RASGEF1B

gene
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Also known as GPIG4FLJ31695

Summary

RASGEF1B (RasGEF domain family member 1B, HGNC:24881) is a protein-coding gene on chromosome 4q21.21, encoding Ras-GEF domain-containing family member 1B (Q0VAM2). Guanine nucleotide exchange factor (GEF) with specificity for RAP2A, it doesn’t seems to activate other Ras family proteins (in vitro).

Enables guanyl-nucleotide exchange factor activity. Predicted to be involved in Ras protein signal transduction. Predicted to be located in early endosome; late endosome; and midbody. Predicted to be active in plasma membrane.

Source: NCBI Gene 153020 — RefSeq curated summary.

At a glance

  • GWAS associations: 28
  • Clinical variants (ClinVar): 73 total
  • MANE Select transcript: NM_152545

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24881
Approved symbolRASGEF1B
NameRasGEF domain family member 1B
Location4q21.21
Locus typegene with protein product
StatusApproved
AliasesGPIG4, FLJ31695
Ensembl geneENSG00000138670
Ensembl biotypeprotein_coding
OMIM614532
Entrez153020

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 12 protein_coding, 4 protein_coding_CDS_not_defined, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000264400, ENST00000335927, ENST00000436139, ENST00000504863, ENST00000507538, ENST00000508294, ENST00000509081, ENST00000510780, ENST00000512343, ENST00000512716, ENST00000514050, ENST00000514889, ENST00000638048, ENST00000900842, ENST00000900843, ENST00000900844, ENST00000939400, ENST00000961893

RefSeq mRNA: 3 — MANE Select: NM_152545 NM_001300735, NM_001300736, NM_152545

CCDS: CCDS34022, CCDS75151, CCDS75152

Canonical transcript exons

ENST00000264400 — 14 exons

ExonStartEnd
ENSE000009698408143384081433963
ENSE000009698428143229981432371
ENSE000010071278145749981457621
ENSE000010731398144806981448284
ENSE000010731418144574381445838
ENSE000010731438144552681445628
ENSE000010731448144083481440929
ENSE000010731458144750481447578
ENSE000016872028145933281459514
ENSE000016881198147177081471907
ENSE000020815518142639381427792
ENSE000025154838144229781442376
ENSE000025303108143463981434734
ENSE000035661288145665181456788

Expression profiles

Bgee: expression breadth ubiquitous, 164 present calls, max score 95.53.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.9426 / max 947.5551, expressed in 1009 samples.

FANTOM5 promoters (11 alternative TSS)

Promoter IDTPM avgSamples expressed
5279415.0306898
527938.9078594
527923.0036388
528220.5231211
528210.2238103
528250.086838
528200.055722
528260.041918
528240.038914
528270.02015

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ganglionic eminenceUBERON:000402395.53gold quality
right lobe of liverUBERON:000111488.76gold quality
monocyteCL:000057688.58gold quality
bone marrow cellCL:000209288.53gold quality
right lungUBERON:000216788.24gold quality
buccal mucosa cellCL:000233687.81gold quality
leukocyteCL:000073887.69gold quality
skin of abdomenUBERON:000141687.44gold quality
skin of legUBERON:000151186.21gold quality
lower esophagus mucosaUBERON:003583486.03gold quality
gall bladderUBERON:000211085.92gold quality
upper lobe of left lungUBERON:000895285.05gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.34gold quality
cortical plateUBERON:000534383.68gold quality
islet of LangerhansUBERON:000000682.69gold quality
sural nerveUBERON:001548882.10gold quality
calcaneal tendonUBERON:000370181.80gold quality
olfactory segment of nasal mucosaUBERON:000538681.79gold quality
zone of skinUBERON:000001481.78gold quality
upper lobe of lungUBERON:000894881.74gold quality
vermiform appendixUBERON:000115481.35gold quality
metanephros cortexUBERON:001053380.61gold quality
esophagus mucosaUBERON:000246980.46gold quality
caudate nucleusUBERON:000187380.25gold quality
putamenUBERON:000187480.24gold quality
minor salivary glandUBERON:000183079.92gold quality
omental fat padUBERON:001041479.50gold quality
peritoneumUBERON:000235879.40gold quality
right uterine tubeUBERON:000130279.13gold quality
colonic epitheliumUBERON:000039779.05gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-2yes7331.84
E-GEOD-75688yes1577.26
E-GEOD-75140yes1287.68
E-CURD-7yes749.70
E-GEOD-84465yes35.91
E-ANND-3yes26.36
E-MTAB-9467yes18.86
E-GEOD-93593yes8.60
E-CURD-11no97.03
E-GEOD-124858no12.03
E-CURD-112no2.15

