GMIP

gene
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Also known as ARHGAP46

Summary

GMIP (GEM interacting protein, HGNC:24852) is a protein-coding gene on chromosome 19p13.11, encoding GEM-interacting protein (Q9P107). Stimulates, in vitro and in vivo, the GTPase activity of RhoA.

This gene encodes a member of the ARHGAP family of Rho/Rac/Cdc42-like GTPase activating proteins. The encoded protein interacts with the Ras-related protein Gem through its N-terminal domain. Separately, it interacts with RhoA through a RhoGAP domain, and stimulates RhoA-dependent GTPase activity. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 51291 — RefSeq curated summary.

At a glance

  • GWAS associations: 26
  • Clinical variants (ClinVar): 148 total
  • MANE Select transcript: NM_016573

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24852
Approved symbolGMIP
NameGEM interacting protein
Location19p13.11
Locus typegene with protein product
StatusApproved
AliasesARHGAP46
Ensembl geneENSG00000089639
Ensembl biotypeprotein_coding
OMIM609694
Entrez51291

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 8 protein_coding, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000203556, ENST00000586269, ENST00000587205, ENST00000587238, ENST00000587713, ENST00000588171, ENST00000591047, ENST00000593186, ENST00000905971, ENST00000905972, ENST00000916819, ENST00000940889

RefSeq mRNA: 3 — MANE Select: NM_016573 NM_001288998, NM_001288999, NM_016573

CCDS: CCDS12408, CCDS74318

Canonical transcript exons

ENST00000203556 — 21 exons

ExonStartEnd
ENSE000005707741963380319634190
ENSE000006917101963047119630537
ENSE000006917251963450719634703
ENSE000006917281963541519635569
ENSE000006917301963564419635721
ENSE000006917371963736519637561
ENSE000006917411963792019638057
ENSE000009518361963815919638329
ENSE000011135541962947619630336
ENSE000012244671964351119643657
ENSE000034592131964008519640192
ENSE000034722561963502519635213
ENSE000034979231963670719636796
ENSE000035199351964181019641867
ENSE000035224231964044619640571
ENSE000035235071963691719637029
ENSE000035704291963840219638482
ENSE000035797021964029619640360
ENSE000035836691964253519642619
ENSE000036079331964197619642051
ENSE000036397461963479219634929

Expression profiles

Bgee: expression breadth ubiquitous, 219 present calls, max score 97.46.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.9896 / max 1234.6092, expressed in 1774 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
18016416.61711774
1801630.3482169
1801610.024318

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009497.46gold quality
bloodUBERON:000017895.56gold quality
monocyteCL:000057695.14gold quality
leukocyteCL:000073895.02gold quality
mononuclear cellCL:000084294.91gold quality
spleenUBERON:000210693.27gold quality
vermiform appendixUBERON:000115491.89gold quality
lymph nodeUBERON:000002990.26gold quality
bone marrow cellCL:000209290.22gold quality
caecumUBERON:000115389.09gold quality
cortical plateUBERON:000534387.45gold quality
mucosa of transverse colonUBERON:000499186.92gold quality
ganglionic eminenceUBERON:000402386.45gold quality
right lungUBERON:000216785.80gold quality
small intestine Peyer’s patchUBERON:000345485.68gold quality
bone marrowUBERON:000237185.17gold quality
upper lobe of left lungUBERON:000895284.45gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.15gold quality
gall bladderUBERON:000211083.89gold quality
sural nerveUBERON:001548883.86gold quality
small intestineUBERON:000210883.85gold quality
upper lobe of lungUBERON:000894883.51gold quality
rectumUBERON:000105282.54gold quality
superficial temporal arteryUBERON:000161482.44gold quality
tonsilUBERON:000237282.30gold quality
stromal cell of endometriumCL:000225581.86gold quality
lower esophagus mucosaUBERON:003583481.45gold quality
transverse colonUBERON:000115781.41gold quality
body of stomachUBERON:000116181.29gold quality
periodontal ligamentUBERON:000826681.17silver quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes7.17
E-MTAB-6142no94.85

