RALGPS1

gene
On this page

Also known as RALGPS1ARALGEF2KIAA0351

Summary

RALGPS1 (Ral GEF with PH domain and SH3 binding motif 1, HGNC:16851) is a protein-coding gene on chromosome 9q33.3, encoding Ras-specific guanine nucleotide-releasing factor RalGPS1 (Q5JS13). Guanine nucleotide exchange factor (GEF) for the small GTPase RALA.

Enables guanyl-nucleotide exchange factor activity. Involved in regulation of Ral protein signal transduction. Predicted to be located in cytoplasm. Predicted to be active in plasma membrane.

Source: NCBI Gene 9649 — RefSeq curated summary.

At a glance

  • GWAS associations: 14
  • Clinical variants (ClinVar): 54 total
  • MANE Select transcript: NM_014636

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16851
Approved symbolRALGPS1
NameRal GEF with PH domain and SH3 binding motif 1
Location9q33.3
Locus typegene with protein product
StatusApproved
AliasesRALGPS1A, RALGEF2, KIAA0351
Ensembl geneENSG00000136828
Ensembl biotypeprotein_coding
OMIM614444
Entrez9649

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 16 protein_coding, 5 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000259351, ENST00000319107, ENST00000373434, ENST00000373436, ENST00000373439, ENST00000394011, ENST00000394022, ENST00000424082, ENST00000438723, ENST00000467325, ENST00000471643, ENST00000472427, ENST00000477700, ENST00000480993, ENST00000903174, ENST00000903175, ENST00000903176, ENST00000921398, ENST00000921399, ENST00000921400, ENST00000921401, ENST00000968097

RefSeq mRNA: 13 — MANE Select: NM_014636 NM_001190728, NM_001190729, NM_001190730, NM_001322320, NM_001322321, NM_001322322, NM_001322323, NM_001322324, NM_001322325, NM_001366399, NM_001366400, NM_001366401, NM_014636

CCDS: CCDS35143, CCDS55344, CCDS55345, CCDS55346, CCDS94484

Canonical transcript exons

ENST00000259351 — 19 exons

ExonStartEnd
ENSE00000806793127196474127196631
ENSE00000806794127199015127199066
ENSE00001399772126914782126914975
ENSE00001615084127174715127174782
ENSE00001642587127218740127223166
ENSE00001705184127168679127168772
ENSE00001758580127166069127166206
ENSE00001782812127195091127195217
ENSE00003467780127034431127034514
ENSE00003478854127052847127052939
ENSE00003529241127212131127212236
ENSE00003548747127212944127213049
ENSE00003550853127212627127212719
ENSE00003617599126965844126965951
ENSE00003618467127214751127214842
ENSE00003620578126977695126977745
ENSE00003628748127050043127050132
ENSE00003651353126962225126962346
ENSE00003660119127069230127069356

Expression profiles

Bgee: expression breadth ubiquitous, 260 present calls, max score 96.79.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.8756 / max 217.5538, expressed in 1287 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
985806.56061283
985820.1984119
985810.116765

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534396.79gold quality
jejunal mucosaUBERON:000039993.19gold quality
right hemisphere of cerebellumUBERON:001489092.77gold quality
cerebellar cortexUBERON:000212992.15gold quality
cerebellar hemisphereUBERON:000224592.13gold quality
cerebellumUBERON:000203791.73gold quality
C1 segment of cervical spinal cordUBERON:000646991.71gold quality
spinal cordUBERON:000224090.42gold quality
duodenumUBERON:000211490.30gold quality
Brodmann (1909) area 23UBERON:001355490.29gold quality
cerebellar vermisUBERON:000472090.25gold quality
endothelial cellCL:000011589.71gold quality
primary visual cortexUBERON:000243689.69gold quality
ganglionic eminenceUBERON:000402389.59gold quality
middle temporal gyrusUBERON:000277189.57gold quality
apex of heartUBERON:000209888.57gold quality
prefrontal cortexUBERON:000045187.94gold quality
occipital lobeUBERON:000202187.85gold quality
small intestineUBERON:000210887.83gold quality
right uterine tubeUBERON:000130287.73gold quality
small intestine Peyer’s patchUBERON:000345487.66gold quality
right frontal lobeUBERON:000281087.59gold quality
neocortexUBERON:000195087.29gold quality
frontal cortexUBERON:000187087.28gold quality
postcentral gyrusUBERON:000258187.22gold quality
pituitary glandUBERON:000000787.20gold quality
Brodmann (1909) area 9UBERON:001354087.01gold quality
corpus callosumUBERON:000233686.87gold quality
cerebral cortexUBERON:000095686.85gold quality
central nervous systemUBERON:000101786.82gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.97

