RASA1

gene
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Also known as GAPCM-AVMp120GAPp120RASGAPp120

Summary

RASA1 (RAS p21 protein activator 1, HGNC:9871) is a protein-coding gene on chromosome 5q14.3, encoding Ras GTPase-activating protein 1 (P20936). GTPase-activating protein (GAP) that stimulates the intrinsic GTPase activity of Ras proteins, such as NRAS, facilitating their transition from the active GTP-bound state to the inactive GDP-bound state, thereby terminating Ras signaling. In precision oncology, RASA1 Loss-of-function confers sensitivity to Trametinib in Lung Non-small Cell Carcinoma (CIViC Level D). It is haploinsufficient (ClinGen: sufficient evidence).

The protein encoded by this gene is located in the cytoplasm and is part of the GAP1 family of GTPase-activating proteins. The gene product stimulates the GTPase activity of normal RAS p21 but not its oncogenic counterpart. Acting as a suppressor of RAS function, the protein enhances the weak intrinsic GTPase activity of RAS proteins resulting in the inactive GDP-bound form of RAS, thereby allowing control of cellular proliferation and differentiation. Mutations leading to changes in the binding sites of either protein are associated with basal cell carcinomas. Mutations also have been associated with hereditary capillary malformations (CM) with or without arteriovenous malformations (AVM) and Parkes Weber syndrome. Alternative splicing results in two isoforms where the shorter isoform, lacking the N-terminal hydrophobic region but retaining the same activity, appears to be abundantly expressed in placental but not adult tissues.

Source: NCBI Gene 5921 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): capillary malformation-arteriovenous malformation 1 (Definitive, GenCC) — +4 more curated relationships
  • GWAS associations: 7
  • Clinical variants (ClinVar): 400 total — 32 pathogenic, 7 likely-pathogenic
  • Phenotypes (HPO): 47
  • Precision-oncology evidence (CIViC): 1 curated variant–drug association
  • Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 2 cancer types
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_002890

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9871
Approved symbolRASA1
NameRAS p21 protein activator 1
Location5q14.3
Locus typegene with protein product
StatusApproved
AliasesGAP, CM-AVM, p120GAP, p120RASGAP, p120
Ensembl geneENSG00000145715
Ensembl biotypeprotein_coding
OMIM139150
Entrez5921

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000274376, ENST00000456692, ENST00000506290, ENST00000509953, ENST00000512763, ENST00000515800, ENST00000888488, ENST00000888489, ENST00000888490, ENST00000962098

RefSeq mRNA: 2 — MANE Select: NM_002890 NM_002890, NM_022650

CCDS: CCDS34200, CCDS47243

Canonical transcript exons

ENST00000274376 — 25 exons

ExonStartEnd
ENSE000010821488738939387389527
ENSE000011625728733134887331500
ENSE000015053288733326787333337
ENSE000015053298733250787332642
ENSE000020514678739080087391916
ENSE000022423288733797487338091
ENSE000034671458737639387376565
ENSE000034754078736334887363504
ENSE000034790758738682687386903
ENSE000034834418735315787353235
ENSE000034848398734921487349364
ENSE000035032898734667287346724
ENSE000035051778738371387383780
ENSE000035100218736981387369900
ENSE000035387968738530187385389
ENSE000035638738734129087341321
ENSE000035790868737839687378538
ENSE000035801628737688187377040
ENSE000035932598738050987380595
ENSE000036263458737211887372195
ENSE000036421718737973587379850
ENSE000036447958736255187362671
ENSE000036554778737484087374916
ENSE000036754978737416387374320
ENSE000038899728726788387268990

Expression profiles

Bgee: expression breadth ubiquitous, 298 present calls, max score 98.98.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.6003 / max 945.7019, expressed in 1808 samples.

FANTOM5 promoters (12 alternative TSS)

Promoter IDTPM avgSamples expressed
5745517.39401800
574642.0837334
574611.92581072
574581.3580696
574620.9450577
574570.5622335
574540.5032227
574560.2991128
574600.2630116
574590.198967

Top tissues by expression

301 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011598.98gold quality
placentaUBERON:000198798.07gold quality
choroid plexus epitheliumUBERON:000391197.69gold quality
Brodmann (1909) area 23UBERON:001355497.46gold quality
middle temporal gyrusUBERON:000277196.53gold quality
pigmented layer of retinaUBERON:000178296.32gold quality
retinaUBERON:000096696.29gold quality
skin of hipUBERON:000155496.02gold quality
tibiaUBERON:000097995.73gold quality
CA1 field of hippocampusUBERON:000388195.63gold quality
Brodmann (1909) area 46UBERON:000648395.62gold quality
parietal pleuraUBERON:000240095.61gold quality
pleuraUBERON:000097795.50gold quality
corpus epididymisUBERON:000435995.40gold quality
visceral pleuraUBERON:000240195.27gold quality
cervix squamous epitheliumUBERON:000692295.08gold quality
caput epididymisUBERON:000435895.01gold quality
tongue squamous epitheliumUBERON:000691994.90gold quality
oocyteCL:000002394.57gold quality
germinal epithelium of ovaryUBERON:000130494.49gold quality
entorhinal cortexUBERON:000272894.46gold quality
orbitofrontal cortexUBERON:000416794.37gold quality
periodontal ligamentUBERON:000826694.34gold quality
cauda epididymisUBERON:000436094.23gold quality
cranial nerve IIUBERON:000094194.15gold quality
mucosa of paranasal sinusUBERON:000503094.09gold quality
postcentral gyrusUBERON:000258194.01gold quality
mucosa of sigmoid colonUBERON:000499393.93gold quality
dorsal motor nucleus of vagus nerveUBERON:000287093.89gold quality
mammary ductUBERON:000176593.87gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-6701yes114.12
E-ANND-3yes9.93