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ARX, E2F1

miRNA regulators (miRDB)

110 targeting RASGEF1B, 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-518D-5P100.0067.51979
HSA-MIR-518E-5P100.0067.66954
HSA-MIR-518F-5P100.0067.51979
HSA-MIR-519A-5P100.0067.66954
HSA-MIR-519B-5P100.0067.66954
HSA-MIR-519C-5P100.0067.66954
HSA-MIR-520C-5P100.0067.51979
HSA-MIR-522-5P100.0067.66954
HSA-MIR-523-5P100.0067.66954
HSA-MIR-526A-5P100.0067.51979
HSA-MIR-5692A100.0074.406850
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-8485100.0077.574731
HSA-MIR-1277-5P100.0073.955056
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-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-118499.9968.191458
HSA-MIR-150-5P99.9966.691976
HSA-MIR-569699.9872.364487
HSA-MIR-548P99.9872.253784
HSA-MIR-314899.9775.066478
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197

Literature-anchored findings (GeneRIF, showing 4)

  • Mutation of the Ser39 in Rap1 changed the specificity and allowed the nucleotide exchange of Rap1(S39F) to be stimulated by RasGEF1B (PMID:19645719)
  • As an addition to PRKG2 and RASGEFIB genes, we propose to include BMP3 gene as the principal determinant of the observed common phenotype. (PMID:22303795)
  • We show that knockdown of the expression of mcircRasGEF1B reduces LPS-induced ICAM-1 expression. Additionally, we demonstrate that mcircRasGEF1B regulates the stability of mature ICAM-1 mRNAs. (PMID:27362560)
  • study provides evidence for two novel candidate genes, SPG7 and RASGEF1B, associating with white coat effect (PMID:31044621)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_reriorasgef1baENSDARG00000033614
danio_reriorasgef1bbENSDARG00000044251
mus_musculusRasgef1bENSMUSG00000089809
rattus_norvegicusRasgef1bENSRNOG00000002345
drosophila_melanogasterCG4853FBGN0034230
drosophila_melanogasterCG7369FBGN0037188
caenorhabditis_elegansWBGENE00019902

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), RALGPS1 (ENSG00000136828), 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-GEF domain-containing family member 1BQ0VAM2 (reviewed: Q0VAM2)

Alternative names: GPI gamma-4

All UniProt accessions (6): A0A0G2JLL4, A0A1B0GVA7, A0A1B0GW78, D6RE71, Q0VAM2, Q8N437

UniProt curated annotations — full annotation on UniProt →

Function. Guanine nucleotide exchange factor (GEF) with specificity for RAP2A, it doesn’t seems to activate other Ras family proteins (in vitro).

Subunit / interactions. Interacts with Ras family proteins. Interacts with CCDC124 during cytokinesis.

Subcellular location. Early endosome. Late endosome. Midbody.

Induction. Up-regulated in macrophages stimulated with IFNG, GPI-mucins or bacterial lipopolysaccharides (LPS).

