RASA4

gene
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Also known as KIAA0538CAPRIGAPL

Summary

RASA4 (RAS p21 protein activator 4, HGNC:23181) is a protein-coding gene on chromosome 7q22.1, encoding Ras GTPase-activating protein 4 (O43374). Ca(2+)-dependent Ras GTPase-activating protein, that switches off the Ras-MAPK pathway following a stimulus that elevates intracellular calcium. It is a selective cancer dependency (DepMap: 27.8% of cell lines).

This gene encodes a member of the GAP1 family of GTPase-activating proteins that suppresses the Ras/mitogen-activated protein kinase pathway in response to Ca(2+). Stimuli that increase intracellular Ca(2+) levels result in the translocation of this protein to the plasma membrane, where it activates Ras GTPase activity. Consequently, Ras is converted from the active GTP-bound state to the inactive GDP-bound state and no longer activates downstream pathways that regulate gene expression, cell growth, and differentiation. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 10156 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 7 total
  • Cancer dependency (DepMap): dependent in 27.8% of screened cell lines
  • MANE Select transcript: NM_006989

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23181
Approved symbolRASA4
NameRAS p21 protein activator 4
Location7q22.1
Locus typegene with protein product
StatusApproved
AliasesKIAA0538, CAPRI, GAPL
Ensembl geneENSG00000105808
Ensembl biotypeprotein_coding
OMIM607943
Entrez10156

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 17 protein_coding, 6 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000262940, ENST00000449970, ENST00000461209, ENST00000462172, ENST00000519539, ENST00000519878, ENST00000520042, ENST00000520577, ENST00000521076, ENST00000521397, ENST00000521822, ENST00000521892, ENST00000522223, ENST00000522443, ENST00000522801, ENST00000523568, ENST00000903861, ENST00000903862, ENST00000903864, ENST00000903865, ENST00000916277, ENST00000960941, ENST00000960942, ENST00000960943, ENST00000960944

RefSeq mRNA: 2 — MANE Select: NM_006989 NM_001079877, NM_006989

CCDS: CCDS47674, CCDS5725

Canonical transcript exons

ENST00000262940 — 21 exons

ExonStartEnd
ENSE00001940252102579646102582892
ENSE00003462000102593707102593844
ENSE00003472352102584218102584338
ENSE00003473120102592285102592454
ENSE00003500506102587635102587770
ENSE00003517971102596012102596129
ENSE00003522646102590159102590296
ENSE00003527553102595634102595784
ENSE00003541845102600257102600388
ENSE00003564446102605858102605987
ENSE00003609935102592994102593138
ENSE00003629408102609341102609454
ENSE00003633920102608761102608822
ENSE00003640475102611086102611142
ENSE00003644844102599860102599954
ENSE00003648115102595305102595369
ENSE00003649430102583004102583068
ENSE00003674737102594447102594559
ENSE00003684400102594050102594242
ENSE00003791683102602324102602405
ENSE00003901398102616625102616756

Expression profiles

Bgee: expression breadth ubiquitous, 137 present calls, max score 98.61.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1199 / max 9.7597, expressed in 55 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
853590.119955