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CIC, GATA4, JUN, MAFB, NR2E1, STAT3, TBP

miRNA regulators (miRDB)

126 targeting RASA1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-3163100.0077.238605
HSA-MIR-3134100.0066.43777
HSA-MIR-223-3P99.9970.141140
HSA-MIR-33A-5P99.9968.621055
HSA-MIR-33B-5P99.9968.581062
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-480399.9871.993117
HSA-MIR-548N99.9871.944170
HSA-MIR-548P99.9872.253784
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-807599.9767.20962
HSA-MIR-9-3P99.9670.882068
HSA-MIR-545-3P99.9570.742783
HSA-MIR-96-5P99.9572.802140
HSA-MIR-101-3P99.9475.032230
HSA-MIR-144-3P99.9473.982698
HSA-MIR-20699.9372.501893
HSA-MIR-1-3P99.9372.351914
HSA-MIR-145-5P99.9271.131836
HSA-MIR-5195-3P99.9270.921877

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

  • We show a novel alternative pathway of apoptosis in human primary cells that is mediated by transcriptionally dependent decreases in p53 and c-Myc and decreases in p21. (PMID:11751853)
  • N-terminal fragment generated by caspase cleavage protects cells in a Ras/PI3K/Akt-dependent manner that does not rely on NFkappa B activation (PMID:11847220)
  • mutual regulation of Ras and NF1-GAP is essential for normal neuronal differentiation (PMID:12730209)
  • p21Ras, hSOS1, and p120GAP are not involved in polycystic ovary disease (PMID:15010862)
  • The induction of p21 gene expression is mediated by PPARgamma ligands in lung carcinoma. (PMID:15041706)
  • ligation of CD40 on EC increased association of Ras with its effector molecules Raf, Rho, and PI3K. But, it was determined that only PI3K was functional for Ras-induced VEGF transcription. (PMID:15187129)
  • executioner caspases control the extent of their own activation by a feedback regulatory mechanism initiated by the partial cleavage of RasGAP that is crucial for cell survival under adverse conditions (PMID:15542850)
  • p52Shc couples tyrosine kinase receptors to Ras by recruiting Grb2/Sos complexes. (PMID:15688026)
  • an uncleavable N-terminal RasGAP fragment in insulin-secreting cells has a role in increasing resistance toward apoptotic stimuli without affecting glucose-induced insulin secretion (PMID:16046410)
  • These results demonstrate that integrin signaling through Arg activates p190 by promoting its association with p120, resulting in recruitment of p190 to the cell periphery where it inhibits Rho. (PMID:16971514)
  • novel mutation is decribed, which causes capillary malformation and limb enlargement in a patient from a family with vascular malformations (PMID:18327598)
  • the spectrum of clinical manifestations due to mutations in RASA1 is wider than previously thought and also includes typical CMs not associated with AVM/AVF. (PMID:18363760)
  • 42 novel RASA1 mutations and the associated phenotype in 44 families. (PMID:18446851)
  • RasGAP and Capns1 interaction in oncogenic Ras cells is involved in regulating migration and cell survival. (PMID:18761085)
  • found a mean Ras activation of 23.1% in cell lines with known constitutively activating ras mutations (PMID:18784923)
  • p120Ras-GAP binds the DLC1 Rho-GAP tumor suppressor protein and inhibits its RhoA GTPase and growth-suppressing activities. (PMID:19151751)
  • Data show that fibroblast, endothelial and carcinoma polarity during cell migration requires FAK and is associated with a complex between FAK, p120RasGAP and p190RhoGAP (p190A), leading to p190A tyrosine phosphorylation. (PMID:19435801)
  • CD200R inhibits the activation of human myeloid cells through direct recruitment of Dok2 and subsequent activation of RAS p21 protein activator 1. (PMID:19786546)
  • the monomeric intracellular plexin-B1 binds R-Ras but not H-Ras. These findings suggest that the monomeric form of the intracellular region is primed for GAP activity and extend a model for plexin activation. (PMID:19843518)
  • In a collaborative study, 5 index patients (2 females, 3 males) with spinal AVMs or AVFs and cutaneous multifocal capillary lesions were investigated for the RASA1 gene mutation. (PMID:20007727)
  • Sema4D/Plexin-B1 promotes the dephosphorylation and activation of PTEN through the R-Ras GAP activity, inducing growth cone collapse. (PMID:20610402)
  • miR-132 acts as an angiogenic switch by suppressing endothelial p120RasGAP expression. (PMID:20676106)
  • A novel synonymous mutation (c.1229 G > A [p.K420K]) of RASA1 was identified in a Chinese population with sporadic Sturge-Weber syndrome (PMID:20821215)
  • Ras mutation cooperates with beta-catenin activation to drive bladder tumourigenesis. (PMID:21368895)
  • Ca2+-dependent monomer and dimer formation switches CAPRI Protein between Ras GTPase-activating protein (GAP) and RapGAP activities (PMID:21460216)
  • An important role is revealed for p120 RasGAP (RASA1) as a transgenic regulator of CD4+CD8+ double-positive cell survival and positive selection in the thymus as well as naive T cell survival in the periphery. (PMID:21646295)
  • Cell adhesion to the substrate is necessary for RasGAP to bind Nck1. Cell detachment makes RasGAP incapable of associating with Nck1 and decreases RasGAP activity. (PMID:21664272)
  • Nck1 activates RasGAP by direct binding in the substrate-attached but not in the suspended cells. (PMID:21664272)
  • The results assign an unexpected role for p120RasGAP in the regulation of integrin traffic in cancer cells and reveal a new concept of competitive binding of Rab GTPases and GAP proteins to receptors as a regulatory mechanism in trafficking. (PMID:21768288)
  • multifocal capillary malformations is the key clinical finding to suggest a RASA1 mutation (PMID:22200646)
  • arguments against G3BP1 being a genuine RasGAP-binding partner (PMID:22205990)
  • An update of the associated phenotype variability in a family with hereditary capillary malformations caused by a mutation in the RASA1 gene. (PMID:22342634)
  • Ras and GTPase-activating protein (GAP) drive GTP into a precatalytic state as revealed by combining FTIR and biomolecular simulations (PMID:22949691)
  • capillary malformation-arteriovenous malformation syndrome; study reports a family with a novel mutation in the RASA1 gene - a truncating mutation in exon 11 of RASA1 (Q503X) (PMID:23158644)
  • MicroRNA-31 activates the RAS pathway and functions as an oncogenic MicroRNA by repressing RAS p21 GTPase activating protein 1 (RASA1) (PMID:23322774)
  • 14-3-3 negatively regulates the RGC downstream of the PI3-kinase/Akt signaling pathway (PMID:23386617)
  • The results of the present study indicate that P110, in combination with chemotherapeutics, is likely to represent a potential therapeutic strategy for cancer. (PMID:23447049)
  • RASA1 mutation is responsible for the aberrant lymphatic architecture and functional abnormalities, as visualized in the PKWS subject and in the animal model. (PMID:23650393)
  • results indicate that, mTOR, Bad, or Survivin are not required for p120 RasGAP fragment N to protect cells from cell death; conclude that downstream targets of Akt other than mTORC1, Bad, or survivin mediate fragment N-induced protection or that several Akt effectors can compensate for each other to induce the pro-survival fragment N-dependent responses (PMID:23826368)
  • Multifocal, small, round-to-oval, pinkish-to-red cutaneous capillary malformations are seen in more than 90% of people with RASA1 mutations. (PMID:23829194)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriorasa1aENSDARG00000035535
danio_reriorasa1bENSDARG00000073665
mus_musculusRasa1ENSMUSG00000021549
rattus_norvegicusRasa1ENSRNOG00000029185
drosophila_melanogastervapFBGN0003969

