RASA3

gene
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Also known as GAP1IP4BPGAPIII

Summary

RASA3 (RAS p21 protein activator 3, HGNC:20331) is a protein-coding gene on chromosome 13q34, encoding Ras GTPase-activating protein 3 (Q14644). Inhibitory regulator of the Ras-cyclic AMP pathway.

This gene encodes a protein that binds inositol 1,3,4,5-tetrakisphosphate and stimulates the GTPase activity of Ras p21. This protein functions as a negative regulator of the Ras signalling pathway. It is localized to the cell membrane via a pleckstrin homology (PH) domain in the C-terminal region. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 22821 — RefSeq curated summary.

At a glance

  • GWAS associations: 10
  • Clinical variants (ClinVar): 165 total — 1 pathogenic, 1 likely-pathogenic
  • MANE Select transcript: NM_007368

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20331
Approved symbolRASA3
NameRAS p21 protein activator 3
Location13q34
Locus typegene with protein product
StatusApproved
AliasesGAP1IP4BP, GAPIII
Ensembl geneENSG00000185989
Ensembl biotypeprotein_coding
OMIM605182
Entrez22821

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000334062, ENST00000542651, ENST00000881265, ENST00000881266, ENST00000912835, ENST00000947915, ENST00000947916, ENST00000947917

RefSeq mRNA: 3 — MANE Select: NM_007368 NM_001320821, NM_001320822, NM_007368

CCDS: CCDS32016

Canonical transcript exons

ENST00000334062 — 24 exons

ExonStartEnd
ENSE00001334925113981675113981858
ENSE00001334926113992485113992588
ENSE00001334928113996531113996739
ENSE00001334932113999585113999667
ENSE00001334935114000826114000932
ENSE00001334936114007533114007606
ENSE00001334938114009387114009464
ENSE00001334940114011171114011248
ENSE00001334941114013142114013248
ENSE00001334942114015209114015332
ENSE00001334944114016197114016271
ENSE00001334946114017237114017351
ENSE00001334956114041000114041094
ENSE00001334957114052052114052155
ENSE00001603051113977783113979422
ENSE00001912227114132435114132623
ENSE00003514006114021404114021508
ENSE00003517174114018104114018252
ENSE00003560806114024279114024355
ENSE00003600219114073720114073837
ENSE00003621816114027389114027461
ENSE00003624165114027847114027927
ENSE00003628538114018763114018919
ENSE00003683454114029811114029887

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 96.15.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.5094 / max 362.0558, expressed in 1765 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
13840722.54691758
1384050.8437499
1384060.8288480
1383880.132552
1383960.102754
1383890.054832

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009496.15gold quality
stromal cell of endometriumCL:000225592.74gold quality
leukocyteCL:000073892.64gold quality
sural nerveUBERON:001548892.33gold quality
monocyteCL:000057692.32gold quality
bloodUBERON:000017890.83gold quality
subcutaneous adipose tissueUBERON:000219090.38gold quality
lymph nodeUBERON:000002989.88gold quality
adipose tissueUBERON:000101389.64gold quality
right uterine tubeUBERON:000130289.38gold quality
tibial nerveUBERON:000132388.98gold quality
omental fat padUBERON:001041488.70gold quality
endocervixUBERON:000045888.64gold quality
vermiform appendixUBERON:000115488.27gold quality
mucosa of stomachUBERON:000119986.99gold quality
temporal lobeUBERON:000187186.70gold quality
amygdalaUBERON:000187686.68gold quality
ascending aortaUBERON:000149686.66gold quality
thoracic aortaUBERON:000151586.62gold quality
spleenUBERON:000210686.50gold quality
primary visual cortexUBERON:000243686.48gold quality
lower esophagus muscularis layerUBERON:003583386.47gold quality
thoracic mammary glandUBERON:000520086.41gold quality
lower esophagusUBERON:001347386.40gold quality
right frontal lobeUBERON:000281086.33gold quality
Ammon’s hornUBERON:000195486.10gold quality
descending thoracic aortaUBERON:000234586.04gold quality
left uterine tubeUBERON:000130386.02gold quality
ectocervixUBERON:001224985.85gold quality
C1 segment of cervical spinal cordUBERON:000646985.81gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.70
E-CURD-119yes4.40

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

37 targeting RASA3, 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-4682100.0068.891258
HSA-MIR-340-5P100.0072.504437
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-139-5P99.8069.501399
HSA-MIR-204-5P99.7971.622439
HSA-MIR-211-5P99.7971.652440
HSA-MIR-494-3P99.7071.452795
HSA-MIR-451699.6167.783390
HSA-MIR-3120-3P99.5470.282669
HSA-MIR-6507-5P99.3670.462524
HSA-MIR-1211399.3267.541072
HSA-MIR-6731-5P99.2867.422375
HSA-MIR-808599.2867.562362
HSA-MIR-450499.1069.141328
HSA-MIR-129498.9169.261030
HSA-MIR-998698.9169.281024
HSA-MIR-4716-5P98.8268.571168
HSA-MIR-429798.7766.952013
HSA-MIR-758-3P98.4268.601122
HSA-MIR-4691-5P98.4166.771343
HSA-MIR-6792-3P98.4166.861359
HSA-MIR-5088-3P98.2966.631310
HSA-MIR-6771-3P98.2066.53971
HSA-MIR-4769-3P97.9568.171002
HSA-MIR-6817-5P97.9567.861026
HSA-MIR-5581-5P97.9166.50965
HSA-MIR-466097.7967.441328
HSA-MIR-194-3P97.3665.961027
HSA-MIR-10398-5P97.1264.941051
HSA-MIR-335-5P97.1068.121022

Literature-anchored findings (GeneRIF, showing 6)

  • role in intracellular calcium homeostasis (PMID:12356770)
  • model in which the Ras GAP-related domain of GAP1(IP4BP) functions to stabilize the switch II region of Rap1, allowing stabilization of the transition state during GTP hydrolysis initiated by the arginine finger (PMID:19433443)
  • the function of RASA3 during megakaryopoiesis, megakaryocyte adhesion and migration as well as integrin signaling has been reported. (PMID:25294679)
  • these results support an important role for Rasa3 in PI3K-dependent integrin alphaIIbbeta3-mediated outside-in signaling and cell spreading. (PMID:27903653)
  • Rasa3 is a critical regulator of Rap1 in endothelial cells which controls adhesions properties and vascular lumen integrity; its specific endothelial cell inactivation results in occluded blood vessels, hemorrhages and early embryonic death in mouse, mimicking thus the Rasa3-/- mouse phenotype. (PMID:29381707)
  • GAP1IP4BP is an inositol 1,3,4,5-tetrakisphosphate regulated plasma membrane associated Ras and Rap GAP. Membrane association results from its PH domain binding phosphatidylinositol 4,5-bisphosphate. (PMID:7637787)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriorasa3ENSDARG00000063371
mus_musculusRasa3ENSMUSG00000031453
rattus_norvegicusRasa3ENSRNOG00000017671
drosophila_melanogasterRasGAP1FBGN0004390
drosophila_melanogasterraskolFBGN0261570
caenorhabditis_elegansWBGENE00001515
caenorhabditis_elegansWBGENE00001516

Paralogs (10): RASAL2 (ENSG00000075391), RASAL3 (ENSG00000105122), RASA4 (ENSG00000105808), RASAL1 (ENSG00000111344), DAB2IP (ENSG00000136848), RASA1 (ENSG00000145715), RASA2 (ENSG00000155903), RASA4B (ENSG00000170667), NF1 (ENSG00000196712), SYNGAP1 (ENSG00000197283)

Protein

Protein identifiers

Ras GTPase-activating protein 3Q14644 (reviewed: Q14644)

Alternative names: GAP1(IP4BP), Ins P4-binding protein

All UniProt accessions (1): Q14644

UniProt curated annotations — full annotation on UniProt →

Function. Inhibitory regulator of the Ras-cyclic AMP pathway. Binds inositol tetrakisphosphate (IP4) with high affinity. Might be a specific IP4 receptor.

Subcellular location. Cell membrane.

Isoforms (2)

UniProt IDNamesCanonical?
Q14644-11yes
Q14644-22

RefSeq proteins (3): NP_001307750, NP_001307751, NP_031394* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000008C2_domDomain
IPR001562Znf_Btk_motifConserved_site
IPR001849PH_domainDomain
IPR001936RasGAP_domDomain
IPR008936Rho_GTPase_activation_protHomologous_superfamily
IPR011993PH-like_dom_sfHomologous_superfamily
IPR023152RasGAP_CSConserved_site
IPR035892C2_domain_sfHomologous_superfamily
IPR037774RASA3_PHDomain
IPR039360Ras_GTPaseFamily

Pfam: PF00168, PF00169, PF00616, PF00779

UniProt features (23 total): modified residue 6, binding site 4, domain 4, mutagenesis site 3, initiator methionine 1, chain 1, site 1, splice variant 1, sequence conflict 1, zinc finger region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q14644-F184.790.51

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): 371 (arginine finger; crucial for gtp hydrolysis by stabilizing the transition state)

Ligand- & substrate-binding residues (4): 709; 687; 698; 699

Post-translational modifications (6): 2, 66, 77, 110, 809, 833

Mutagenesis-validated functional residues (3):

PositionPhenotype
599no binding to ip4 and loss of plasma membrane localization.
600no binding to ip4 and loss of plasma membrane localization.
601no binding to ip4 and loss of plasma membrane localization.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-5658442Regulation of RAS by GAPs

MSigDB gene sets: 252 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_DN, GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, GOBP_PLATELET_ACTIVATION, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOBP_NEGATIVE_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_WOUND_HEALING, chr13q34, GOBP_RAS_PROTEIN_SIGNAL_TRANSDUCTION, SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_DN, ATTCTTT_MIR186, TGACATY_UNKNOWN, MYB_Q3, ABBUD_LIF_SIGNALING_1_UP, RYTTCCTG_ETS2_B

GO Biological Process (7): signal transduction (GO:0007165), platelet activation (GO:0030168), intracellular signal transduction (GO:0035556), negative regulation of Ras protein signal transduction (GO:0046580), regulation of intracellular signal transduction (GO:1902531), response to stress (GO:0006950), regulation of GTPase activity (GO:0043087)

GO Molecular Function (4): GTPase activator activity (GO:0005096), calcium channel regulator activity (GO:0005246), zinc ion binding (GO:0008270), metal ion binding (GO:0046872)

GO Cellular Component (4): cytosol (GO:0005829), cytoplasmic side of plasma membrane (GO:0009898), plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
RAF/MAP kinase cascade1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
GTPase activity2
cellular anatomical structure2
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
cell activation1
blood coagulation1
intracellular anatomical structure1
signal transduction1
Ras protein signal transduction1
regulation of Ras protein signal transduction1
negative regulation of small GTPase mediated signal transduction1
regulation of signal transduction1
intracellular signal transduction1
response to stimulus1
regulation of hydrolase activity1
enzyme activator activity1
GTPase regulator activity1
calcium channel activity1
ion channel regulator activity1
transition metal ion binding1
cation binding1
cytoplasm1
plasma membrane1
cytoplasmic side of membrane1
membrane1
cell periphery1

Protein interactions and networks

STRING

796 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RASA3RAP1AP10113716
RASA3PLEK2Q9NYT0622
RASA3PLEKP08567622
RASA3RASGRP2Q7LDG7571
RASA3RRASP10301570
RASA3RASA1P20936512
RASA3RASGRP1O95267508
RASA3RASAL2Q9UJF2480
RASA3RAP1GAPP47736475
RASA3AKT1P31749454
RASA3RAP1BP09526453
RASA3CBLP22681421
RASA3TNFAIP8O95379416
RASA3DAPP1Q9UN19410
RASA3ADAP1O75689399

IntAct

4 interactions, top by confidence:

ABTypeScore
Mbd2MTA3psi-mi:“MI:0914”(association)0.350
PPP2R2DBAG2psi-mi:“MI:0914”(association)0.350
ZBTB18DNASE1L1psi-mi:“MI:0914”(association)0.350