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
hindlimb stylopod muscleUBERON:000425298.61gold quality
gastrocnemiusUBERON:000138898.53gold quality
skeletal muscle tissueUBERON:000113498.11gold quality
muscle of legUBERON:000138398.04gold quality
sural nerveUBERON:001548896.43gold quality
right coronary arteryUBERON:000162595.78gold quality
granulocyteCL:000009495.28gold quality
myometriumUBERON:000129694.87gold quality
body of uterusUBERON:000985394.75gold quality
subcutaneous adipose tissueUBERON:000219094.59gold quality
endocervixUBERON:000045894.24gold quality
mucosa of stomachUBERON:000119994.12gold quality
vaginaUBERON:000099694.02gold quality
ganglionic eminenceUBERON:000402394.02gold quality
ectocervixUBERON:001224993.89gold quality
muscle tissueUBERON:000238593.85gold quality
tibial nerveUBERON:000132393.60gold quality
right ovaryUBERON:000211893.48gold quality
adipose tissueUBERON:000101393.29gold quality
uterine cervixUBERON:000000293.24gold quality
stromal cell of endometriumCL:000225593.19gold quality
right uterine tubeUBERON:000130293.07gold quality
lower esophagusUBERON:001347392.80gold quality
lower esophagus muscularis layerUBERON:003583392.80gold quality
pituitary glandUBERON:000000792.51gold quality
temporal lobeUBERON:000187192.51gold quality
fundus of stomachUBERON:000116092.48gold quality
esophagogastric junction muscularis propriaUBERON:003584192.48gold quality
amygdalaUBERON:000187692.44gold quality
adenohypophysisUBERON:000219692.20gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-5061yes14.60
E-GEOD-81547yes10.53
E-ANND-3yes8.12
E-MTAB-7303no582.48
E-GEOD-100618no91.87
E-MTAB-10137no7.16
E-GEOD-125970no3.57

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

110 targeting RASA4, 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-4776-3P100.0068.731340
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4481100.0066.421669
HSA-MIR-4262100.0073.263931
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-450099.9972.722367
HSA-MIR-806899.9873.852376
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-MIR-477599.9875.006394
HSA-LET-7D-5P99.9671.761632
HSA-MIR-445899.9671.641650
HSA-MIR-552-5P99.9368.561583
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-464899.9167.00710
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-7162-3P99.8968.161682
HSA-MIR-1343-3P99.8966.781815
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-7845-5P99.8864.88771

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 27.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 7)

  • CAPRI (Ca2+-promoted Ras inactivator) a Ca2+-dependent Ras GTPase-activating protein (Ras GAP). Switches off the Ras-MAPK pathway following G protein-coupled receptor stimulated intracellular Ca2+ elevation that recruits CAPRI to the plasma membrane. (PMID:11448776)
  • CAPRI seems to low-pass filter the Ca2+ signal, converting different intensities of stimulation into different durations of Ras activity. (PMID:16009725)
  • Ca2+-dependent monomer and dimer formation switches CAPRI Protein between Ras GTPase-activating protein (GAP) and RapGAP activities (PMID:21460216)
  • RASA4 isoform 2 promoter methylation correlated with clinical parameters predicting poor prognosis (older age, elevated fetal hemoglobin), with higher risk of relapse after hematopoietic stem cell transplantation, and with PTPN11 mutation. (PMID:25147919)
  • Treponema denticola-Induced RASA4 Upregulation Mediates Cytoskeletal Dysfunction and MMP-2 Activity in Periodontal Fibroblasts. (PMID:34094999)
  • Ras inhibitor CAPRI enables neutrophil-like cells to chemotax through a higher-concentration range of gradients. (PMID:34675073)
  • RASA4 inhibits the HIFalpha signaling pathway to suppress proliferation of cervical cancer cells. (PMID:34752201)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriorasa4ENSDARG00000029372
mus_musculusRasa4ENSMUSG00000004952
rattus_norvegicusRasa4ENSRNOG00000001431
drosophila_melanogasterRasGAP1FBGN0004390
drosophila_melanogasterraskolFBGN0261570
caenorhabditis_elegansWBGENE00001515
caenorhabditis_elegansWBGENE00001516

Paralogs (10): RASAL2 (ENSG00000075391), RASAL3 (ENSG00000105122), RASAL1 (ENSG00000111344), DAB2IP (ENSG00000136848), RASA1 (ENSG00000145715), RASA2 (ENSG00000155903), RASA4B (ENSG00000170667), RASA3 (ENSG00000185989), NF1 (ENSG00000196712), SYNGAP1 (ENSG00000197283)

Protein

Protein identifiers

Ras GTPase-activating protein 4O43374 (reviewed: O43374)