Paralogs (10): RASAL2 (ENSG00000075391), RASAL3 (ENSG00000105122), RASA4 (ENSG00000105808), RASAL1 (ENSG00000111344), DAB2IP (ENSG00000136848), RASA2 (ENSG00000155903), RASA4B (ENSG00000170667), RASA3 (ENSG00000185989), NF1 (ENSG00000196712), SYNGAP1 (ENSG00000197283)

Protein

Protein identifiers

Ras GTPase-activating protein 1P20936 (reviewed: P20936)

Alternative names: Ras p21 protein activator, p120GAP

All UniProt accessions (2): E9PGC0, P20936

UniProt curated annotations — full annotation on UniProt →

Function. GTPase-activating protein (GAP) that stimulates the intrinsic GTPase activity of Ras proteins, such as NRAS, facilitating their transition from the active GTP-bound state to the inactive GDP-bound state, thereby terminating Ras signaling.

Subunit / interactions. Interacts with SQSTM1. Interacts with SPSB1; the interaction does not promote degradation. Interacts with CAV2 (tyrosine phosphorylated form). Directly interacts with NCK1. Interacts with PDGFRB (tyrosine phosphorylated). Interacts (via SH2 domain) with the ‘Tyr-9’ phosphorylated form of PDPK1. Interacts with tyrosine-phosphorylated EPHB4.

Subcellular location. Cytoplasm.

Tissue specificity. In placental villi, detected only in the trophoblast layer (cytotrophoblast and syncytiotrophoblast). Not detected in stromal, endothelial or Hofbauer cells (at protein level).

Post-translational modifications. The N-terminus is blocked. Phosphorylated by SRC and LCK. The phosphorylation SRC inhibits its ability to stimulate the Ras-GTPase activity, whereas phosphorylation by LCK does not display any effect on stimulation activity.

Disease relevance. Mutations in the SH2 domain of RASA seem to be oncogenic and cause basal cell carcinomas. Capillary malformation-arteriovenous malformation 1 (CMAVM1) [MIM:608354] A disorder characterized by atypical capillary malformations that are multiple, small, round to oval in shape and pinkish red in color. These capillary malformations are associated with either arteriovenous malformation, arteriovenous fistula, or Parkes Weber syndrome. CMAVM1 inheritance is autosomal dominant. The disease is caused by variants affecting the gene represented in this entry.

Isoforms (4)

UniProt IDNamesCanonical?
P20936-11, Longyes
P20936-22, Short
P20936-33
P20936-44

RefSeq proteins (2): NP_002881, NP_072179 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000008C2_domDomain
IPR000980SH2Domain
IPR001452SH3_domainDomain
IPR001849PH_domainDomain
IPR001936RasGAP_domDomain
IPR008936Rho_GTPase_activation_protHomologous_superfamily
IPR011993PH-like_dom_sfHomologous_superfamily
IPR023152RasGAP_CSConserved_site
IPR035652RasGAP_SH3Domain
IPR035841RasGAP_N_SH2Domain
IPR035842RasGAP_C_SH2Domain
IPR035892C2_domain_sfHomologous_superfamily
IPR036028SH3-like_dom_sfHomologous_superfamily
IPR036860SH2_dom_sfHomologous_superfamily
IPR039360Ras_GTPaseFamily

Pfam: PF00017, PF00018, PF00168, PF00169, PF00616

UniProt features (94 total): strand 33, helix 28, sequence variant 8, turn 7, domain 6, splice variant 6, modified residue 3, chain 1, sequence conflict 1, site 1

Structure

Experimental structures (PDB)

15 structures.

PDBMethodResolution (Å)
2J05X-RAY DIFFRACTION1.5
6WAXX-RAY DIFFRACTION1.5
6WAYX-RAY DIFFRACTION1.5
1WERX-RAY DIFFRACTION1.6
6PXCX-RAY DIFFRACTION1.6
6PXBX-RAY DIFFRACTION1.75
2J06X-RAY DIFFRACTION1.8
8DGQX-RAY DIFFRACTION1.95
8BOSX-RAY DIFFRACTION2.1
4FSSX-RAY DIFFRACTION2.25
9BZ4X-RAY DIFFRACTION2.45
1WQ1X-RAY DIFFRACTION2.5
2GQISOLUTION NMR
2GSBSOLUTION NMR
2M51SOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P20936-F177.370.34

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 789 (arginine finger; crucial for gtp hydrolysis by stabilizing the transition state)

Post-translational modifications (3): 831, 1, 615

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-186763Downstream signal transduction
R-HSA-3928662EPHB-mediated forward signaling
R-HSA-5218921VEGFR2 mediated cell proliferation
R-HSA-5658442Regulation of RAS by GAPs
R-HSA-8849471PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases

MSigDB gene sets: 453 (showing top): PID_BCR_5PATHWAY, GOBP_MITOTIC_CYTOKINESIS, GOBP_NEGATIVE_REGULATION_OF_NEURON_APOPTOTIC_PROCESS, BORCZUK_MALIGNANT_MESOTHELIOMA_UP, GOBP_REGULATION_OF_PROTEIN_POLYMERIZATION, GOBP_REGULATION_OF_CELL_MORPHOGENESIS, TGCGCANK_UNKNOWN, PAL_PRMT5_TARGETS_UP, KEGG_MAPK_SIGNALING_PATHWAY, THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN, GOCC_RUFFLE, GOMF_GTPASE_BINDING, BIOCARTA_TPO_PATHWAY, CTATGCA_MIR153, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS

GO Biological Process (17): mitotic cytokinesis (GO:0000281), angiogenesis (GO:0001525), vasculogenesis (GO:0001570), negative regulation of cell-matrix adhesion (GO:0001953), negative regulation of cell adhesion (GO:0007162), signal transduction (GO:0007165), regulation of cell shape (GO:0008360), regulation of actin filament polymerization (GO:0030833), intracellular signal transduction (GO:0035556), negative regulation of apoptotic process (GO:0043066), negative regulation of neuron apoptotic process (GO:0043524), ephrin receptor signaling pathway (GO:0048013), blood vessel morphogenesis (GO:0048514), regulation of RNA metabolic process (GO:0051252), regulation of intracellular signal transduction (GO:1902531), regulation of GTPase activity (GO:0043087), system development (GO:0048731)

GO Molecular Function (8): phosphotyrosine residue binding (GO:0001784), GTPase activity (GO:0003924), GTPase activator activity (GO:0005096), signaling receptor binding (GO:0005102), potassium channel inhibitor activity (GO:0019870), GTPase binding (GO:0051020), protein binding (GO:0005515), enzyme binding (GO:0019899)

GO Cellular Component (4): ruffle (GO:0001726), cytoplasm (GO:0005737), cytosol (GO:0005829), plasma membrane (GO:0005886)

Reactome top-level categories

Rollup of top-5 pathways:

CategoryPathways
Signaling by PDGF1
EPH-Ephrin signaling1
VEGFA-VEGFR2 Pathway1
RAF/MAP kinase cascade1
Signaling by PTK61

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
blood vessel morphogenesis2
intracellular anatomical structure2
GTPase activity2
protein binding2
cellular anatomical structure2
mitotic cell cycle1
cytoskeleton-dependent cytokinesis1
mitotic cell cycle process1
anatomical structure formation involved in morphogenesis1
cell differentiation1
regulation of cell-matrix adhesion1
cell-matrix adhesion1
negative regulation of cell-substrate adhesion1
cell adhesion1
regulation of cell adhesion1
negative regulation of cellular process1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
regulation of cell morphogenesis1
regulation of biological quality1
regulation of actin polymerization or depolymerization1
actin filament polymerization1
regulation of protein polymerization1
signal transduction1
apoptotic process1
regulation of apoptotic process1
negative regulation of programmed cell death1
negative regulation of apoptotic process1
regulation of neuron apoptotic process1
neuron apoptotic process1
cell surface receptor protein tyrosine kinase signaling pathway1
blood vessel development1
tube morphogenesis1
RNA metabolic process1
regulation of nucleobase-containing compound metabolic process1
regulation of macromolecule metabolic process1
regulation of signal transduction1

Protein interactions and networks

STRING

4002 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RASA1G3BP1Q13283993
RASA1ARHGAP35Q9NRY4993
RASA1RALAP11233987
RASA1DOK1Q99704983
RASA1HRASP01112977
RASA1DOK2O60496963
RASA1PXNP49023943
RASA1RABIFP47224930
RASA1TSC2P49815928
RASA1CDC42P21181928
RASA1ARHGAP1Q07960913
RASA1TSC1Q92574913
RASA1EGFRP00533902
RASA1AKT1P31749901
RASA1SOS1Q07889891

IntAct

197 interactions, top by confidence:

ABTypeScore
DLC1RASA1psi-mi:“MI:0915”(physical association)0.710
RASA1DLC1psi-mi:“MI:0915”(physical association)0.710
RASA1NCK1psi-mi:“MI:0915”(physical association)0.670
NCK1RASA1psi-mi:“MI:0915”(physical association)0.670
RASA1NCK1psi-mi:“MI:0407”(direct interaction)0.670
RASA1PDGFRBpsi-mi:“MI:0914”(association)0.640
FYB1NCK2psi-mi:“MI:0914”(association)0.620
CAV1RASA1psi-mi:“MI:0407”(direct interaction)0.590
RASA1CAV1psi-mi:“MI:0914”(association)0.590
RASA1GAB1psi-mi:“MI:0914”(association)0.590
RASA1ERBB2psi-mi:“MI:0407”(direct interaction)0.590
RASA1ERBB2psi-mi:“MI:0915”(physical association)0.590
RASA1GAB1psi-mi:“MI:0407”(direct interaction)0.590

BioGRID (208): RASA1 (Affinity Capture-Western), RASA1 (Affinity Capture-MS), OLIG1 (Two-hybrid), RASA1 (Affinity Capture-Western), HRAS (Reconstituted Complex), HRAS (Affinity Capture-Western), RASA1 (Affinity Capture-MS), RASA1 (Affinity Capture-Western), RASA1 (Affinity Capture-RNA), RASA1 (Reconstituted Complex), DOK1 (Affinity Capture-Western), DOK2 (Affinity Capture-Western), RASA1 (Affinity Capture-MS), RASA1 (Affinity Capture-MS), RASA1 (Two-hybrid)

ESM2 similar proteins: A0A0G2JTR4, A1A4S6, A2AWA9, A4FUD6, A4II46, A6H6A9, A6QNS3, A6QQZ7, O60890, P09851, P0CAX5, P20936, P23727, P26450, P27986, P50904, Q08DP6, Q12979, Q5R372, Q5R5M3, Q5R685, Q5R6F2, Q5R8I6, Q5RCC1, Q5RCW6, Q5SSL4, Q5T2T1, Q5U2Y3, Q5ZJ17, Q5ZLX4, Q5ZMW5, Q62696, Q63787, Q6Y5D8, Q6ZQ82, Q7YQL5, Q7YQL6, Q8AVG0, Q8BPU7, Q8K0F1

Diamond homologs: A0A8I3NFE2, A0FI79, A0JNB0, A1Y2K1, A6QLK6, B2RZ59, B5KFD7, D3ZGS3, D7PF45, F1RDG9, G5ECJ6, O14306, O14796, O15357, O35324, O60880, O88890, O88900, P00519, P00520, P00521, P00522, P03949, P06239, P06241, P09851, P0CE43, P10447, P17713, P20936, P29350, P29351, P32019, P34370, P39688, P42684, P42685, P42686, P50904, P53356

SIGNOR signaling

7 interactions.

AEffectBMechanism
PDGFRBup-regulatesRASA1binding
EGFRunknownRASA1phosphorylation
hsa-miR-31-5p“down-regulates quantity by repression”RASA1“post transcriptional regulation”
RASA1down-regulatesHRASbinding
EPHB2up-regulatesRASA1binding
SRCdown-regulatesRASA1phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 72 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Signaling by ERBB2 ECD mutants669.5×1e-08
Constitutive Signaling by EGFRvIII561.5×8e-07
Signaling by ERBB2 KD Mutants858.3×1e-10
PI3K events in ERBB2 signaling557.9×1e-06
Signaling by ERBB2 TMD/JMD mutants757.4×3e-09
GRB2 events in ERBB2 signaling554.7×1e-06
SHC1 events in ERBB2 signaling649.2×1e-07
Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants549.2×2e-06

GO biological processes:

GO termPartnersFoldFDR
epidermal growth factor receptor signaling pathway831.5×7e-08
cell surface receptor protein tyrosine kinase signaling pathway1027.6×3e-09
ephrin receptor signaling pathway527.3×8e-05
cellular response to epidermal growth factor stimulus525.2×1e-04
epithelial cell proliferation524.8×1e-04
positive regulation of epithelial cell proliferation623.3×2e-05
insulin receptor signaling pathway621.1×3e-05
protein autophosphorylation920.8×7e-08

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 2 cancer types — HNSC, LUSC.

Clinical variants and AI predictions

ClinVar

400 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic32
Likely pathogenic7
Uncertain significance207
Likely benign113
Benign4