BioGRID (53): RASA3 (Co-fractionation), RASA3 (Affinity Capture-MS), RASA3 (Affinity Capture-MS), GNAI2 (Reconstituted Complex), GNAI3 (Reconstituted Complex), GNAI2 (Affinity Capture-Western), GNAI3 (Affinity Capture-Western), RASA3 (Affinity Capture-RNA), RASA3 (Affinity Capture-MS), RASA3 (Affinity Capture-MS), RASA3 (Proximity Label-MS), RASA3 (Proximity Label-MS), RASA3 (Proximity Label-MS), RASA3 (Proximity Label-MS), RASA3 (Affinity Capture-MS)

ESM2 similar proteins: A0AVI2, A0FGR9, A2AP18, A3KGK3, A6QQP7, F1LYQ8, F8VPU2, O00329, O08835, O14976, O15068, O35904, O75038, O75923, O94887, P19687, P40749, P50232, P58069, P97610, P97874, Q14644, Q15283, Q28013, Q5DTI8, Q5FWL4, Q5M7N9, Q5RAB8, Q5RJH2, Q60790, Q63406, Q63713, Q64096, Q6DN12, Q6P7F1, Q7L8C5, Q7ZWU7, Q8IV01, Q8VHQ7, Q91VS8

Diamond homologs: A6QQ91, F6SEU4, P48423, P97526, Q14644, Q15283, Q28013, Q3UHC7, Q54Y08, Q5VWQ8, Q60790, Q6P730, Q86YV0, Q8C2K5, Q8MLZ5, Q8T498, Q96PV0, Q9QUH6, Q9QYJ2, Q9UJF2, Q9Z268, A3KGK3, A8KBH6, B2RUP2, B3DLH6, C9J798, K8FE10, O00445, O08625, O35681, O43374, O43581, O75923, O95294, P04409, P05126, P05128, P05129, P05130, P05696

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic1
Uncertain significance121
Likely benign10
Benign3

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
599497NM_007368.4(RASA3):c.892_895del (p.Asp298fs)Pathogenic
599498NM_007368.4(RASA3):c.254T>C (p.Val85Ala)Likely pathogenic

SpliceAI

6593 predictions. Top by Δscore:

VariantEffectΔscore
13:113979418:GCTCC:Gacceptor_gain1.0000
13:113979419:CTCC:Cacceptor_gain1.0000
13:113979419:CTCCC:Cacceptor_gain1.0000
13:113979420:TCC:Tacceptor_gain1.0000
13:113979420:TCCCT:Tacceptor_gain1.0000
13:113979421:CC:Cacceptor_gain1.0000
13:113979421:CCC:Cacceptor_gain1.0000
13:113979422:CC:Cacceptor_gain1.0000
13:113979423:C:CCacceptor_gain1.0000
13:113979423:C:Tacceptor_gain1.0000
13:113979423:CTGA:Cacceptor_loss1.0000
13:113979424:T:Cacceptor_loss1.0000
13:113981671:TCACT:Tdonor_loss1.0000
13:113981672:CAC:Cdonor_loss1.0000
13:113981673:A:ACdonor_gain1.0000
13:113981673:ACT:Adonor_loss1.0000
13:113981673:ACTGG:Adonor_gain1.0000
13:113981674:C:CAdonor_gain1.0000
13:113981674:CT:Cdonor_gain1.0000
13:113981674:CTGG:Cdonor_gain1.0000
13:113981674:CTGGC:Cdonor_gain1.0000
13:113981859:C:CCacceptor_gain1.0000
13:113992480:CTCA:Cdonor_loss1.0000
13:113992481:TCACC:Tdonor_loss1.0000
13:113992482:CAC:Cdonor_loss1.0000
13:113992483:A:ACdonor_gain1.0000
13:113992483:AC:Adonor_gain1.0000
13:113992484:C:Adonor_loss1.0000
13:113992484:C:CCdonor_gain1.0000
13:113992484:CC:Cdonor_gain1.0000