Alternative names: Calcium-promoted Ras inactivator, Ras p21 protein activator 4, RasGAP-activating-like protein 2

All UniProt accessions (7): O43374, E5RGQ8, E5RID2, E5RK78, E7ERK1, H0YB35, H0YBU2

UniProt curated annotations — full annotation on UniProt →

Function. Ca(2+)-dependent Ras GTPase-activating protein, that switches off the Ras-MAPK pathway following a stimulus that elevates intracellular calcium. Functions as an adaptor for Cdc42 and Rac1 during FcR-mediated phagocytosis.

Subcellular location. Cytoplasm. Cytosol. Cell membrane.

Tissue specificity. Widely expressed.

Cofactor. Binds 3 Ca(2+) ions per C2 domain.

Domain organisation. The PH domain does not bind phosphatidylinositol 4,5-bisphosphate or phosphatidylinositol 3,4,5-trisphosphate. This lack of binding activity is due to Leu-592, compared to Arg found in other family members.

Isoforms (2)

UniProt IDNamesCanonical?
O43374-11yes
O43374-22

RefSeq proteins (2): NP_001073346, NP_008920* (*=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
IPR037777RASA4_PHDomain
IPR039360Ras_GTPaseFamily

Pfam: PF00168, PF00169, PF00616, PF00779

UniProt features (43 total): binding site 26, sequence conflict 6, domain 4, sequence variant 2, chain 1, site 1, splice variant 1, zinc finger region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O43374-F186.330.56

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

Ligand- & substrate-binding residues (26): 74; 74; 76; 76; 76; 79; 82; 82; 149; 149; 155; 202

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-5658442Regulation of RAS by GAPs

MSigDB gene sets: 186 (showing top): WALLACE_PROSTATE_CANCER_RACE_UP, RORA1_01, GOBP_NEGATIVE_REGULATION_OF_HYDROLASE_ACTIVITY, GOBP_REGULATION_OF_GTPASE_ACTIVITY, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOBP_NEGATIVE_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOBP_RESPONSE_TO_METAL_ION, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, BROWNE_HCMV_INFECTION_48HR_DN, GOBP_REGULATION_OF_HYDROLASE_ACTIVITY, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_RAS_PROTEIN_SIGNAL_TRANSDUCTION, GOBP_NEGATIVE_REGULATION_OF_MOLECULAR_FUNCTION, LIAO_METASTASIS

GO Biological Process (6): negative regulation of GTPase activity (GO:0034260), intracellular signal transduction (GO:0035556), negative regulation of Ras protein signal transduction (GO:0046580), cellular response to calcium ion (GO:0071277), regulation of intracellular signal transduction (GO:1902531), regulation of GTPase activity (GO:0043087)

GO Molecular Function (4): GTPase activator activity (GO:0005096), phospholipid binding (GO:0005543), zinc ion binding (GO:0008270), metal ion binding (GO:0046872)

GO Cellular Component (4): cytosol (GO:0005829), plasma membrane (GO:0005886), cytoplasm (GO:0005737), 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 activity3
cellular anatomical structure3
intracellular anatomical structure2
regulation of GTPase activity1
negative regulation of biological process1
negative regulation of hydrolase activity1
signal transduction1
Ras protein signal transduction1
regulation of Ras protein signal transduction1
negative regulation of small GTPase mediated signal transduction1
response to calcium ion1
cellular response to metal ion1
regulation of signal transduction1
intracellular signal transduction1
regulation of hydrolase activity1
enzyme activator activity1
GTPase regulator activity1
lipid binding1
transition metal ion binding1
cation binding1
cytoplasm1
membrane1
cell periphery1