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1075206NM_002890.3(RASA1):c.172_173del (p.Ala58fs)Pathogenic
1075680NM_002890.3(RASA1):c.442dup (p.Ala148fs)Pathogenic
1354503NM_002890.3(RASA1):c.538del (p.Gln180fs)Pathogenic
1451377NC_000005.9:g.(?86564269)(86686700_?)delPathogenic
1457368NC_000005.9:g.(?86564269)(86659341_?)delPathogenic
1477458NC_000005.9:g.(?86633771)(86659341_?)delPathogenic
1527177GRCh37/hg19 5q14.3(chr5:86426877-86614352)Pathogenic
15999NM_002890.3(RASA1):c.475_476del (p.Leu159fs)Pathogenic
1992410NM_002890.2:c.540-406_692+21735delPathogenic
2001480NM_002890.3(RASA1):c.474dup (p.Leu159fs)Pathogenic
2001727NM_002890.3(RASA1):c.132_152delinsACAGCGAAACTCCATCTCTCAAAAAAAAAAAAAAAAAAAAAGAAGTCTACTAAAAACAGTTTTTTTTAACTACAATATCCTAAATATACCTAATTTAGTTATAAACTAGCATAAGACTAGATTCTTTCAGTATGAAAAGTT (p.Ala45_Gly51delinsGlnArgAsnSerIleSerGlnLysLysLysLysLysLysArgSerLeuLeuLysThrValPhePheAsnTyrAsnIleLeuAsnIleProAsnLeuValIleAsnTer)Pathogenic
2042873NM_002890.3(RASA1):c.78del (p.Ser27fs)Pathogenic
2051636NM_002890.3(RASA1):c.539+4A>GPathogenic
2115938NM_002890.3(RASA1):c.539+4dupPathogenic
2195273NM_002890.3(RASA1):c.383_384del (p.Leu128fs)Pathogenic
2424564NC_000005.9:g.(?86564269)(86564827_?)delPathogenic
2732232NM_002890.3(RASA1):c.496G>T (p.Glu166Ter)Pathogenic
2746283NM_002890.3(RASA1):c.426C>G (p.Tyr142Ter)Pathogenic
2877034NM_002890.3(RASA1):c.434_451delinsA (p.Pro145fs)Pathogenic
2893369NM_002890.3(RASA1):c.402del (p.Pro136fs)Pathogenic
3246331NC_000005.9:g.(?86669960)(86670753_?)delPathogenic
3391888GRCh37/hg19 5q14.3(chr5:86011540-86616649)x1Pathogenic
3659038NM_002890.3(RASA1):c.231_232del (p.Ala78fs)Pathogenic
3660323NM_002890.3(RASA1):c.217G>T (p.Gly73Ter)Pathogenic
4279976NM_002890.3(RASA1):c.463G>T (p.Glu155Ter)Pathogenic
452663NM_002890.3(RASA1):c.297del (p.Ala100fs)Pathogenic
4724217NM_002890.3(RASA1):c.117dup (p.Ala40fs)Pathogenic
503721NM_002890.3(RASA1):c.261_262del (p.Gly89fs)Pathogenic
811221NM_002890.3(RASA1):c.431_438del (p.Pro144fs)Pathogenic
952905NM_002890.3(RASA1):c.365C>A (p.Ser122Ter)Pathogenic

SpliceAI

4926 predictions. Top by Δscore:

VariantEffectΔscore
5:87268991:G:GGdonor_gain1.0000
5:87331344:CTAG:Cacceptor_loss1.0000
5:87331345:TAGG:Tacceptor_loss1.0000
5:87331346:A:AGacceptor_gain1.0000
5:87331346:AG:Aacceptor_gain1.0000
5:87331346:AGGT:Aacceptor_gain1.0000
5:87331346:AGGTG:Aacceptor_gain1.0000
5:87331347:G:Aacceptor_gain1.0000
5:87331347:G:GTacceptor_gain1.0000
5:87331347:GGT:Gacceptor_gain1.0000
5:87331347:GGTG:Gacceptor_gain1.0000
5:87331347:GGTGG:Gacceptor_gain1.0000
5:87331405:G:Tdonor_gain1.0000
5:87331499:AGG:Adonor_loss1.0000
5:87331501:G:GGdonor_gain1.0000
5:87331501:GTA:Gdonor_loss1.0000
5:87331502:T:Adonor_loss1.0000
5:87332505:A:AGacceptor_gain1.0000
5:87332506:G:GGacceptor_gain1.0000
5:87333256:AT:Aacceptor_gain1.0000
5:87333257:T:TAacceptor_gain1.0000
5:87333265:A:AGacceptor_gain1.0000
5:87333266:G:GGacceptor_gain1.0000
5:87333266:GCCA:Gacceptor_gain1.0000
5:87337972:A:AGacceptor_gain1.0000
5:87337973:G:GGacceptor_gain1.0000
5:87337973:GTTT:Gacceptor_gain1.0000
5:87338092:G:GAdonor_loss1.0000
5:87338093:TAAGT:Tdonor_loss1.0000
5:87341322:G:GGdonor_gain1.0000

AlphaMissense

6849 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:87331349:T:AW181R1.000
5:87331349:T:CW181R1.000
5:87331359:G:AG184E1.000
5:87331365:T:CL186P1.000
5:87331371:G:CR188T1.000
5:87331372:A:CR188S1.000
5:87331372:A:TR188S1.000
5:87331389:G:CR194P1.000
5:87331392:T:AL195H1.000
5:87331392:T:CL195P1.000
5:87331418:T:GY204D1.000
5:87331422:T:AL205H1.000
5:87331422:T:CL205P1.000
5:87331425:T:AI206K1.000
5:87331428:G:CR207T1.000
5:87331428:G:TR207I1.000
5:87331429:A:CR207S1.000
5:87331429:A:TR207S1.000
5:87331461:T:AL218H1.000
5:87331461:T:CL218P1.000
5:87331461:T:GL218R1.000
5:87331463:T:CS219P1.000
5:87331493:C:GH229D1.000
5:87331495:T:AH229Q1.000
5:87331495:T:GH229Q1.000
5:87331496:T:CF230L1.000
5:87331497:T:CF230S1.000
5:87331498:T:AF230L1.000
5:87331498:T:GF230L1.000
5:87331500:G:TR231M1.000

dbSNP variants (sampled 300 via entrez): RS1000035296 (5:87332782 A>G,T), RS1000081869 (5:87267702 A>C,G), RS1000119777 (5:87347379 G>A,T), RS1000123902 (5:87314405 G>A,C), RS1000125560 (5:87378098 T>G), RS1000128628 (5:87302530 T>C,G), RS1000139410 (5:87331770 A>C,T), RS1000158306 (5:87323455 G>A,C), RS1000192507 (5:87351682 CCTGA>C), RS1000224192 (5:87374351 T>C), RS1000324352 (5:87357887 T>C), RS1000359888 (5:87333855 C>G), RS1000359906 (5:87271216 C>T), RS1000386220 (5:87285158 C>T), RS1000412441 (5:87318675 C>G,T)

