not only including hypoplastic and malformed teeth, and mucosal papillomatosis, but also ankyloglossia, hemihyperplastic tongue, intraoral nevus, giant cell granuloma, ameloblastoma, bone cysts, follicular cysts, oligodontia, and odontodysplasia. Sebaceous nevi follow the lines of Blaschko and these can continue as linear intraoral lesions, as in mucosal papillomatosis. {ECO:0000269|PubMed:22683711}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 1.00
Intolerance Scores
- LoFtool
- 0.205
- RVIS EVS
- -0.34
- RVIS percentile EVS
- 30.07
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.873
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |