RALGAPA2

gene
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Also known as dJ1049G11.4AS250KIAA1272RapGAPalpha2

Summary

RALGAPA2 (Ral GTPase activating protein catalytic subunit alpha 2, HGNC:16207) is a protein-coding gene on chromosome 20p11.23, encoding Ral GTPase-activating protein subunit alpha-2 (Q2PPJ7). Catalytic subunit of the heterodimeric RalGAP2 complex which acts as a GTPase activator for the Ras-like small GTPases RALA and RALB.

Predicted to enable GTPase activator activity and protein heterodimerization activity. Predicted to be involved in activation of GTPase activity. Predicted to act upstream of or within Ral protein signal transduction; regulation of exocyst localization; and regulation of protein localization. Located in cytosol and plasma membrane.

Source: NCBI Gene 57186 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 342 total
  • MANE Select transcript: NM_020343

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16207
Approved symbolRALGAPA2
NameRal GTPase activating protein catalytic subunit alpha 2
Location20p11.23
Locus typegene with protein product
StatusApproved
AliasesdJ1049G11.4, AS250, KIAA1272, RapGAPalpha2
Ensembl geneENSG00000188559
Ensembl biotypeprotein_coding
OMIM618836
Entrez57186

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 retained_intron

ENST00000202677, ENST00000424981, ENST00000427175, ENST00000430436, ENST00000495793, ENST00000909985, ENST00000934890

RefSeq mRNA: 1 — MANE Select: NM_020343 NM_020343

CCDS: CCDS46584

Canonical transcript exons

ENST00000202677 — 40 exons

ExonStartEnd
ENSE000006608092050541120505534
ENSE000006608112051251320513284
ENSE000006608122052091720521100
ENSE000006608132052440620524543
ENSE000006608152052625220526362
ENSE000006608162053168720531795
ENSE000006608172053574520535803
ENSE000006608312062046320620630
ENSE000006608322062936320629590
ENSE000006608332063541820635617
ENSE000008593852049511720495275
ENSE000008593862050335120503506
ENSE000008593882051125420511325
ENSE000008593922052483020524898
ENSE000008593952053665620536784
ENSE000011298502061131520611426
ENSE000012054192061604320616191
ENSE000012054222061927720619414
ENSE000012055332041202720412148
ENSE000012055512047282920472956
ENSE000013550682054670420546832
ENSE000013550742057145820571613
ENSE000013550812057287520573068
ENSE000013550862058305020583226
ENSE000013550902058486520584955
ENSE000014192472059117720591314
ENSE000014198352058926820589365
ENSE000014234082057184820571946
ENSE000015435992039669520396734
ENSE000015942922068069120680801
ENSE000016033292064070120640878
ENSE000016115962067623620676288
ENSE000016404102065353020653587
ENSE000017717112071237520712644
ENSE000017749922038953020393253
ENSE000017879532064350620643549
ENSE000036211702060168220601846
ENSE000036312572060517520605412
ENSE000037081802063978520639900
ENSE000037104222063736320637501

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 95.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.4276 / max 279.1550, expressed in 1632 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
18659410.42761632

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
tibialis anteriorUBERON:000138595.29gold quality
spermCL:000001995.06gold quality
pancreatic ductal cellCL:000207994.79gold quality
deltoidUBERON:000147693.77gold quality
nasal cavity epitheliumUBERON:000538493.57gold quality
ileal mucosaUBERON:000033192.88gold quality
upper arm skinUBERON:000426392.62gold quality
visceral pleuraUBERON:000240192.33gold quality
bronchial epithelial cellCL:000232892.28gold quality
buccal mucosa cellCL:000233691.95gold quality
bronchusUBERON:000218591.93gold quality
vastus lateralisUBERON:000137991.87gold quality
skeletal muscle tissueUBERON:000113491.66gold quality
quadriceps femorisUBERON:000137791.59gold quality
skeletal muscle organUBERON:001489290.46gold quality
gastrocnemiusUBERON:000138890.42gold quality
trabecular bone tissueUBERON:000248390.38gold quality
muscle of legUBERON:000138390.18gold quality
muscle tissueUBERON:000238590.16gold quality
ganglionic eminenceUBERON:000402389.53gold quality
embryoUBERON:000092289.52gold quality
kidney epitheliumUBERON:000481989.46silver quality
ventricular zoneUBERON:000305389.34gold quality
biceps brachiiUBERON:000150789.33gold quality
mucosa of paranasal sinusUBERON:000503089.13gold quality
parotid glandUBERON:000183188.97gold quality
sural nerveUBERON:001548888.75gold quality
liverUBERON:000210788.69gold quality
pylorusUBERON:000116688.68gold quality
bloodUBERON:000017888.58gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-GEOD-135922yes35.34
E-CURD-119yes17.22
E-MTAB-6678yes13.72
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

