GPSM3

gene
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Also known as NG1G18G18.1aG18.1bG18.2AGS4

Summary

GPSM3 (G protein signaling modulator 3, HGNC:13945) is a protein-coding gene on chromosome 6p21.32, encoding G-protein-signaling modulator 3 (Q9Y4H4). Interacts with subunit of G(i) alpha proteins and regulates the activation of G(i) alpha proteins.

Predicted to enable GTPase regulator activity. Predicted to be involved in positive regulation of inflammatory response. Predicted to act upstream of or within positive regulation of cytokine production involved in inflammatory response and positive regulation of leukocyte chemotaxis. Predicted to be located in cytoplasm and plasma membrane.

Source: NCBI Gene 63940 — RefSeq curated summary.

At a glance

  • GWAS associations: 33
  • Clinical variants (ClinVar): 29 total
  • MANE Select transcript: NM_001276501

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13945
Approved symbolGPSM3
NameG protein signaling modulator 3
Location6p21.32
Locus typegene with protein product
StatusApproved
AliasesNG1, G18, G18.1a, G18.1b, G18.2, AGS4
Ensembl geneENSG00000213654
Ensembl biotypeprotein_coding
OMIM618558
Entrez63940

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 nonsense_mediated_decay

ENST00000375040, ENST00000375043, ENST00000472768, ENST00000487761, ENST00000619085, ENST00000874270, ENST00000874271, ENST00000934374

RefSeq mRNA: 2 — MANE Select: NM_001276501 NM_001276501, NM_022107

CCDS: CCDS34419

Canonical transcript exons

ENST00000375040 — 4 exons

ExonStartEnd
ENSE000016601633219214832192250
ENSE000017274993219170932191908
ENSE000018113533219247232192643
ENSE000036457923219076632191503

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 99.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 48.9197 / max 2505.6758, expressed in 1578 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
7293323.68941245
7293613.02221334
7293211.7123752
729300.192593
729340.123758
729350.113854
729310.065720

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009499.44gold quality
bloodUBERON:000017899.34gold quality
spleenUBERON:000210698.96gold quality
lymph nodeUBERON:000002998.55gold quality
leukocyteCL:000073898.52gold quality
monocyteCL:000057698.44gold quality
vermiform appendixUBERON:000115498.37gold quality
bone marrowUBERON:000237198.33gold quality
bone marrow cellCL:000209298.23gold quality
right lungUBERON:000216796.13gold quality
upper lobe of left lungUBERON:000895294.72gold quality
placentaUBERON:000198792.87gold quality
small intestine Peyer’s patchUBERON:000345492.50gold quality
lungUBERON:000204891.95gold quality
gall bladderUBERON:000211091.89gold quality
small intestineUBERON:000210891.77gold quality
omental fat padUBERON:001041490.78gold quality
adipose tissueUBERON:000101388.72gold quality
right coronary arteryUBERON:000162588.05gold quality
mucosa of transverse colonUBERON:000499187.75gold quality
duodenumUBERON:000211487.71gold quality
apex of heartUBERON:000209887.27gold quality
subcutaneous adipose tissueUBERON:000219087.14gold quality
tonsilUBERON:000237286.55gold quality
C1 segment of cervical spinal cordUBERON:000646986.51gold quality
left uterine tubeUBERON:000130386.37gold quality
rectumUBERON:000105286.24gold quality
olfactory segment of nasal mucosaUBERON:000538685.98gold quality
transverse colonUBERON:000115785.93gold quality
intestineUBERON:000016085.46gold quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 8.

ExperimentMarker?Max mean expression
E-MTAB-6701yes89.03
E-MTAB-10287yes32.88
E-HCAD-10yes26.98
E-GEOD-134144yes25.42
E-CURD-112yes19.13
E-MTAB-8410yes13.24
E-ANND-3yes11.73
E-MTAB-9388yes10.60
E-HCAD-8no175.97
E-CURD-89no96.31
E-MTAB-5061no3.84