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): IRX1

miRNA regulators (miRDB)

251 targeting RALGPS1, 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-8485100.0077.574731
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-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-196A-5P100.0068.16684
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-196B-5P100.0068.16681
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-188-3P100.0068.761240
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-366299.9973.825684
HSA-MIR-450099.9972.722367
HSA-MIR-453199.9969.703181
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-806899.9873.852376
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580

Literature-anchored findings (GeneRIF, showing 2)

  • The guanine-nucleotide exchange factor (GEF) RalGPS1a activates small GTPase Ral proteins such as RalA and RalB by stimulating the exchange of Ral bound GDP to GTP, thus regulating various downstream cellular processes. (PMID:21494904)
  • Ral GEF with the PH Domain and SH3 Binding Motif 1 Regulated by Splicing Factor Junction Plakoglobin and Pyrimidine Metabolism Are Prognostic in Uterine Carcinosarcoma. (PMID:34745385)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioralgps1ENSDARG00000068370
mus_musculusRalgps1ENSMUSG00000038831
rattus_norvegicusRalgps1ENSRNOG00000016910

Paralogs (24): RASGRF1 (ENSG00000058335), RASGRP2 (ENSG00000068831), RAPGEF3 (ENSG00000079337), RAPGEF4 (ENSG00000091428), SOS2 (ENSG00000100485), RAPGEF1 (ENSG00000107263), RAPGEFL1 (ENSG00000108352), RAPGEF2 (ENSG00000109756), RASGRF2 (ENSG00000113319), SOS1 (ENSG00000115904), RALGPS2 (ENSG00000116191), RAPGEF5 (ENSG00000136237), RASGEF1B (ENSG00000138670), RGL1 (ENSG00000143344), RASGEF1C (ENSG00000146090), RASGRP3 (ENSG00000152689), RAPGEF6 (ENSG00000158987), RGL4 (ENSG00000159496), RALGDS (ENSG00000160271), RASGRP4 (ENSG00000171777), RASGRP1 (ENSG00000172575), RASGEF1A (ENSG00000198915), RGL3 (ENSG00000205517), RGL2 (ENSG00000237441)

Protein

Protein identifiers

Ras-specific guanine nucleotide-releasing factor RalGPS1Q5JS13 (reviewed: Q5JS13)

Alternative names: Ral GEF with PH domain and SH3-binding motif 1, Ral guanine nucleotide exchange factor 2, RalA exchange factor RalGPS1

All UniProt accessions (3): Q5JS13, H0Y6A2, Q5JT61

UniProt curated annotations — full annotation on UniProt →

Function. Guanine nucleotide exchange factor (GEF) for the small GTPase RALA. May be involved in cytoskeletal organization. Guanine nucleotide exchange factor for.

Subunit / interactions. Interacts with the SH3 domains of GRB2, NCK1, PLCG1 and SRC.

Subcellular location. Cytoplasm. Cell membrane.

Tissue specificity. Widely expressed (at protein level). Isoform 2 is expressed in brain, colon, kidney, pancreas, prostate, skeletal muscle, small intestine, testis, thymus and uterus. Isoform 1 is expressed at high levels in heart and testis and at lower levels in brain, pancreas, skeletal muscle, small intestine and thymus.

Domain organisation. The PH domain mediates binding to membranes. It is required for efficient GEF activity.