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting GMIP, 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-4692100.0067.322066
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-451499.9967.101870
HSA-MIR-34C-5P99.9770.451577
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-444799.8567.812900
HSA-MIR-370-5P99.7866.81706
HSA-MIR-431999.7669.832586
HSA-MIR-119799.7067.751027
HSA-MIR-3689A-3P99.7065.732306
HSA-MIR-3689B-3P99.7065.712311
HSA-MIR-3689C99.7065.712311
HSA-MIR-447299.5666.081478
HSA-MIR-6808-5P99.3166.232150
HSA-MIR-6799-5P99.1465.722093
HSA-MIR-4725-5P98.6765.42628
HSA-MIR-504-5P98.6765.40631
HSA-MIR-4701-5P96.4568.411121
HSA-MIR-58896.4568.361127
HSA-MIR-129196.2865.891224
HSA-MIR-6775-3P95.7665.91982

Literature-anchored findings (GeneRIF, showing 4)

  • signalling pathways controlled by two proteins of the Ras superfamily, RhoA and Gem, are linked via the action of the RhoGAP protein Gmip (PMID:12093360)
  • Variations in the GMIP gene can confer susceptibility to major depressive disorder. (PMID:16086184)
  • during exocytosis, actin depolymerization commences near the secretory organelle, not the plasma membrane, and secretory granules use a JFC1- and GMIP-dependent molecular mechanism to traverse cortical actin. (PMID:22438581)
  • These findings demonstrate a new role of Gem/Gmip/RhoA signaling in cortical actin regulation during early mitotic stages (PMID:25173885)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriogmipENSDARG00000077249
mus_musculusGmipENSMUSG00000036246
rattus_norvegicusGmipENSRNOG00000027257
caenorhabditis_elegansWBGENE00014051

Paralogs (2): ARHGAP29 (ENSG00000137962), ARHGAP45 (ENSG00000180448)

Protein

Protein identifiers

GEM-interacting proteinQ9P107 (reviewed: Q9P107)

All UniProt accessions (5): Q9P107, A0A024R7N1, K7EJC2, K7ELE8, K7EQR5

UniProt curated annotations — full annotation on UniProt →

Function. Stimulates, in vitro and in vivo, the GTPase activity of RhoA.

Subunit / interactions. Interacts with GEM through its N-terminal.

Isoforms (2)

UniProt IDNamesCanonical?
Q9P107-11yes
Q9P107-22

RefSeq proteins (3): NP_001275927, NP_001275928, NP_057657* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000198RhoGAP_domDomain
IPR002219PKC_DAG/PEDomain
IPR008936Rho_GTPase_activation_protHomologous_superfamily
IPR027267AH/BAR_dom_sfHomologous_superfamily
IPR031160F_BAR_domDomain
IPR046349C1-like_sfHomologous_superfamily
IPR051025RhoGAPFamily
IPR054713GMIP/FCHO2-like_FCHDomain

Pfam: PF00620, PF22699

UniProt features (44 total): modified residue 13, compositionally biased region 8, helix 7, region of interest 5, sequence conflict 3, domain 2, chain 1, site 1, zinc finger region 1, splice variant 1, sequence variant 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
3QWEX-RAY DIFFRACTION2.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9P107-F170.020.48

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

Post-translational modifications (13): 19, 71, 231, 234, 243, 437, 441, 660, 885, 907, 914, 919, 923

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-8980692RHOA GTPase cycle
R-HSA-9013148CDC42 GTPase cycle
R-HSA-9013149RAC1 GTPase cycle

MSigDB gene sets: 142 (showing top): GCANCTGNY_MYOD_Q6, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, MORI_IMMATURE_B_LYMPHOCYTE_UP, GGGTGGRR_PAX4_03, GOBP_NEGATIVE_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GNF2_MCL1, GNF2_ICAM3, GNF2_S100A4, GNF2_MYD88, GNF2_HCK, DANG_BOUND_BY_MYC, GOBP_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, AP2GAMMA_01