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

46 targeting GPSM3, 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-6825-5P99.9669.813431
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-464899.9167.00710
HSA-MIR-449299.8768.253611
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-6764-5P99.7567.892304
HSA-MIR-149-3P99.7268.223963
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-320299.6667.702737
HSA-MIR-1915-3P99.5866.791988
HSA-MIR-76299.5866.611994
HSA-MIR-7106-5P99.5367.473574
HSA-MIR-143-3P99.4969.051457
HSA-MIR-477099.4969.091451
HSA-MIR-449899.4767.422360
HSA-MIR-132499.4666.571302
HSA-MIR-377-3P99.3770.181905
HSA-MIR-608899.2968.451284
HSA-MIR-6731-5P99.2867.422375
HSA-MIR-319999.1765.19696
HSA-MIR-805299.1765.01719
HSA-MIR-6809-5P99.1368.451223
HSA-MIR-5001-5P99.0566.761972
HSA-MIR-6895-3P98.7965.69996
HSA-MIR-797798.6566.182590
HSA-MIR-6830-3P98.6268.071760
HSA-MIR-6878-5P98.4967.912142
HSA-MIR-6824-3P98.4467.621154
HSA-MIR-6764-3P98.4467.641153

Literature-anchored findings (GeneRIF, showing 7)

  • Mutational analysis of the role of GoLoco motifs in guanine nucleotide dissociation inhibitor activity of G18 protein. (PMID:14656218)
  • AGS4-Galpha(i) complexes directly couple to a G-protein-coupled receptor and may serve as substrates for agonist-induced G-protein activation. (PMID:20452976)
  • GPSM3 increases Gbeta stability until formation of the Gbetagamma dimer, including association of the Gbeta-GPSM3 complex with phosducin-like protein PhLP and T-complex protein 1 subunit eta (CCT7), two known chaperones of neosynthesized Gbeta subunits. (PMID:22167191)
  • Phosphorylation of GPSM3 by a proline-directed serine/threonine kinase and the resultant association of 14-3-3 is the first description of post-translational regulation of GPSM3 subcellular localization (PMID:22843681)
  • findings suggest that GPSM3 acts as a direct negative regulator of NLRP3 function. (PMID:25271165)
  • Genetic variations in GPSM3 which are associated with protection from rheumatoid arthritis affect its transcript abundance. (PMID:26821282)
  • role for GPSM3 in neutrophil migration toward proinflammatory chemoattractants LTB4 and CXCL8-a discovery that helps strengthen the association between the promoter-weakening GPSM3 SNP rs204989 and a reduced risk of rheumatoid arthritis (PMID:27307211)

Cross-species orthologs

1 orthologs

OrganismSymbolGene ID
mus_musculusGpsm3ENSMUSG00000034786

Paralogs (6): TTC28 (ENSG00000100154), GPSM2 (ENSG00000121957), TTC29 (ENSG00000137473), GPSM1 (ENSG00000160360), RAPSN (ENSG00000165917), TTC24 (ENSG00000187862)

Protein

Protein identifiers

G-protein-signaling modulator 3Q9Y4H4 (reviewed: Q9Y4H4)

Alternative names: Activator of G-protein signaling 4, G18.1b, Protein G18

All UniProt accessions (6): A0A024RCP6, E9PIE9, E9PIP3, P78548, Q9Y4H4, Q9Y4H5

UniProt curated annotations — full annotation on UniProt →

Function. Interacts with subunit of G(i) alpha proteins and regulates the activation of G(i) alpha proteins.

Subcellular location. Cytoplasm.

Tissue specificity. Expressed in heart, placenta, lung and liver.

Domain organisation. The GoLoco 1 and/or GoLoco 3 domains exhibit GDI activity towards GDP-bound G(i) alpha protein, but not the GoLoco 2 domain.

RefSeq proteins (2): NP_001263430, NP_071390 (=MANE)

Domains & families (InterPro)

IDNameType
IPR003109GoLoco_motifConserved_site
IPR011990TPR-like_helical_dom_sfHomologous_superfamily
IPR042888GPSM3Family

Pfam: PF02188

UniProt features (14 total): modified residue 5, domain 3, compositionally biased region 2, chain 1, mutagenesis site 1, sequence conflict 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y4H4-F171.770.24

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 (5): 59, 62, 35, 39, 56

Mutagenesis-validated functional residues (1):

PositionPhenotype
121restores g(i) alpha binding and gdi activity of the goloco 2 domain.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-418594G alpha (i) signalling events