AlphaMissense

5561 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
13:113996670:A:GW668R1.000
13:113996670:A:TW668R1.000
13:114000920:C:AK585N1.000
13:114000920:C:GK585N1.000
13:114011210:C:AK517N1.000
13:114011210:C:GK517N1.000
13:114011231:C:AR510S1.000
13:114011231:C:GR510S1.000
13:114011232:C:AR510M1.000
13:114011232:C:GR510T1.000
13:114013185:G:TA490D1.000
13:114013200:C:AR485M1.000
13:114013200:C:GR485T1.000
13:114013203:A:GL484P1.000
13:114015325:A:GL430P1.000
13:114018851:A:GL285P1.000
13:114018857:A:GL283P1.000
13:114021458:C:TG244E1.000
13:114029887:C:GG125R1.000
13:114041041:A:GW111R1.000
13:114041041:A:TW111R1.000
13:114073768:A:GL42P1.000
13:113981681:C:TG808E0.999
13:113996729:A:TV648D0.999
13:114000872:T:AR601S0.999
13:114000872:T:GR601S0.999
13:114000917:C:AR586S0.999
13:114000917:C:GR586S0.999
13:114000918:C:GR586T0.999
13:114011193:C:TG523D0.999

dbSNP variants (sampled 300 via entrez): RS1000065173 (13:114042317 A>T), RS1000069060 (13:114002466 C>G,T), RS1000080103 (13:114090375 G>A), RS1000089611 (13:114109458 C>G), RS1000097152 (13:114063390 G>A,C), RS1000108898 (13:114100127 C>A,G,T), RS1000114781 (13:114016069 T>G), RS1000139018 (13:114055332 C>A,T), RS1000153473 (13:114109846 C>T), RS1000165958 (13:114039987 G>A,T), RS1000181054 (13:114073632 GA>G), RS1000189465 (13:114054979 T>C), RS1000198421 (13:114110323 C>T), RS1000205640 (13:114089951 G>A), RS1000221837 (13:114130933 C>T)

Disease associations

OMIM: gene MIM:605182 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

10 associations (top):

StudyTraitp-value
GCST007465_12Phoneme awareness6.000000e-06
GCST009200_12Whole brain grey matter density3.000000e-06
GCST010302_7Cutaneous melanoma or hair colour5.000000e-12
GCST90002388_127Lymphocyte count3.000000e-34
GCST90002388_128Lymphocyte count9.000000e-13
GCST90002389_481Lymphocyte percentage of white cells2.000000e-13
GCST90002389_482Lymphocyte percentage of white cells1.000000e-17
GCST90002401_69Platelet distribution width1.000000e-10
GCST90002407_616White blood cell count8.000000e-10
GCST90006897_1Anti-Epstein-Barr virus IgG seropositivity2.000000e-08

EFO canonical traits (7, from GWAS)

EFO IDTrait name
EFO:0005301reading and spelling ability
EFO:0010306Grey matter density measurement
EFO:0003924hair color
EFO:0004587lymphocyte count
EFO:0007993lymphocyte percentage of leukocytes
EFO:0007984platelet component distribution width
EFO:0007034seropositivity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
trichostatin Aaffects cotreatment, increases expression3
Estradiolaffects expression, affects cotreatment, increases expression3
sodium arsenitedecreases expression, affects methylation2
Benzo(a)pyreneincreases expression, affects methylation2
Cisplatindecreases expression2
Smokedecreases expression, increases abundance, increases expression2
Tobacco Smoke Pollutiondecreases expression2
Valproic Acidincreases expression, increases methylation2
aristolochic acid Idecreases expression1
GSK-J4increases expression1
FR900359decreases phosphorylation1
methylmercuric chlorideincreases expression1
triphenyl phosphateaffects expression1
bisphenol Aaffects methylation, affects cotreatment1
tris(2-butoxyethyl) phosphateaffects expression1
benzo(e)pyreneincreases methylation1
aflatoxin B2decreases methylation1
2-palmitoylglycerolincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
abrinedecreases expression1
quinocetonedecreases expression1
dorsomorphinaffects cotreatment, increases expression1
jinfukangincreases expression1
Temozolomidedecreases expression1
Sunitinibincreases expression1
Fulvestrantaffects methylation, affects cotreatment1
Glyphosateincreases expression1
Air Pollutantsincreases expression, increases abundance1
Arsenicaffects methylation1
Azacitidineincreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): cutaneous melanoma