143 targeting RALGAPA2, 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-3646100.0073.565283
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-4262100.0073.263931
HSA-MIR-5193100.0067.261744
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-548P99.9872.253784
HSA-MIR-1213699.9872.815713
HSA-MIR-477599.9875.006394
HSA-MIR-569699.9872.364487
HSA-MIR-480399.9871.993117
HSA-MIR-570-3P99.9672.414910
HSA-MIR-365899.9673.874379
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-590-3P99.9674.346478
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-545-3P99.9570.742783
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-651-3P99.9473.485177
HSA-MIR-971899.9468.91918
HSA-MIR-627-3P99.9071.423316
HSA-MIR-3529-3P99.9073.553045

Literature-anchored findings (GeneRIF, showing 5)

  • The cDNA sequence for human AS250 is reported, and the sites that undergo phosphorylation upon insulin treatment of adipocytes have been identified by tandem mass spectrometry. (PMID:16490346)
  • Downregulation of Ral GTPase-activating protein promotes tumor invasion and metastasis of bladder cancer. (PMID:22450745)
  • loss of RalGAP function has a distinct role in promoting progression from prostatic intraepithelial neoplasia to invasive adenocarcinoma. (PMID:31058283)
  • Low RalGAPalpha2 expression was associated with a reduced survival rate in patients with oral squamous cell carcinoma (PMID:31329042)
  • The interaction between MALAT1 target, miR-143-3p, and RALGAPA2 is affected by functional SNP rs3827693 in breast cancer. (PMID:32880825)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioralgapa2ENSDARG00000005861
mus_musculusRalgapa2ENSMUSG00000037110
rattus_norvegicusRalgapa2ENSRNOG00000036964
drosophila_melanogasterCG5521FBGN0039466
caenorhabditis_eleganshgap-1WBGENE00021209

Paralogs (2): TSC2 (ENSG00000103197), RALGAPA1 (ENSG00000174373)

Protein

Protein identifiers

Ral GTPase-activating protein subunit alpha-2Q2PPJ7 (reviewed: Q2PPJ7)

Alternative names: 250 kDa substrate of Akt, p220

All UniProt accessions (4): A0A3B3IS41, Q2PPJ7, H7BZA8, H7C1F9

UniProt curated annotations — full annotation on UniProt →

Function. Catalytic subunit of the heterodimeric RalGAP2 complex which acts as a GTPase activator for the Ras-like small GTPases RALA and RALB.

Subunit / interactions. Component of the heterodimeric RalGAP2 complex with RALGAPB. Heterodimerization is required for activity.

Subcellular location. Cytoplasm.

Isoforms (3)

UniProt IDNamesCanonical?
Q2PPJ7-11yes
Q2PPJ7-22
Q2PPJ7-33

RefSeq proteins (1): NP_065076* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000331Rap/Ran_GAP_domDomain
IPR016024ARM-type_foldHomologous_superfamily
IPR027107Tuberin/Ral-act_asuFamily
IPR035974Rap/Ran-GAP_sfHomologous_superfamily
IPR046859RGPA/RALGAPB_NDomain

Pfam: PF02145, PF20412

UniProt features (24 total): modified residue 9, compositionally biased region 6, region of interest 3, splice variant 2, chain 1, domain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
9QU1X-RAY DIFFRACTION2.72
9QWPELECTRON MICROSCOPY3.8