Disease associations

OMIM: gene MIM:139150 | disease phenotypes: MIM:605462, MIM:608354, MIM:608355, MIM:123880

GenCC curated gene-disease

DiseaseClassificationInheritance
capillary malformation-arteriovenous malformation 1DefinitiveAutosomal dominant
capillary malformation-arteriovenous malformation syndromeSupportiveAutosomal dominant
Parkes Weber syndromeSupportiveAutosomal dominant
Noonan syndromeDisputed EvidenceAutosomal dominant
telangiectasia, hereditary hemorrhagic, type 1No Known Disease RelationshipAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
Noonan syndromeDisputedAD

Mondo (7): basal cell carcinoma, susceptibility to, 1 (MONDO:0011556), capillary malformation-arteriovenous malformation syndrome (MONDO:0012016), capillary malformation-arteriovenous malformation 1 (MONDO:0020783), Gorham-Stout disease (MONDO:0007414), Noonan syndrome (MONDO:0018997), telangiectasia, hereditary hemorrhagic, type 1 (MONDO:0008535), (MONDO:0012017)

Orphanet (4): Capillary malformation-arteriovenous malformation (Orphanet:137667), RASA1-related capillary malformation-arteriovenous malformation (Orphanet:693907), Gorham-Stout disease (Orphanet:73), Parkes Weber syndrome (Orphanet:90307)

HPO phenotypes

47 total (30 of 47 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000016Urinary retention
HP:0000079Abnormality of the urinary system
HP:0000100Nephrotic syndrome
HP:0001722High-output congestive heart failure
HP:0001892Abnormal bleeding
HP:0002138Subarachnoid hemorrhage
HP:0002196Myelopathy
HP:0002315Headache
HP:0002390Spinal arteriovenous malformation
HP:0002408Cerebral arteriovenous malformation
HP:0002617Vascular dilatation
HP:0002619Varicose veins
HP:0002671Basal cell carcinoma
HP:0002814Abnormality of the lower limb
HP:0002817Abnormality of the upper limb
HP:0002936Distal sensory impairment
HP:0003418Back pain
HP:0003474Somatic sensory dysfunction
HP:0004947Arteriovenous fistula
HP:0004948Vascular tortuosity
HP:0005306Capillary hemangioma
HP:0005521Disseminated intravascular coagulation
HP:0006489Abnormal femoral metaphysis morphology
HP:0007340Lower limb muscle weakness
HP:0007394Prominent superficial blood vessels
HP:0007461Hemangiomatosis
HP:0008968Muscle hypertrophy of the lower extremities
HP:0010484Hypertrophy of the upper limb
HP:0010550Paraplegia

GWAS associations

7 associations (top):

StudyTraitp-value
GCST000922_1Openness2.000000e-06
GCST001850_35Major depressive disorder4.000000e-06
GCST002886_1Prostate cancer aggressiveness6.000000e-09
GCST006976_58Macular thickness4.000000e-10
GCST007576_417Chronotype5.000000e-10
GCST007576_47Chronotype4.000000e-11
GCST009379_40Type 2 diabetes2.000000e-08

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0007914openness measurement
EFO:0006999cancer aggressiveness measurement
EFO:0007000Gleason score measurement
EFO:0008328chronotype measurement

MeSH disease descriptors (2)

DescriptorNameTree numbers
D009634Noonan SyndromeC05.660.207.690; C14.240.400.787; C14.280.400.787; C16.131.240.400.784; C16.131.621.207.690; C17.300.690
C564254Capillary Malformation-Arteriovenous Malformation (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

Clinical evidence (CIViC)

Drug × variant × indication: 1 predictive associations from 1 curated evidence items.

VariantTherapyIndicationEffectLevelCIViC
RASA1 Loss-of-functionTrametinibLung Non-small Cell CarcinomaSensitivity/ResponseCIViC DEID5994

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

61 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Faffects cotreatment, decreases expression, increases expression2
bisphenol Aaffects cotreatment, decreases methylation, increases expression2
Benzo(a)pyrenedecreases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression2
Cadmium Chloridedecreases expression, increases abundance, increases expression2
aristolochic acid Idecreases expression1
taxifolindecreases expression1
triphenyl phosphateaffects expression1
pyrogallol 1,3-dimethyl etherincreases expression, affects cotreatment, affects localization, decreases expression1
arseniteaffects binding, decreases reaction1
sodium arseniteincreases expression1
cobaltous chloridedecreases expression1
potassium chromate(VI)decreases expression1
S-(1,2-dichlorovinyl)cysteinedecreases expression, affects response to substance, increases expression, affects cotreatment1
di-n-butylphosphoric acidaffects expression1
rofecoxibaffects expression1
CP 31398increases expression1
bisphenol Bincreases expression1
abrinedecreases expression1
asparanin Adecreases expression1
jinfukangdecreases expression, increases reaction1
7-(benzylamino)-1,3,4,8-tetrahydropyrrolo(4,3,2-de)quinolin-8(1H)-onedecreases expression1
Irinotecandecreases expression1
Temozolomidedecreases expression1
Sunitinibincreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Acetaminophendecreases expression1
Aerosolsincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicincreases methylation1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E2IIHAP1 RASA1 (-)Cancer cell lineMale

Clinical trials (associated diseases)