Isoforms (7)

UniProt IDNamesCanonical?
Q5JS13-11, RALGPS1Byes
Q5JS13-22, RALGPS1A
Q5JS13-33
Q5JS13-44
Q5JS13-55
Q5JS13-66
Q5JS13-77

RefSeq proteins (13): NP_001177657, NP_001177658, NP_001177659, NP_001309249, NP_001309250, NP_001309251, NP_001309252, NP_001309253, NP_001309254, NP_001353328, NP_001353329, NP_001353330, NP_055451* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001849PH_domainDomain
IPR001895RASGEF_cat_domDomain
IPR008937Ras-like_GEFFamily
IPR011993PH-like_dom_sfHomologous_superfamily
IPR023578Ras_GEF_dom_sfHomologous_superfamily
IPR036964RASGEF_cat_dom_sfHomologous_superfamily

Pfam: PF00169, PF00617

UniProt features (43 total): helix 16, splice variant 11, sequence conflict 3, region of interest 3, domain 2, compositionally biased region 2, chain 1, sequence variant 1, mutagenesis site 1, turn 1, strand 1, short sequence motif 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
3QXLX-RAY DIFFRACTION2.24

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5JS13-F175.960.57

Functional residue map

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

Mutagenesis-validated functional residues (1):

PositionPhenotype
148loss of activity.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 168 (showing top): BROWNE_HCMV_INFECTION_30MIN_DN, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, CACCAGC_MIR138, RODWELL_AGING_KIDNEY_NO_BLOOD_DN, MODULE_66, BLALOCK_ALZHEIMERS_DISEASE_UP, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, GCM_NF2, GGTGAAG_MIR412, MODULE_11, GOBP_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, TGCCTTA_MIR124A

GO Biological Process (4): Ras protein signal transduction (GO:0007265), regulation of Ral protein signal transduction (GO:0032485), intracellular signal transduction (GO:0035556), small GTPase-mediated signal transduction (GO:0007264)

GO Molecular Function (2): guanyl-nucleotide exchange factor activity (GO:0005085), protein binding (GO:0005515)

GO Cellular Component (3): cytoplasm (GO:0005737), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular anatomical structure2
cellular anatomical structure2
small GTPase-mediated signal transduction1
Ral protein signal transduction1
regulation of small GTPase mediated signal transduction1
signal transduction1
intracellular signaling cassette1
GTP binding1
GDP binding1
GTPase regulator activity1
binding1
membrane1
cell periphery1

Protein interactions and networks

STRING

1382 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RALGPS1NUTM2GQ5VZR2594
RALGPS1GARNL3Q5VVW2548
RALGPS1RALBP11234510
RALGPS1RALAP11233508
RALGPS1RALGAPBQ86X10508
RALGPS1RTL9Q8NET4486
RALGPS1DPM2O94777475
RALGPS1NUGGCQ68CJ6450
RALGPS1MAP7D2Q96T17427
RALGPS1UQCC6Q69YU5425
RALGPS1RALGAPA1Q6GYQ0417
RALGPS1REPS2Q8NFH8403
RALGPS1VPS50Q96JG6380
RALGPS1GASK1BQ6UWH4361
RALGPS1SPNS3Q6ZMD2360
RALGPS1ZNF395Q9H8N7360

IntAct

4 interactions, top by confidence:

ABTypeScore
Dlg4RALGPS1psi-mi:“MI:0407”(direct interaction)0.440
C2orf88RALGPS1psi-mi:“MI:0915”(physical association)0.370
RHOGCOPEpsi-mi:“MI:0914”(association)0.350

BioGRID (15): RALGPS1 (Affinity Capture-RNA), RALGPS1 (Positive Genetic), RALGPS1 (Synthetic Lethality), RALGPS1 (Two-hybrid), RALA (Biochemical Activity), GRB2 (Affinity Capture-Western), NCK1 (Affinity Capture-Western), RALGPS1 (Affinity Capture-RNA), RALGPS1 (Cross-Linking-MS (XL-MS)), RALGPS1 (Co-fractionation), RALGPS1 (Co-fractionation), RALGPS1 (Reconstituted Complex), RALGPS1 (Affinity Capture-RNA), APP (Reconstituted Complex), RALGPS1 (Two-hybrid)

