HRAS

protein-coding

HRas 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]

Previous symbols:
  • HRAS1

MANE transcript

NM_005343.4

Inheritance

AD

ClinVar variants

P:42U:272B:200

Top phenotype

Costello syndrome

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr11:532,242-537,321

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~5.1 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Costello syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0009026

Submitter: Orphanet

rhabdomyosarcomaMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0005212

Submitter: Genomics England PanelApp

Noonan syndrome-like disorder with loose anagen hairNO_KNOWN

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).

Costello syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0009026

Submitter: Labcorp Genetics (formerly Invitae)

Costello syndromeDEFINITIVE

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).

Costello syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0009026

Submitter: PanelApp Australia

Costello syndromeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0009026

Submitter: G2P

Costello syndromeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0009026

Submitter: Genomics England PanelApp

Clinical Genomic Database (CGD)

Costello syndromeAD

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

Refs: 907573; 8882404; 8834040; 9863604; 9521961; 10424828; 10449656; 10678668; 11857557; 11857556; 12210337; 12561057; 12605434; 16170316; 15940703; 16372351; 16329078; 16969868; 16443854; 17551924; 17412879; 17054105; 18042262; 18247425; 18302240; 19213030; 19288554; 19206176; 20301680; 20425820; 21438134; 21495179; 21834037; 22098123; 22261753; 22420426; 22488832; 22495831; 22495892; 22510203; 22887473; 22926243; 23429430; 23751039; 23813656; 23918324; 24057668Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HRAS variants in ClinVar

50 Conditions Cataloged
Costello syndromeTotal: 578
not providedTotal: 153
Cardiovascular phenotypeTotal: 112
not specifiedTotal: 109
HRAS-related disorderTotal: 47
Epidermal nevusTotal: 26
Linear nevus sebaceous syndromeTotal: 25
Malignant tumor of urinary bladderTotal: 23

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
174
clinvar
5
clinvar
182
missense
18
clinvar
22
clinvar
231
clinvar
16
clinvar
2
clinvar
289
nonsense
1
clinvar
12
clinvar
1
clinvar
14
start loss
0
frameshift
21
clinvar
1
clinvar
22
splice donor/acceptor (+/-2bp)
1
clinvar
5
clinvar
1
clinvar
7
Total19232721937514

Highest pathogenic variant AF is 0.0000047909766

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_005343.4RefSeqNP_005334.14MANE Select
ENST00000311189.8EnsemblENSP00000309845.74MANE Select
NM_001130442.3RefSeqNP_001123914.14Standard
NM_001318054.2RefSeqNP_001304983.13Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.51751220.6150.000008911232
Missense (PolyPhen)1840.1670.44813409
Synonymous-2.277453.01.400.00000405372
Loss of Function1.7238.370.3584.54e-790

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000880.000088rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumLowMedium
Primary ImmunodeficiencyMediumLowMedium
CancerMediumMediumMedium
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