MSigDB gene sets: 240 (showing top): BROWNE_HCMV_INFECTION_30MIN_DN, GSE45365_NK_CELL_VS_CD11B_DC_DN, AP1_01, GOBP_CELL_CHEMOTAXIS, MODULE_255, GOBP_INFLAMMATORY_RESPONSE, GCM_MSN, MODULE_45, MODULE_317, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION, MODULE_16, GOBP_REGULATION_OF_LEUKOCYTE_MIGRATION, GOBP_LEUKOCYTE_CHEMOTAXIS, MODULE_118

GO Biological Process (4): positive regulation of leukocyte chemotaxis (GO:0002690), positive regulation of inflammatory response (GO:0050729), positive regulation of cytokine production involved in inflammatory response (GO:1900017), regulation of inflammatory response (GO:0050727)

GO Molecular Function (2): GTPase regulator activity (GO:0030695), protein binding (GO:0005515)

GO Cellular Component (3): cytoplasm (GO:0005737), plasma membrane (GO:0005886), cellular_component (GO:0005575)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
GPCR downstream signalling1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
inflammatory response2
positive regulation of leukocyte migration1
regulation of leukocyte chemotaxis1
leukocyte chemotaxis1
positive regulation of chemotaxis1
positive regulation of defense response1
positive regulation of response to external stimulus1
regulation of inflammatory response1
positive regulation of cytokine production1
cytokine production involved in inflammatory response1
regulation of cytokine production involved in inflammatory response1
regulation of defense response1
regulation of response to external stimulus1
GTPase activity1
nucleoside-triphosphatase regulator activity1
binding1
intracellular anatomical structure1
cellular anatomical structure1
membrane1
cell periphery1

Protein interactions and networks

STRING

1490 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GPSM3EGFL8Q99944721
GPSM3SUCLG2Q96I99718
GPSM3PRRT1Q99946641
GPSM3GPSM1Q86YR5599
GPSM3PCP2Q8IVA1570
GPSM3FGD2Q7Z6J4558
GPSM3GPSM2P81274521
GPSM3DXOO77932447
GPSM3FKBPLQ9UIM3422
GPSM3FBP1P09467419
GPSM3FPR3P25089416
GPSM3TDRD5Q8NAT2402
GPSM3LYZP00695394
GPSM3TCF19Q9Y242381
GPSM3PBX2P40425379

IntAct

184 interactions, top by confidence:

ABTypeScore
GPSM3GNAI1psi-mi:“MI:0915”(physical association)0.830
GNAI1GPSM3psi-mi:“MI:0915”(physical association)0.830
GPSM3GNAI3psi-mi:“MI:0915”(physical association)0.780
GNAI3GPSM3psi-mi:“MI:0915”(physical association)0.780
YWHAZGPSM3psi-mi:“MI:0915”(physical association)0.740
GNAI2GPSM3psi-mi:“MI:0915”(physical association)0.670
GPSM3GNAI2psi-mi:“MI:0915”(physical association)0.670
MEOX2GPSM3psi-mi:“MI:0915”(physical association)0.560
TADA2AGPSM3psi-mi:“MI:0915”(physical association)0.560
GPSM3USHBP1psi-mi:“MI:0915”(physical association)0.560
GPSM3MEOX2psi-mi:“MI:0915”(physical association)0.560
GPSM3TADA2Apsi-mi:“MI:0915”(physical association)0.560
HSF2BPGPSM3psi-mi:“MI:0915”(physical association)0.560
TEX11GPSM3psi-mi:“MI:0915”(physical association)0.560
CTAG1AGPSM3psi-mi:“MI:0915”(physical association)0.560
SPRY3GPSM3psi-mi:“MI:0915”(physical association)0.560
FAM86C1PGPSM3psi-mi:“MI:0915”(physical association)0.560
IQCEGPSM3psi-mi:“MI:0915”(physical association)0.560
ZNF581GPSM3psi-mi:“MI:0915”(physical association)0.560
P4HA3GPSM3psi-mi:“MI:0915”(physical association)0.560
RIPK4GPSM3psi-mi:“MI:0915”(physical association)0.560