Isoforms (3)

UniProt IDNamesCanonical?
Q0VAM2-11yes
Q0VAM2-22
Q0VAM2-33

RefSeq proteins (3): NP_001287664, NP_001287665, NP_689758* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000651Ras-like_Gua-exchang_fac_NDomain
IPR001895RASGEF_cat_domDomain
IPR008937Ras-like_GEFFamily
IPR019804Ras_G-nucl-exch_fac_CSConserved_site
IPR023578Ras_GEF_dom_sfHomologous_superfamily
IPR036964RASGEF_cat_dom_sfHomologous_superfamily

Pfam: PF00617, PF00618

UniProt features (5 total): domain 2, splice variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q0VAM2-F187.310.72

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 209 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, FREAC2_01, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GCANCTGNY_MYOD_Q6, MEF2_02, FOXO1_01, GOBP_RAS_PROTEIN_SIGNAL_TRANSDUCTION, POU3F2_02, GOBP_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, MEF2_Q6_01, CTAWWWATA_RSRFC4_Q2, FOXO4_02, chr4q21, MEF2_03, GOMF_GUANYL_NUCLEOTIDE_EXCHANGE_FACTOR_ACTIVITY

GO Biological Process (2): Ras protein signal transduction (GO:0007265), 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 (5): early endosome (GO:0005769), late endosome (GO:0005770), plasma membrane (GO:0005886), midbody (GO:0030496), endosome (GO:0005768)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
endosome2
small GTPase-mediated signal transduction1
intracellular signaling cassette1
GTP binding1
GDP binding1
GTPase regulator activity1
binding1
membrane1
cell periphery1
cellular anatomical structure1
endomembrane system1
cytoplasmic vesicle1

Protein interactions and networks

STRING

752 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RASGEF1BPRKG2Q13237918
RASGEF1BICAM1P05362532
RASGEF1BENOPH1Q9UHY7505
RASGEF1BHAUS8Q9BT25441
RASGEF1BLINGO1Q96FE5436
RASGEF1BSLC26A3P40879432
RASGEF1BUNC5DQ6UXZ4411
RASGEF1BARHGAP12Q8IWW6389
RASGEF1BGDF10P55107377
RASGEF1BGDF3Q9NR23367
RASGEF1BWSCD1Q658N2363
RASGEF1BZC3H4Q9UPT8362
RASGEF1BCUX2O14529357
RASGEF1BGDF2Q9UK05355
RASGEF1BDLL1O00548349

IntAct

2 interactions, top by confidence:

ABTypeScore
RASGEF1BGAPDHSpsi-mi:“MI:0914”(association)0.350

BioGRID (13): RASGEF1B (Affinity Capture-MS), COL1A1 (Affinity Capture-MS), GAPDHS (Affinity Capture-MS), RASGEF1B (Affinity Capture-RNA), RASGEF1B (Two-hybrid), TSGA10IP (Two-hybrid), PLEKHF2 (Two-hybrid), PDLIM7 (Two-hybrid), RASGEF1B (Affinity Capture-RNA), GAPDHS (Affinity Capture-MS), COL1A1 (Affinity Capture-MS), RASGEF1B (Positive Genetic), RASGEF1B (Affinity Capture-RNA)

ESM2 similar proteins: A0A0G2JTR4, A0A2R8QFQ6, A0JM95, A4IFE4, A6QNS3, C1C3R6, D3Z649, D4ABL6, E9PV86, F1QH17, G3MWR8, O46404, Q0VAM2, Q12800, Q12979, Q13507, Q28EC1, Q3ULA2, Q3UNW5, Q4V860, Q5R6F2, Q5RB16, Q5RC04, Q5SSL4, Q5VWJ9, Q5ZLX4, Q63789, Q64143, Q6DHR3, Q6NZH6, Q6UVM3, Q6UVM4, Q6ZPR4, Q7RTP6, Q7T2U9, Q7Z6J6, Q8CE50, Q8CJ19, Q8JZL7, Q8N431

Diamond homologs: A0JM95, A4IFE4, F1M386, F1MSG6, F1PBJ0, Q0VAM2, Q28EC1, Q5RC04, Q6DBW1, Q6DHR3, Q8CHG7, Q8IS18, Q8IS19, Q8JZL7, Q8MVR1, Q8N431, Q8N9B8, Q95KH6, Q9D300, Q9Y4G8, O95398, P28818, P83900, Q02342, Q8C0Q9, Q8VCC8, Q8WZA2, Q92565, Q9EQZ6, Q9UHV5, Q9Z1C7, Q9Z1C8, A2AR50, A2CEA7, A7A0P0, B0M0P8, B3LTF3, B5VMS9, C8ZCV7, E9Q9W7

SIGNOR signaling

5 interactions.