Protein interactions and networks

STRING

574 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RASA4RASGRP1O95267825
RASA4RABIFP47224625
RASA4SCAF11Q99590624
RASA4RASGRP4Q8TDF6581
RASA4PLEK2Q9NYT0557
RASA4PLEKP08567554
RASA4CASP14P31944550
RASA4TRPC3Q13507531
RASA4CCDC70Q6NSX1524
RASA4RND1Q92730523
RASA4SRCP12931515
RASA4CDC42P21181489
RASA4TBL1XO60907478
RASA4PUS10Q3MIT2443
RASA4PLCG2P16885428

IntAct

10 interactions, top by confidence:

ABTypeScore
PCNARASA4psi-mi:“MI:0915”(physical association)0.370
Prdm16ESYT2psi-mi:“MI:0914”(association)0.350
BMI1HMGB1P1psi-mi:“MI:0914”(association)0.350
ACKR3PDE2Apsi-mi:“MI:0914”(association)0.350
TUBBVWA8psi-mi:“MI:0914”(association)0.350
RASA4JPT2psi-mi:“MI:0915”(physical association)0.000
RASA4APMAPpsi-mi:“MI:0915”(physical association)0.000
RASA4ERBB3psi-mi:“MI:0915”(physical association)0.000
RASA4OVGP1psi-mi:“MI:0915”(physical association)0.000

BioGRID (5): RASA4 (Affinity Capture-MS), RASA4 (Reconstituted Complex), RASA4 (Affinity Capture-MS), RASA4 (Affinity Capture-MS), RASA4 (Affinity Capture-MS)

ESM2 similar proteins: A0A0B4J1F4, A0A0G2JXN2, A2AWP8, A2RRH5, C9J798, O43374, O70277, O95294, P04629, P59926, Q0GA42, Q13368, Q14318, Q16512, Q29RM4, Q2HY40, Q2T9P3, Q2TBA3, Q5BIM1, Q5M7W1, Q5R5M3, Q5R811, Q5T7P8, Q5XIS9, Q62746, Q6PFQ7, Q6PFY8, Q7TNM2, Q7TP90, Q7Z4K8, Q8BG60, Q8BHT7, Q8BQC3, Q8C6N3, Q8CIW5, Q8IZ69, Q8NCT1, Q920N2, Q92546, Q925B4

Diamond homologs: A0AVI2, A0JJX5, A3KGK3, B2RUP2, C9J798, O43374, O95294, P48231, Q2WGJ9, Q54E35, Q5SPC5, Q8L706, Q8L7A4, Q8W4D4, Q9ERC5, Q9ESF1, Q9FVJ3, Q9HC10, Q9R189, Q9UT00, A0A075F932, A0FGR9, K8FE10, O00445, O35681, O43581, O94812, P04409, P05128, P10829, P13677, P21521, P21579, P21707, P24505, P24506, P24507, P29101, P34693, P40748

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance4
Likely benign1
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

3356 predictions. Top by Δscore:

VariantEffectΔscore
7:102582748:G:Cdonor_gain1.0000
7:102582774:CGT:Cdonor_gain1.0000
7:102582893:C:CCacceptor_gain1.0000
7:102583067:CC:Cacceptor_gain1.0000
7:102583068:CC:Cacceptor_gain1.0000
7:102584211:GACTC:Gdonor_loss1.0000
7:102584212:ACTCA:Adonor_loss1.0000
7:102584214:TCA:Tdonor_loss1.0000
7:102584215:CA:Cdonor_loss1.0000
7:102584216:A:ACdonor_gain1.0000
7:102584216:A:Cdonor_loss1.0000
7:102584216:AC:Adonor_gain1.0000
7:102584217:C:Adonor_loss1.0000
7:102584217:C:CCdonor_gain1.0000
7:102584217:CC:Cdonor_gain1.0000
7:102584217:CCA:Cdonor_gain1.0000
7:102584334:CTGAC:Cacceptor_gain1.0000
7:102584335:TGAC:Tacceptor_gain1.0000
7:102584336:GAC:Gacceptor_gain1.0000
7:102584337:AC:Aacceptor_gain1.0000
7:102584338:CC:Cacceptor_gain1.0000
7:102584339:C:CCacceptor_gain1.0000
7:102584346:C:CTacceptor_gain1.0000
7:102587769:CA:Cacceptor_gain1.0000
7:102587771:C:CCacceptor_gain1.0000
7:102592280:CCCA:Cdonor_gain1.0000
7:102592281:CCA:Cdonor_loss1.0000
7:102592283:A:Tdonor_loss1.0000
7:102592284:CC:Cdonor_loss1.0000
7:102592453:CT:Cacceptor_gain1.0000