ESM2 similar proteins: A2AR50, B0UXH6, D3ZAZ5, D4AB98, F1M386, F1MSG6, F1PBJ0, F7EL49, O60343, O75044, O97790, P0CE43, P42331, Q00IB7, Q13905, Q14155, Q15678, Q28CB1, Q4R7W3, Q58DL5, Q5JS13, Q5U2Z7, Q5ZJK0, Q60695, Q60949, Q62130, Q62136, Q6INE5, Q6INP9, Q6P112, Q6P549, Q7Z6B7, Q80TI1, Q86TI0, Q86X27, Q8BYJ6, Q8BYW1, Q8C4V1, Q8CHG7, Q8IV61

Diamond homologs: A2AR50, A2CEA7, B0M0P8, B0UXH6, F1M386, F1MSG6, F1PBJ0, O14827, P27671, P28818, P70392, Q03385, Q03386, Q07889, Q07890, Q12967, Q13905, Q13972, Q3MIN7, Q3UYI5, Q4R7W3, Q54FF3, Q54PQ4, Q54TK8, Q552M5, Q55GH9, Q5JS13, Q5ZJK0, Q60695, Q86G47, Q86X27, Q8CHG7, Q8IS14, Q8IS15, Q8IS16, Q8IS18, Q8IS20, Q8IS21, Q8SSQ0, Q8SSW7

SIGNOR signaling

1 interactions.

AEffectBMechanism
IRX1“up-regulates quantity by expression”RALGPS1“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance39
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

6291 predictions. Top by Δscore:

VariantEffectΔscore
9:126952903:G:GTdonor_gain1.0000
9:126952960:G:GTdonor_gain1.0000
9:126965842:AG:Aacceptor_gain1.0000
9:126965843:GG:Gacceptor_gain1.0000
9:126965843:GGGC:Gacceptor_gain1.0000
9:126965843:GGGCA:Gacceptor_gain1.0000
9:126965948:TGCT:Tdonor_gain1.0000
9:126965948:TGCTG:Tdonor_loss1.0000
9:126965949:GCT:Gdonor_gain1.0000
9:126965949:GCTG:Gdonor_gain1.0000
9:126965950:CT:Cdonor_gain1.0000
9:126965950:CTGT:Cdonor_loss1.0000
9:126965951:TGTAA:Tdonor_loss1.0000
9:126965952:G:GGdonor_gain1.0000
9:126965952:GT:Gdonor_loss1.0000
9:126965953:TAAGT:Tdonor_loss1.0000
9:127052935:GGGCT:Gdonor_gain1.0000
9:127052936:GGCT:Gdonor_gain1.0000
9:127052936:GGCTG:Gdonor_gain1.0000
9:127052937:GCT:Gdonor_gain1.0000
9:127052937:GCTG:Gdonor_gain1.0000
9:127052940:G:GGdonor_gain1.0000
9:127069223:A:AGacceptor_gain1.0000
9:127069226:CTA:Cacceptor_loss1.0000
9:127069227:TA:Tacceptor_loss1.0000
9:127069228:A:AGacceptor_gain1.0000
9:127069228:AGCT:Aacceptor_loss1.0000
9:127069229:G:GAacceptor_gain1.0000
9:127069229:GC:Gacceptor_gain1.0000
9:127069229:GCT:Gacceptor_gain1.0000