BioGRID (90): GPSM3 (Two-hybrid), GPSM3 (Two-hybrid), GPSM3 (Two-hybrid), GPSM3 (Two-hybrid), GPSM3 (Two-hybrid), USHBP1 (Two-hybrid), GPSM3 (Synthetic Growth Defect), GPSM3 (Two-hybrid), GPSM3 (Two-hybrid), GPSM3 (Affinity Capture-Western), GPSM3 (Reconstituted Complex), GPSM3 (Reconstituted Complex), GPSM3 (Two-hybrid), GPSM3 (Two-hybrid), GPSM3 (Two-hybrid)

ESM2 similar proteins: A7YY62, A7Z026, B2RYF1, H3BV60, O12972, O35393, O54951, O70141, O75078, O75864, P01344, P05524, P11487, P23695, P28686, P33717, P42642, P56717, Q00961, Q01098, Q02833, Q06643, Q06AS9, Q14957, Q15768, Q1LZB9, Q3SXP7, Q3U2I3, Q5R8V2, Q5TM22, Q6PCB0, Q862Z7, Q86VR8, Q8BKR5, Q8K4Q6, Q8N612, Q8TAD2, Q8WXS5, Q96FI4, Q96FT7

Diamond homologs: Q3U1Z5, Q6MG88, Q9Y4H4

SIGNOR signaling

4 interactions.

AEffectBMechanism
GSK3A“down-regulates quantity by destabilization”GPSM3phosphorylation
GPSM3“down-regulates activity”GNAI1binding
14-3-3“up-regulates quantity by stabilization”GPSM3binding
GPSM3“down-regulates quantity by destabilization”GNB1binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance18
Likely benign2
Benign4

Top pathogenic / likely-pathogenic (0)

SpliceAI

490 predictions. Top by Δscore:

VariantEffectΔscore
6:32191703:TCTTA:Tdonor_loss0.9900
6:32191704:CTTA:Cdonor_loss0.9900
6:32191705:TTA:Tdonor_loss0.9900
6:32191706:TA:Tdonor_loss0.9900
6:32191707:ACCT:Adonor_loss0.9900
6:32191708:C:CTdonor_loss0.9900
6:32191850:C:CTacceptor_gain0.9900
6:32191866:TCAGT:Tacceptor_gain0.9900
6:32191867:CAGTC:Cacceptor_gain0.9900
6:32192703:T:TAdonor_gain0.9900
6:32191504:C:CCacceptor_gain0.9800
6:32191707:A:ACdonor_gain0.9800
6:32191708:C:CCdonor_gain0.9800
6:32191867:CAGT:Cacceptor_gain0.9800
6:32191871:C:CCacceptor_gain0.9800
6:32192468:TCA:Tdonor_loss0.9800
6:32192469:CACCT:Cdonor_loss0.9800
6:32192470:A:Cdonor_loss0.9800
6:32192471:C:Adonor_loss0.9800
6:32191512:G:GCacceptor_gain0.9700
6:32191868:AGT:Aacceptor_gain0.9700
6:32191868:AGTCT:Aacceptor_loss0.9600
6:32191869:GT:Gacceptor_gain0.9600
6:32191869:GTC:Gacceptor_loss0.9600
6:32191870:TCTGC:Tacceptor_loss0.9600
6:32191871:C:Gacceptor_loss0.9600
6:32191872:T:Aacceptor_loss0.9600
6:32192471:CCTG:Cdonor_gain0.9600
6:32192717:C:Adonor_gain0.9600
6:32191873:G:Cacceptor_loss0.9500

AlphaMissense

1003 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:32191722:A:GI111T0.996
6:32191722:A:TI111N0.995
6:32191722:A:CI111S0.992
6:32191824:A:GL77P0.989
6:32191433:A:TL139Q0.988
6:32191846:C:GA70P0.988
6:32191396:T:AQ151H0.987
6:32191396:T:GQ151H0.987
6:32191433:A:GL139P0.986
6:32191483:C:AQ122H0.986
6:32191483:C:GQ122H0.986
6:32191496:C:GR118P0.986
6:32191828:G:TR76S0.985
6:32191430:A:GL140P0.983
6:32191811:C:AR81S0.983
6:32191811:C:GR81S0.983
6:32191436:A:GL138S0.982
6:32191814:C:AQ80H0.981
6:32191814:C:GQ80H0.981
6:32191433:A:CL139R0.978
6:32191709:C:AQ115H0.978
6:32191709:C:GQ115H0.978
6:32191719:A:GL112P0.977
6:32191827:C:GR76P0.977
6:32191393:C:AR152S0.976
6:32191393:C:GR152S0.976
6:32191420:C:AQ143H0.976
6:32191420:C:GQ143H0.976
6:32191834:A:GS74P0.975
6:32191835:C:AQ73H0.975