AlphaMissense

5224 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:102609420:A:GW53R0.999
7:102609420:A:TW53R0.999
7:102587665:A:GW692R0.998
7:102587665:A:TW692R0.998
7:102587749:A:GW664R0.998
7:102587749:A:TW664R0.998
7:102600361:A:GW180R0.998
7:102600361:A:TW180R0.998
7:102609418:C:AW53C0.998
7:102609418:C:GW53C0.998
7:102593707:C:AK505N0.997
7:102593707:C:GK505N0.997
7:102593789:G:TA478D0.997
7:102600359:C:AW180C0.997
7:102600359:C:GW180C0.997
7:102602361:A:TV158D0.997
7:102608805:C:TG85E0.997
7:102609362:A:TV72D0.997
7:102609419:C:GW53S0.997
7:102611120:A:GC30R0.997
7:102616650:C:AG14W0.997
7:102593767:G:CF485L0.996
7:102593767:G:TF485L0.996
7:102593769:A:GF485L0.996
7:102593777:G:TP482H0.996
7:102593818:G:CS468R0.996
7:102593818:G:TS468R0.996
7:102593820:T:GS468R0.996
7:102611123:A:CY29D0.996
7:102616650:C:GG14R0.996

dbSNP variants (sampled 300 via entrez): RS1003473758 (7:102612371 G>T), RS1004679248 (7:102603865 C>A), RS1005660489 (7:102612329 G>GC), RS1006043556 (7:102596457 T>A,G), RS1012904728 (7:102613734 G>A), RS1014670600 (7:102603879 C>A), RS1028830161 (7:102595278 T>A,G), RS1035236572 (7:102612500 G>C), RS1041002414 (7:102608085 C>T), RS1049617355 (7:102611015 A>C,G), RS1060228 (7:102584251 T>C), RS111387683 (7:102589132 C>T), RS111563401 (7:102618273 C>T), RS112003076 (7:102603241 G>A,T), RS112083455 (7:102601172 C>A)

Disease associations

OMIM: gene MIM:607943 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST003837_4Chronotype8.000000e-15
GCST003838_4Morning vs. evening chronotype7.000000e-07
GCST010118_153Type 2 diabetes3.000000e-11

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases methylation, decreases expression4
sodium arseniteincreases abundance, increases expression, affects cotreatment, decreases expression3
aristolochic acid Iincreases expression1
afuresertibincreases expression1
sotorasibaffects cotreatment, decreases expression1
triphenyl phosphateaffects expression1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidineincreases expression, increases response to substance1
asparanin Aincreases expression1
trametinibaffects cotreatment, decreases expression1
NVP-BKM120affects cotreatment, decreases expression1
Arsenic Trioxidedecreases expression1
Acetaminophenincreases expression1
Glyphosateincreases expression1
Arsenicaffects cotreatment, decreases expression, increases abundance1
Benzo(a)pyrenedecreases expression1
Cisplatindecreases expression1
Drugs, Chinese Herbalincreases expression1
Estradioldecreases expression1
Ethyl Methanesulfonatedecreases expression1
Methyl Methanesulfonatedecreases expression1
Niclosamideincreases expression1
Phenylmercuric Acetatedecreases expression1
Smokedecreases expression1
Okadaic Aciddecreases expression1
Lactic Acidaffects expression1
S-Nitrosoglutathionedecreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.