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q2PPJ7-F172.970.33

Functional residue map

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

Post-translational modifications (9): 373, 376, 379, 486, 696, 715, 820, 821, 1593

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-1445148Translocation of SLC2A4 (GLUT4) to the plasma membrane

MSigDB gene sets: 113 (showing top): WANG_CLIM2_TARGETS_UP, GOBP_ACTIVATION_OF_GTPASE_ACTIVITY, GOBP_REGULATION_OF_GTPASE_ACTIVITY, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, REACTOME_MEMBRANE_TRAFFICKING, GOBP_POSITIVE_REGULATION_OF_CATALYTIC_ACTIVITY, GOBP_REGULATION_OF_HYDROLASE_ACTIVITY, GOBP_POSITIVE_REGULATION_OF_MOLECULAR_FUNCTION, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_DN, GOBP_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, GOMF_PROTEIN_HETERODIMERIZATION_ACTIVITY, GOMF_PROTEIN_DIMERIZATION_ACTIVITY, NUYTTEN_NIPP1_TARGETS_DN

GO Biological Process (6): Ral protein signal transduction (GO:0032484), regulation of protein localization (GO:0032880), regulation of small GTPase mediated signal transduction (GO:0051056), regulation of exocyst localization (GO:0060178), activation of GTPase activity (GO:0090630), positive regulation of GTPase activity (GO:0043547)

GO Molecular Function (3): GTPase activator activity (GO:0005096), protein heterodimerization activity (GO:0046982), protein binding (GO:0005515)

GO Cellular Component (5): obsolete extracellular space (GO:0005615), nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829), plasma membrane (GO:0005886)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Membrane Trafficking1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
small GTPase-mediated signal transduction2
regulation of localization2
GTPase activity2
cellular anatomical structure2
intracellular protein localization1
regulation of intracellular signal transduction1
exocyst localization1
positive regulation of GTPase activity1
regulation of GTPase activity1
positive regulation of hydrolase activity1
enzyme activator activity1
GTPase regulator activity1
protein dimerization activity1
binding1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cytoplasm1
membrane1
cell periphery1

Protein interactions and networks

STRING

588 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RALGAPA2CFAP61Q8NHU2495
RALGAPA2RALGAPBQ86X10483
RALGAPA2SLC25A13Q9UJS0448
RALGAPA2SPMAP2LP0DJG4441
RALGAPA2FYB2Q5VWT5417
RALGAPA2CFAP418Q96NL8409
RALGAPA2SLC25A5P05141404
RALGAPA2RALAP11233400
RALGAPA2NFX1Q12986388
RALGAPA2SLC34A2O95436374
RALGAPA2DCDC2CA8MYV0360
RALGAPA2ORMDL2Q53FV1356
RALGAPA2ACOT8O14734352
RALGAPA2ARHGAP4P98171350
RALGAPA2MYEOVQ96EZ4338

IntAct

19 interactions, top by confidence:

ABTypeScore
RALGAPA2DDI1psi-mi:“MI:0915”(physical association)0.560
GFOD1PER1psi-mi:“MI:0914”(association)0.530
GFOD1RALGAPA2psi-mi:“MI:0914”(association)0.530
NKIRAS2RALGAPA2psi-mi:“MI:0914”(association)0.530
BMI1HMGB1P1psi-mi:“MI:0914”(association)0.350
NKIRAS2RAP1GDS1psi-mi:“MI:0914”(association)0.350
DPH7CCT2psi-mi:“MI:0914”(association)0.350
DLG3DLG1psi-mi:“MI:0914”(association)0.350
MTMR7RALGAPA2psi-mi:“MI:0914”(association)0.350
DPH7RALGAPA2psi-mi:“MI:0914”(association)0.350
GFOD1SBF1psi-mi:“MI:0914”(association)0.350
GFOD1B4GAT1psi-mi:“MI:0914”(association)0.350
NKIRAS2GABARAPL2psi-mi:“MI:0914”(association)0.350
ORF66RALGAPA1psi-mi:“MI:0914”(association)0.350
RALGAPBDHX15psi-mi:“MI:0914”(association)0.350
LAMP1TRAPPC13psi-mi:“MI:2364”(proximity)0.270
RALGAPA2DDI1psi-mi:“MI:0915”(physical association)0.000