AlphaMissense

3656 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:126965950:C:AA55D1.000
9:126977705:C:AT59K1.000
9:126977735:T:AI69N1.000
9:127034435:T:CL74P1.000
9:127034449:T:AW79R1.000
9:127034449:T:CW79R1.000
9:127034451:G:CW79C1.000
9:127034451:G:TW79C1.000
9:127034506:T:CF98L1.000
9:127034508:T:AF98L1.000
9:127034508:T:GF98L1.000
9:127034511:C:AN99K1.000
9:127034511:C:GN99K1.000
9:127050052:T:AW104R1.000
9:127050052:T:CW104R1.000
9:127050071:T:AL110Q1.000
9:127050071:T:CL110P1.000
9:127050094:A:GR118G1.000
9:127050094:A:TR118W1.000
9:127050095:G:CR118T1.000
9:127050095:G:TR118M1.000
9:127050096:G:CR118S1.000
9:127050096:G:TR118S1.000
9:127050097:G:CA119P1.000
9:127050107:T:CL122P1.000
9:127050128:C:AA129D1.000
9:127052851:T:CL132P1.000
9:127052867:C:AN137K1.000
9:127052867:C:GN137K1.000
9:127052896:C:AA147E1.000

dbSNP variants (sampled 300 via entrez): RS1000015196 (9:127189256 C>T), RS1000026958 (9:127051755 C>G), RS1000030645 (9:126941300 A>G), RS1000045052 (9:127052025 T>C), RS1000049814 (9:127090893 G>A), RS1000054131 (9:127097175 T>G), RS1000060252 (9:127059533 T>C,G), RS1000063748 (9:126913304 G>A), RS1000078808 (9:126918827 C>A,T), RS1000081401 (9:127173579 C>T), RS1000087395 (9:127003306 T>G), RS1000105970 (9:127087935 A>C), RS1000123215 (9:127103644 G>C), RS1000123747 (9:127132268 T>C), RS1000124582 (9:127064438 T>C)

Disease associations

OMIM: gene MIM:614444 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

14 associations (top):

StudyTraitp-value
GCST003264_163Post bronchodilator FEV1/FVC ratio3.000000e-06
GCST005580_229Intraocular pressure1.000000e-17
GCST005580_246Intraocular pressure9.000000e-11
GCST006412_109Intraocular pressure2.000000e-18
GCST007201_109Schizophrenia1.000000e-07
GCST007294_106Body fat distribution (trunk fat ratio)2.000000e-08
GCST007294_69Body fat distribution (trunk fat ratio)1.000000e-09
GCST007295_19Body fat distribution (leg fat ratio)1.000000e-09
GCST007295_78Body fat distribution (leg fat ratio)3.000000e-13
GCST009066_19Mosaic loss of chromosome Y (Y chromosome dosage)1.000000e-12
GCST009725_26Intraocular pressure2.000000e-14
GCST010703_39Brain morphology (MOSTest)9.000000e-09
GCST012368_6Early-onset schizophrenia4.000000e-11
GCST90000025_381Appendicular lean mass1.000000e-17

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0004713FEV/FVC ratio
EFO:0004695intraocular pressure measurement
EFO:0004341body fat distribution
EFO:0007783mosaic loss of chromosome Y measurement
EFO:0004346neuroimaging measurement
EFO:0004980appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression, decreases methylation5
Valproic Acidaffects cotreatment, increases expression, affects expression, increases methylation4
trichostatin Aincreases expression, affects cotreatment, decreases expression3
Aflatoxin B1affects expression, decreases expression, increases methylation3
sodium arseniteaffects cotreatment, decreases expression, increases abundance, increases expression2
Arsenicaffects methylation, affects cotreatment, decreases expression, increases abundance2
Phenylmercuric Acetatedecreases expression, affects cotreatment2
Smokeincreases expression, decreases expression, increases abundance2
Cyclosporinedecreases expression2
aristolochic acid Idecreases expression1
methylmercuric chloridedecreases expression1
methyleugenoldecreases expression1
beta-lapachonedecreases expression1
butyraldehydedecreases expression1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
periodate-oxidized adenosineaffects expression1
aflatoxin B2decreases methylation1
di-n-butylphosphoric acidaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
ICG 001increases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
bisphenol Sincreases methylation1
jinfukangaffects cotreatment, decreases expression, increases expression1
Sunitinibincreases expression1
Arsenic Trioxideincreases expression1
Acetaminophenincreases expression1
Air Pollutantsincreases expression, increases abundance1
Arsenicalsincreases methylation1
Caffeinedecreases phosphorylation1

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.