GO Biological Process (5): small GTPase-mediated signal transduction (GO:0007264), intracellular signal transduction (GO:0035556), regulation of small GTPase mediated signal transduction (GO:0051056), negative regulation of small GTPase mediated signal transduction (GO:0051058), signal transduction (GO:0007165)

GO Molecular Function (4): GTPase activator activity (GO:0005096), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (3): nucleoplasm (GO:0005654), cytosol (GO:0005829), plasma membrane (GO:0005886)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
RHO GTPase cycle3

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
small GTPase-mediated signal transduction2
cellular anatomical structure2
intracellular signaling cassette1
intracellular anatomical structure1
signal transduction1
regulation of intracellular signal transduction1
regulation of small GTPase mediated signal transduction1
negative regulation of intracellular signal transduction1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
GTPase activity1
enzyme activator activity1
GTPase regulator activity1
transition metal ion binding1
binding1
cation binding1
nuclear lumen1
cytoplasm1
membrane1
cell periphery1

Protein interactions and networks

STRING

1138 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GMIPRHOAP06749690
GMIPSYTL1Q8IYJ3682
GMIPRAB27AP51159555
GMIPYJEFN3A6XGL0475
GMIPAKNAQ7Z591456
GMIPZNF101Q8IZC7434
GMIPMYRIPQ8NFW9430
GMIPLARS2Q15031410
GMIPATP13A1Q9HD20406
GMIPTTC21AQ8NDW8388
GMIPSTARD13Q9Y3M8388
GMIPYRDCQ86U90367
GMIPBORCS8Q96FH0364
GMIPZNF14P17017355
GMIPCELSR3Q9NYQ7345

IntAct

11 interactions, top by confidence:

ABTypeScore
ARHGAP45GMIPpsi-mi:“MI:0915”(physical association)0.560
GMIPACAD8psi-mi:“MI:0915”(physical association)0.400
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
ADGRG2CFAP69psi-mi:“MI:0914”(association)0.350
PRPS2SMCHD1psi-mi:“MI:0914”(association)0.350
CTAG1ADPYSL4psi-mi:“MI:0914”(association)0.350
CTAG1APER1psi-mi:“MI:0914”(association)0.350
SLC35E1IPO8psi-mi:“MI:0914”(association)0.350
ARHGAP45GMIPpsi-mi:“MI:0915”(physical association)0.000

BioGRID (35): GMIP (Co-fractionation), GMIP (Affinity Capture-MS), GMIP (Affinity Capture-MS), GMIP (Affinity Capture-MS), HMHA1 (Two-hybrid), GMIP (Two-hybrid), GEM (Affinity Capture-Western), GMIP (FRET), GMIP (FRET), GMIP (FRET), EBNA1BP2 (Affinity Capture-MS), FLOT1 (Affinity Capture-MS), LRPAP1 (Affinity Capture-MS), NUP35 (Affinity Capture-MS), PSPC1 (Affinity Capture-MS)

ESM2 similar proteins: A1IGU3, A1IGU4, A1IGU5, A6QP29, B1AVH7, B2RUP2, B5DFA1, D2H0G5, D3ZFJ3, O15068, O55043, P00530, P07332, P14238, P16879, P55194, P98171, Q0GNC1, Q14155, Q15052, Q27J81, Q3U5C8, Q3UMR0, Q58EX7, Q5VV41, Q5XXR3, Q5ZLR6, Q60I26, Q63406, Q64096, Q6PFY1, Q6PGG2, Q70J99, Q7TNH6, Q80TT2, Q80VK6, Q86WN1, Q8C2K1, Q8C6B2, Q8CJ00

Diamond homologs: A0A0G2JTR4, A1A4S6, A2AB59, A2RUV4, A4IF90, A4II46, A6QNS3, A6X8Z5, A7KAX9, A7YY57, A8WRJ2, D3ZFJ3, E7EZG2, E7F3F0, F1LXF1, O14559, O94466, P11274, P15882, P30337, P34288, P38339, P46941, P52757, P55194, P81128, P97393, Q03070, Q08DP6, Q10164, Q12979, Q13017, Q15311, Q17QN0, Q20498, Q2M1Z3, Q3TBD2, Q3UIA2, Q52LW3, Q53QZ3

SIGNOR signaling

3 interactions.