BioGRID (53): RALGAPA2 (Affinity Capture-MS), RALGAPA2 (Affinity Capture-MS), RALGAPA2 (Affinity Capture-MS), RALGAPA2 (Affinity Capture-MS), RALGAPA2 (Affinity Capture-MS), RALGAPA2 (Affinity Capture-MS), RALGAPA2 (Affinity Capture-MS), RALGAPA2 (Proximity Label-MS), RALGAPA2 (Proximity Label-MS), RALGAPA2 (Proximity Label-MS), RALGAPA2 (Affinity Capture-RNA), RALGAPA2 (Synthetic Lethality), RALGAPA2 (Two-hybrid), RALGAPA2 (Affinity Capture-MS), RALGAPA2 (Affinity Capture-MS)

ESM2 similar proteins: A0A5F9C6I2, A1L3F5, A2BDA5, A3KGS3, A8E4X8, D3ZXK7, F1R7R1, O75129, P21359, P51593, P97526, Q04690, Q1JPG0, Q2PPJ7, Q3SZD5, Q4QQM5, Q4R5A4, Q5RC14, Q5XPI3, Q5XPI4, Q62717, Q66K64, Q6GLR7, Q6NXD8, Q6P4S8, Q6PFH3, Q6VNB8, Q7L4E1, Q7TMY8, Q7Z6Z7, Q80TJ1, Q86UW7, Q8BHR8, Q8BK03, Q8BYR5, Q8CDG3, Q8CF97, Q8CID0, Q8IY22, Q8IZQ1

Diamond homologs: A3KGS3, O55007, P49815, P86409, P86411, Q2PPJ7, Q3V0G7, Q54SS8, Q61037, Q6GYP7, Q6GYQ0, Q9UUG9, Q9VB98, A2ALS5, A5PF44, G3X9J0, O35412, O43166, O60292, P46062, P47736, Q54EH3, Q55AN8, Q5JCS6, Q5SVL6, Q5VVW2, Q5ZJY3, Q5ZMV8, Q684P5, Q75J96, Q80TE4, Q8C0T5, Q96FS4, Q9P2F8, P49816, Q54TK4

SIGNOR signaling

4 interactions.

AEffectBMechanism
RALGAPA2“form complex”RalGAP2binding
AKT2“down-regulates activity”RALGAPA2phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance286
Likely benign12
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

8696 predictions. Top by Δscore:

VariantEffectΔscore
20:20412160:G:Tacceptor_gain1.0000
20:20495112:CGTA:Cdonor_loss1.0000
20:20495113:GTACC:Gdonor_loss1.0000
20:20495114:TA:Tdonor_loss1.0000
20:20495115:A:ACdonor_gain1.0000
20:20495115:AC:Adonor_gain1.0000
20:20495116:C:CCdonor_gain1.0000
20:20495116:CC:Cdonor_gain1.0000
20:20495116:CCT:Cdonor_gain1.0000
20:20495271:CGAAG:Cacceptor_gain1.0000
20:20495272:GAAG:Gacceptor_gain1.0000
20:20495273:AAG:Aacceptor_gain1.0000
20:20495273:AAGCT:Aacceptor_loss1.0000
20:20495274:AG:Aacceptor_gain1.0000
20:20495275:GCTGC:Gacceptor_loss1.0000
20:20495276:C:Aacceptor_loss1.0000
20:20495276:C:CCacceptor_gain1.0000
20:20503346:CTTA:Cdonor_loss1.0000
20:20503347:TTAC:Tdonor_loss1.0000
20:20503349:ACCTT:Adonor_loss1.0000
20:20503350:C:Adonor_loss1.0000
20:20503518:C:CTacceptor_gain1.0000
20:20503520:C:CTacceptor_gain1.0000
20:20505013:TTTG:Tdonor_gain1.0000
20:20505020:T:TAdonor_gain1.0000
20:20505530:CACGG:Cacceptor_gain1.0000
20:20505532:CGG:Cacceptor_gain1.0000
20:20505535:C:CCacceptor_gain1.0000
20:20511246:T:Adonor_gain1.0000
20:20511249:CATA:Cdonor_loss1.0000