AEffectBMechanism
RASGEF1Bup-regulatesNRASbinding
RASGEF1Bup-regulatesHRASbinding
RASGEF1Bup-regulatesKRASbinding
E2F1“up-regulates quantity by expression”RASGEF1B“transcriptional regulation”
PLPPR1“up-regulates activity”RASGEF1Bbinding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance56
Likely benign4
Benign4

Top pathogenic / likely-pathogenic (0)

SpliceAI

1549 predictions. Top by Δscore:

VariantEffectΔscore
4:81432372:C:CCacceptor_gain1.0000
4:81433834:CCTTA:Cdonor_loss1.0000
4:81433835:CTTA:Cdonor_loss1.0000
4:81433836:TTA:Tdonor_loss1.0000
4:81433837:TACCA:Tdonor_loss1.0000
4:81433838:A:ACdonor_gain1.0000
4:81433838:AC:Adonor_gain1.0000
4:81433838:ACC:Adonor_loss1.0000
4:81433838:ACCAT:Adonor_gain1.0000
4:81433839:C:CCdonor_gain1.0000
4:81433839:C:CTdonor_loss1.0000
4:81433839:CC:Cdonor_gain1.0000
4:81433839:CCA:Cdonor_gain1.0000
4:81433839:CCAT:Cdonor_gain1.0000
4:81433839:CCATC:Cdonor_gain1.0000
4:81433856:TGG:Tdonor_gain1.0000
4:81433959:AATTT:Aacceptor_gain1.0000
4:81433960:ATTT:Aacceptor_gain1.0000
4:81433961:TTT:Tacceptor_gain1.0000
4:81433961:TTTC:Tacceptor_loss1.0000
4:81433962:TT:Tacceptor_gain1.0000
4:81433963:TC:Tacceptor_loss1.0000
4:81433964:C:CAacceptor_loss1.0000
4:81433964:C:CCacceptor_gain1.0000
4:81433971:A:ACacceptor_gain1.0000
4:81433971:A:Cacceptor_gain1.0000
4:81433975:G:Cacceptor_gain1.0000
4:81433975:G:GCacceptor_gain1.0000
4:81434634:CTCA:Cdonor_loss1.0000
4:81434635:TCA:Tdonor_loss1.0000

AlphaMissense

3170 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:81432356:G:AS447F1.000
4:81434703:T:AK379I1.000
4:81440892:C:GR349P1.000
4:81440903:G:CF345L1.000
4:81440903:G:TF345L1.000
4:81440905:A:GF345L1.000
4:81442346:A:GL320P1.000
4:81442349:C:GR319P1.000
4:81442355:A:TV317D1.000
4:81442373:C:TG311D1.000
4:81442374:C:GG311R1.000
4:81445531:A:TI308K1.000
4:81445545:G:CN303K1.000
4:81445545:G:TN303K1.000
4:81445551:G:CN301K1.000
4:81445551:G:TN301K1.000
4:81445566:A:CC296W1.000
4:81445759:G:TA270D1.000
4:81448085:A:GL213P1.000
4:81456740:A:GW117R1.000
4:81456740:A:TW117R1.000
4:81432356:G:TS447Y0.999
4:81432357:A:GS447P0.999
4:81432368:A:GL443P0.999
4:81433948:C:GA406P0.999
4:81434700:T:AD380V0.999
4:81434700:T:GD380A0.999
4:81434701:C:GD380H0.999
4:81434702:T:AK379N0.999
4:81434702:T:GK379N0.999

dbSNP variants (sampled 300 via entrez): RS1000035766 (4:81466933 T>C), RS1000037505 (4:81464761 A>G), RS1000052272 (4:81436814 T>C), RS1000055130 (4:81460988 G>C), RS1000071995 (4:81460586 C>G), RS1000131240 (4:81453274 A>G), RS1000215211 (4:81432778 T>C), RS1000229927 (4:81467031 G>A), RS1000307172 (4:81454320 G>T), RS1000344335 (4:81429421 G>C), RS1000352961 (4:81446863 C>T), RS1000443301 (4:81440437 G>A), RS1000490578 (4:81449428 T>A,C), RS1000636689 (4:81466237 TCTTC>T), RS1000646290 (4:81434767 G>A,T)