AEffectBMechanism
GMIP“down-regulates activity”RHOA“gtpase-activating protein”
GMIP“down-regulates activity”RAC1“gtpase-activating protein”
GMIP“down-regulates activity”CDC42“gtpase-activating protein”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance122
Likely benign8
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2772 predictions. Top by Δscore:

VariantEffectΔscore
19:19630467:TCA:Tdonor_loss1.0000
19:19630468:CA:Cdonor_loss1.0000
19:19630469:A:ATdonor_loss1.0000
19:19630533:GGAAT:Gacceptor_gain1.0000
19:19630534:GAAT:Gacceptor_gain1.0000
19:19630536:AT:Aacceptor_gain1.0000
19:19630537:TC:Tacceptor_loss1.0000
19:19630538:C:CAacceptor_loss1.0000
19:19630538:C:CCacceptor_gain1.0000
19:19634186:CCACC:Cacceptor_gain1.0000
19:19634187:CACC:Cacceptor_gain1.0000
19:19634187:CACCC:Cacceptor_gain1.0000
19:19634189:CC:Cacceptor_gain1.0000
19:19634190:CC:Cacceptor_gain1.0000
19:19634191:C:CCacceptor_gain1.0000
19:19634790:ACCT:Adonor_gain1.0000
19:19634791:CCTC:Cdonor_gain1.0000
19:19634793:T:TAdonor_gain1.0000
19:19634927:GCCC:Gacceptor_loss1.0000
19:19634928:CCCT:Cacceptor_loss1.0000
19:19634930:CTGC:Cacceptor_loss1.0000
19:19634931:T:Cacceptor_loss1.0000
19:19635086:T:TAdonor_gain1.0000
19:19635416:T:TAdonor_gain1.0000
19:19635422:CA:Cdonor_gain1.0000
19:19635429:T:TAdonor_gain1.0000
19:19635570:C:CCacceptor_gain1.0000
19:19636913:TCACC:Tdonor_loss1.0000
19:19636914:CACCT:Cdonor_loss1.0000
19:19636915:A:ACdonor_gain1.0000

AlphaMissense

6244 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:19635495:G:CH494D0.998
19:19634161:A:GM705T0.997
19:19634910:C:TG590E0.997
19:19634929:C:GG584R0.997
19:19635198:G:CH526D0.997
19:19635423:A:GC518R0.997
19:19635462:A:GC505R0.997
19:19635493:G:CH494Q0.997
19:19635493:G:TH494Q0.997
19:19635503:G:TA491D0.997
19:19638445:C:GR192P0.997
19:19634807:C:AK624N0.996
19:19634807:C:GK624N0.996
19:19634923:A:CY586D0.996
19:19635063:A:GC571R0.996
19:19635164:C:TC537Y0.996
19:19635189:A:GC529R0.996
19:19635213:A:GC521R0.996
19:19635461:C:GC505S0.996
19:19635462:A:TC505S0.996
19:19634513:A:GL693P0.995
19:19634919:C:GR587P0.995
19:19635164:C:GC537S0.995
19:19635165:A:TC537S0.995
19:19635188:C:GC529S0.995
19:19635189:A:TC529S0.995
19:19635196:G:CH526Q0.995
19:19635196:G:TH526Q0.995
19:19635422:C:GC518S0.995
19:19635423:A:TC518S0.995