dbSNP variants (sampled 300 via entrez): RS1000931193 (6:32194571 C>A), RS1001796081 (6:32190465 C>G,T), RS1001845749 (6:32196452 A>C,G), RS1002210751 (6:32190532 A>G), RS1002521536 (6:32196692 CTG>C), RS1003586041 (6:32191890 G>A), RS1003978412 (6:32194990 T>G), RS1004293066 (6:32192244 G>A,C), RS1004674647 (6:32190731 C>T), RS1005024340 (6:32190344 G>A), RS1005435146 (6:32196367 G>T), RS1005739658 (6:32193132 C>T), RS1007388429 (6:32195370 G>A,C), RS1007419485 (6:32194933 G>A), RS1009060447 (6:32196665 C>T)

Disease associations

OMIM: gene MIM:618558 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

33 associations (top):

StudyTraitp-value
GCST001709_6Atopic dermatitis8.000000e-20
GCST001762_173Obesity-related traits1.000000e-06
GCST001942_21Prostate cancer5.000000e-09
GCST002737_5Atopic dermatitis3.000000e-07
GCST004131_25Inflammatory bowel disease2.000000e-31
GCST004133_79Ulcerative colitis5.000000e-65
GCST004521_10Autism spectrum disorder or schizophrenia2.000000e-13
GCST004521_114Autism spectrum disorder or schizophrenia3.000000e-17
GCST004521_117Autism spectrum disorder or schizophrenia3.000000e-15
GCST004521_118Autism spectrum disorder or schizophrenia3.000000e-15
GCST004521_126Autism spectrum disorder or schizophrenia2.000000e-10
GCST004521_13Autism spectrum disorder or schizophrenia2.000000e-12
GCST004521_154Autism spectrum disorder or schizophrenia3.000000e-08
GCST004521_17Autism spectrum disorder or schizophrenia2.000000e-12
GCST004521_170Autism spectrum disorder or schizophrenia4.000000e-14
GCST004521_173Autism spectrum disorder or schizophrenia4.000000e-14
GCST004521_211Autism spectrum disorder or schizophrenia5.000000e-15
GCST004521_213Autism spectrum disorder or schizophrenia5.000000e-13
GCST004521_226Autism spectrum disorder or schizophrenia4.000000e-12
GCST004521_276Autism spectrum disorder or schizophrenia5.000000e-10
GCST004521_296Autism spectrum disorder or schizophrenia6.000000e-18
GCST004521_81Autism spectrum disorder or schizophrenia1.000000e-14
GCST005542_1Sarcoidosis (non-Lofgren’s syndrome without extrapulmonary manifestations)7.000000e-06
GCST008059_3Estimated glomerular filtration rate7.000000e-17
GCST008103_66Bipolar disorder7.000000e-07
GCST008916_27Asthma5.000000e-31
GCST009107_8Body mass index variance2.000000e-13
GCST009109_5Hip circumference variance5.000000e-11
GCST009121_10Body mass index9.000000e-15
GCST009123_7Hip circumference3.000000e-24

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0004626IGFBP-3 measurement
EFO:0004340body mass index
EFO:0007789BMI-adjusted waist circumference
EFO:0007788BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

ChemicalActions (top 5)PubMed papers
Nickelincreases expression2
FR900359increases phosphorylation1
triphenyl phosphateaffects expression1
sulforaphanedecreases expression1
sodium arseniteincreases expression1
entinostatincreases expression1
Bortezomibdecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Arsenic Trioxidedecreases expression1
Benzo(a)pyreneaffects methylation, decreases methylation1
Diazinonincreases methylation1
Plant Extractsaffects cotreatment, decreases expression1
Smokeincreases expression1
Testosteronedecreases expression1
Tretinoinincreases expression1
Valproic Acidincreases expression1
Antirheumatic Agentsdecreases expression1
tert-Butylhydroperoxideincreases 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): atopic eczema, sarcoidosis