39 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT02389959PHASE4COMPLETEDIntranasal Bevacizumab for HHT-Related Epistaxis
NCT04999618PHASE4COMPLETEDA New Approach in Laser Surgery Using the Regenerative Solution in Children Diagnosed With Vascular Pathology
NCT00452725PHASE3COMPLETEDEffect of MAXOMAT ® on the Growth of Small Children to NOONAN’s Syndrome
NCT01529840PHASE3COMPLETEDSomatropin Effect on Linear Growth and Final Height in Subjects With Noonan Syndrome
NCT01529944PHASE3COMPLETEDGenetic Testing of Noonan Subjects Previously Treated With Norditropin®. An Extension to Trial GHNOO-1658
NCT01927861PHASE3COMPLETEDInvestigating the Long-term Efficacy and Safety of Two Doses of NN-220 (Somatropin) in Short Stature Due to Noonan Syndrome
NCT02713945PHASE3COMPLETEDTreatment With HMG-COA Reductase Inhibitor of Growth and Bone Abnormalities in Children With Noonan Syndrome
NCT05723835PHASE3ACTIVE_NOT_RECRUITINGA Research Study Looking at How Safe Somapacitan is and How Well it Works in Children Who Need Help to Grow - REAL 9
NCT00351221PHASE2TERMINATEDResearch Study Using Recombinant Human Insulin-Like Growth Factor-1/Recombinant Human Insulin-Like Growth Factor Binding Protein-3 for Children With Noonan Syndrome
NCT06555237PHASE2RECRUITINGMEK Inhibitors for the Treatment of Hypertrophic Cardiomyopathy in Patients With RASopathies
NCT06668805PHASE2RECRUITINGA Study of Vosoritide in Children With Noonan Syndrome With Inadequate Growth During or After Human Growth Hormone Treatment
NCT01314274PHASE2COMPLETEDIntranasal Submucosal Bevacizumab for Epistaxis in Hereditary Hemorrhagic Telangiectasia (HHT)
NCT00960128Not specifiedCOMPLETEDObservational Prospective Study on Patients Treated With Norditropin®
NCT02486731Not specifiedCOMPLETEDHormonal Sensitivity in Patients With Noonan and LEOPARD Syndromes
NCT03435627Not specifiedCOMPLETEDPost Marketing Surveillance on Long-term Use With Norditropin® (Short Stature Due to Noonan Syndrome)
NCT04395495Not specifiedRECRUITINGRASopathy Biorepository
NCT04463316Not specifiedRECRUITINGGROWing Up With Rare GENEtic Syndromes
NCT04888936Not specifiedRECRUITINGClinical, Genetic, and Epidemiologic Study of Children and Adults With RASopathies
NCT05202210Not specifiedRECRUITINGConstitution of a Biological Collection to Study the Pathophysiology in Noonan Syndrome
NCT05308927Not specifiedENROLLING_BY_INVITATIONFrench Registry of Children Treated With Norditropin® for Short Stature Associated With Noonan Syndrome
NCT05361811Not specifiedRECRUITINGAcceptance and Commitment Therapy for Caregivers of Children With a RASopathy: An Internal Pilot Feasibility Study and Follow-up Randomized Controlled Trial
NCT05761314Not specifiedRECRUITINGSolid Tumors in RASopathies
NCT06267807Not specifiedCOMPLETEDLymphatic Phenotype in Noonan Syndrome Spectrum Disorders
NCT06331117Not specifiedUNKNOWNEffect of RAS/MAPK Pathway Hyperactivation on Growth’ and Bone’ Profile of the RASopathies
NCT06355622Not specifiedUNKNOWNPrevalence and Characterization of Pain in RASopathies
NCT06550635Not specifiedCOMPLETEDJoint and Hematologic Disorders of Noonan Syndrome: French Descriptive Cross-sectional Study
NCT06938542Not specifiedENROLLING_BY_INVITATIONPalliative Care Needs of Children With Rare Diseases and Their Families
NCT07259135Not specifiedNOT_YET_RECRUITINGLink Between Abnormal Bleeding and Coagulation Disorders in Noonan Syndromes
NCT07336394Not specifiedRECRUITINGPrecision Diagnosis and Risk Stratification of Rare Cardiomyopathies Based on Novel Cardiac Magnetic Resonance Techniques
NCT07464821Not specifiedRECRUITINGNational Multicentre Study on Lipid Profile in Noonan Syndrome and Related Disorders: Trends by Age, Gender and Genotype
NCT03850964PHASE2/PHASE3ACTIVE_NOT_RECRUITINGEffects of Pazopanib on Hereditary Hemorrhagic Telangiectasia Related Epistaxis and Anemia (Paz)
NCT04150822Not specifiedACTIVE_NOT_RECRUITINGCHORUS - Comprehensive HHT Outcomes Registry of the United States (Formerly OUR HHT Registry)
NCT05550376Not specifiedCOMPLETEDGenotype-phenotype Association in Hereditary Hemorrhagic Telangiectasia
NCT06039124Not specifiedCOMPLETEDSubsequent Bevacizumab Treatment in Patients With HHT. Follow up BABH
NCT06266624Not specifiedACTIVE_NOT_RECRUITINGTourniquet-Test in HHT
NCT06573723Not specifiedRECRUITINGInstitutional Registry of Rare Diseases
NCT02399527Not specifiedRECRUITINGLymphatic Anomalies Registry for the Assessment of Outcome Data
NCT02744027Not specifiedCOMPLETEDImaging of Lymphatic Anomalies
NCT03001180Not specifiedRECRUITINGIdentification of Biomarkers for Patients with Vascular Anomalies