dbSNP variants (sampled 300 via entrez): RS1000014813 (19:19630685 C>G,T), RS1000299919 (19:19643617 AGCCGCCGCCGCC>A,AGCC,AGCCGCC,AGCCGCCGCC,AGCCGCCGCCGCCGCC,AGCCGCCGCCGCCGCCGCC,AGCCGCCGCCGCCGCCGCCGCC,AGCCGCCGCCGCCGCCGCCGCCGCC,AGCCGCCGCCGCCGCCGCCGCCGCCGCC), RS1000351996 (19:19643709 T>C), RS1000869474 (19:19635878 T>C), RS1001159277 (19:19629719 C>T), RS1001262398 (19:19642907 G>A,C), RS1001423984 (19:19629399 T>C), RS1001605626 (19:19642700 G>A), RS1001850018 (19:19637187 T>C), RS1002159601 (19:19641432 G>A,C), RS1002212002 (19:19641738 G>A), RS1002300955 (19:19637519 G>A,T), RS1002689684 (19:19640630 C>G,T), RS1002917251 (19:19644822 G>A,C), RS1003102951 (19:19645101 C>G)

Disease associations

OMIM: gene MIM:609694 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

26 associations (top):

StudyTraitp-value
GCST002149_11Schizophrenia3.000000e-09
GCST008074_33Triglyceride levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)2.000000e-39
GCST008074_98Triglyceride levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)8.000000e-44
GCST008076_31Triglyceride levels4.000000e-14
GCST008076_59Triglyceride levels1.000000e-20
GCST008077_11LDL cholesterol levels6.000000e-12
GCST008077_62LDL cholesterol levels1.000000e-10
GCST008078_133LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)2.000000e-193
GCST008078_96LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)5.000000e-226
GCST008079_115LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)6.000000e-39
GCST008079_47LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)4.000000e-31
GCST008083_106Triglyceride levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)5.000000e-40
GCST008083_142Triglyceride levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)7.000000e-47
GCST008086_19LDL cholesterol levels in current drinkers8.000000e-20
GCST008086_80LDL cholesterol levels in current drinkers2.000000e-21
GCST008087_118Triglyceride levels in current drinkers1.000000e-23
GCST008087_75Triglyceride levels in current drinkers4.000000e-22
GCST008103_10Bipolar disorder1.000000e-09
GCST008115_2Bipolar I disorder3.000000e-09
GCST008116_4Bipolar II disorder4.000000e-06
GCST009600_14Anorexia nervosa, attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, or Tourette syndrome (pleiotropy)1.000000e-09
GCST010002_52Refractive error4.000000e-29
GCST90002379_198Basophil count1.000000e-18
GCST90002380_13Basophil percentage of white cells3.000000e-17
GCST90002389_401Lymphocyte percentage of white cells3.000000e-10
GCST90002399_231Neutrophil percentage of white cells1.000000e-13

EFO canonical traits (9, from GWAS)

EFO IDTrait name
EFO:0004530triglyceride measurement
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0004329alcohol drinking
EFO:0009963bipolar I disorder
EFO:0009964bipolar II disorder
EFO:0005090basophil count
EFO:0007992basophil percentage of leukocytes
EFO:0007993lymphocyte percentage of leukocytes
EFO:0007990neutrophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Air Pollutantsaffects expression, increases abundance, increases expression2
Benzo(a)pyreneincreases expression, increases methylation2
Nickelincreases expression2
Tobacco Smoke Pollutionincreases expression, increases methylation2
Valproic Acidaffects expression, increases methylation2
aristolochic acid Iincreases expression1
GSK-J4decreases expression1
FR900359affects phosphorylation1
triphenyl phosphateaffects expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
sodium arseniteincreases expression1
cobaltous chloridedecreases expression1
coumarindecreases phosphorylation1
muconaldehydedecreases expression1
N,N,N’,N’-tetrakis(2-pyridylmethyl)ethylenediaminedecreases expression1
di-n-butylphosphoric acidaffects expression1
deguelindecreases expression1
thifluzamidedecreases expression1
abrineincreases expression1
pyrachlostrobindecreases expression1
bisphenol Sdecreases methylation1
Resveratrolaffects cotreatment, decreases expression1
Sunitinibdecreases expression1
Caffeinedecreases phosphorylation1
Diazinonincreases methylation1
Doxorubicindecreases expression1
Ozoneaffects expression, increases abundance1
Plant Extractsaffects cotreatment, decreases expression1
Rotenonedecreases expression1
Tretinoinincreases 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.