Disease associations

OMIM: gene MIM:614532 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

28 associations (top):

StudyTraitp-value
GCST000175_43Height2.000000e-06
GCST001850_15Major depressive disorder6.000000e-06
GCST002702_49Height3.000000e-15
GCST005024_68Pursuit maintenance gain6.000000e-07
GCST006291_54Spherical equivalent or myopia (age of diagnosis)3.000000e-11
GCST006427_39Depression in smokers7.000000e-06
GCST006431_1Plasma parathyroid hormone levels1.000000e-08
GCST006817_4Response to antidepressants in depression2.000000e-06
GCST007637_42Diffusing capacity of carbon monoxide6.000000e-06
GCST008151_106Waist circumference2.000000e-06
GCST008158_110Body mass index2.000000e-06
GCST008160_108Waist circumference2.000000e-06
GCST008399_19Cocaine dependence2.000000e-06
GCST008839_421Height3.000000e-38
GCST008969_5White coat effect (clinic diastolic blood pressure minus ambulatory diastolic blood pressure)5.000000e-06
GCST010002_9Refractive error2.000000e-65
GCST010397_30Gut microbiota (bacterial taxa, rank normal transformation method)2.000000e-06
GCST010479_68Coronary artery disease4.000000e-08
GCST010866_22Coronary artery disease2.000000e-13
GCST011365_61Myocardial infarction5.000000e-11
GCST012226_221Waist circumference adjusted for body mass index6.000000e-11
GCST012226_223Waist circumference adjusted for body mass index6.000000e-10
GCST012227_1287Hip circumference adjusted for BMI3.000000e-12
GCST012227_1288Hip circumference adjusted for BMI4.000000e-10
GCST012400_41Low myopia vs hyperopia6.000000e-09
GCST90000015_4Parkinson’s disease motor subtype (tremor to postural instability/gait difficulty score ratio)1.000000e-06
GCST90020028_1941Hip circumference adjusted for BMI1.000000e-13
GCST90020028_1943Hip circumference adjusted for BMI9.000000e-13

EFO canonical traits (9, from GWAS)

EFO IDTrait name
EFO:0008433pursuit maintenance gain measurement
EFO:0004847age at onset
EFO:0009369diffusing capacity of the lung for carbon monoxide
EFO:0004340body mass index
EFO:0006945diastolic blood pressure change measurement
EFO:0007874gut microbiome measurement
EFO:0007789BMI-adjusted waist circumference
EFO:0008039BMI-adjusted hip circumference
EFO:0600011Parkinson’s disease symptom measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, increases expression, increases methylation2
Estradioldecreases expression2
GSK-J4increases expression1
kojic aciddecreases expression1
ethyl-p-hydroxybenzoateincreases expression1
butyraldehydedecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
lei gong tengincreases expression1
epigallocatechin gallateincreases expression1
pentanaldecreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
abrineincreases expression1
bisphenol Sdecreases methylation1
Sunitinibincreases expression1
Air Pollutantsincreases abundance, increases expression1
Air Pollutants, Occupationalincreases expression1
Arbutindecreases expression1
Arsenicincreases methylation1
Cadmiumincreases expression1
Diquatincreases expression1
Endosulfandecreases expression, decreases reaction1
Lipopolysaccharidesincreases expression, affects response to substance1
Nickelincreases expression1
Phthalic Acidsaffects methylation1
Tetrachlorodibenzodioxindecreases expression, decreases reaction1
Thiramincreases expression1
Tobacco Smoke Pollutionaffects expression1
Urethaneincreases expression1
Cyclosporinedecreases 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): cocaine dependence