AlphaMissense

12324 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:20511278:A:GL1635P1.000
20:20495239:A:GW1749R0.999
20:20495239:A:TW1749R0.999
20:20572982:A:GW932R0.999
20:20572982:A:TW932R0.999
20:20573009:A:GW923R0.999
20:20573009:A:TW923R0.999
20:20640845:A:GW136R0.999
20:20640845:A:TW136R0.999
20:20712389:A:GL31P0.999
20:20472871:G:TA1818D0.998
20:20495189:A:CF1765L0.998
20:20495189:A:TF1765L0.998
20:20495191:A:GF1765L0.998
20:20495274:A:GL1737P0.998
20:20513224:A:GL1382P0.998
20:20605295:A:GW640R0.998
20:20605295:A:TW640R0.998
20:20605397:A:GW606R0.998
20:20605397:A:TW606R0.998
20:20635507:A:GW306R0.998
20:20635507:A:TW306R0.998
20:20637486:A:GW228R0.998
20:20637486:A:TW228R0.998
20:20640866:C:GG129R0.998
20:20640866:C:TG129R0.998
20:20653548:A:GW104R0.998
20:20653548:A:TW104R0.998
20:20653580:A:GL93P0.998
20:20412137:C:GR1836P0.997

dbSNP variants (sampled 300 via entrez): RS1000038343 (20:20654741 T>A), RS1000042763 (20:20521923 T>C), RS1000043963 (20:20455095 T>C), RS1000091645 (20:20654990 G>C), RS1000099160 (20:20540238 A>C), RS1000106147 (20:20582519 A>G), RS1000111133 (20:20709722 C>G), RS1000113168 (20:20495043 C>G,T), RS1000134402 (20:20682032 G>A), RS1000162942 (20:20461866 G>C,T), RS1000168390 (20:20541854 C>A), RS1000188488 (20:20682295 C>T), RS1000226107 (20:20496921 G>A), RS1000227295 (20:20452255 A>C), RS1000247563 (20:20458840 C>A,G,T)

Disease associations

OMIM: gene MIM:618836 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST002386_15Cognitive function2.000000e-06
GCST008163_382Height2.000000e-06
GCST008839_37Height7.000000e-09
GCST010136_17Fruit consumption3.000000e-08

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0003925cognition
EFO:0008111diet measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs3827963RALGAPA20.000

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneincreases expression, affects methylation, decreases expression4
methylmercuric chloridedecreases expression, increases expression3
Air Pollutantsaffects expression, increases abundance, decreases expression3
Valproic Acidaffects expression, increases expression3
sodium arseniteincreases abundance, decreases expression2
Arsenicaffects methylation, decreases expression, increases abundance2
Aflatoxin B1decreases methylation, increases methylation2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
dicrotophosincreases expression1
triphenyl phosphateaffects expression1
propionaldehydeincreases expression1
bisphenol Aincreases expression1
9,10-dihydro-9,10-dihydroxybenzo(a)pyreneincreases expression1
benzo(e)pyreneincreases methylation1
potassium chromate(VI)affects cotreatment, decreases expression1
nickel sulfatedecreases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
entinostatdecreases expression1
abrinedecreases expression1
(+)-JQ1 compoundincreases expression1
Sunitinibincreases expression1
Leflunomideincreases expression1
Acetaminophendecreases expression1
Caffeineaffects phosphorylation1
Calcitriolincreases expression, affects cotreatment1
Cisplatindecreases expression1
Doxorubicindecreases expression1
Estradiolaffects cotreatment, decreases 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.