Incidental Mutation 'R4627:Rapgef3'
ID 348908
Institutional Source Beutler Lab
Gene Symbol Rapgef3
Ensembl Gene ENSMUSG00000022469
Gene Name Rap guanine nucleotide exchange factor (GEF) 3
Synonyms 2310016P22Rik, 9330170P05Rik, Epac1
MMRRC Submission 041892-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.186) question?
Stock # R4627 (G1)
Quality Score 225
Status Not validated
Chromosome 15
Chromosomal Location 97744770-97767972 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) G to T at 97758929 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glutamic Acid at position 318 (D318E)
Ref Sequence ENSEMBL: ENSMUSP00000118148 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000126854] [ENSMUST00000128775] [ENSMUST00000129223] [ENSMUST00000134371] [ENSMUST00000134885] [ENSMUST00000146620] [ENSMUST00000149419] [ENSMUST00000175894] [ENSMUST00000177352]
AlphaFold Q8VCC8
Predicted Effect noncoding transcript
Transcript: ENSMUST00000123397
Predicted Effect probably damaging
Transcript: ENSMUST00000126854
AA Change: D318E

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000116426
Gene: ENSMUSG00000022469
AA Change: D318E

DomainStartEndE-ValueType
DEP 111 186 2.05e-25 SMART
low complexity region 197 208 N/A INTRINSIC
low complexity region 230 241 N/A INTRINSIC
cNMP 245 364 2.53e-12 SMART
RasGEFN 383 514 7.04e-10 SMART
Blast:RasGEF 547 644 6e-45 BLAST
RasGEF 661 926 7.98e-95 SMART
Predicted Effect possibly damaging
Transcript: ENSMUST00000128775
AA Change: D318E

PolyPhen 2 Score 0.832 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000120126
Gene: ENSMUSG00000022469
AA Change: D318E

DomainStartEndE-ValueType
DEP 111 186 2.05e-25 SMART
low complexity region 197 208 N/A INTRINSIC
low complexity region 230 241 N/A INTRINSIC
cNMP 245 364 2.53e-12 SMART
RasGEFN 383 514 7.04e-10 SMART
Blast:RasGEF 547 644 7e-45 BLAST
RasGEF 661 909 5.53e-80 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000129223
AA Change: D318E

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000118148
Gene: ENSMUSG00000022469
AA Change: D318E

DomainStartEndE-ValueType
DEP 111 186 2.05e-25 SMART
low complexity region 197 208 N/A INTRINSIC
low complexity region 230 241 N/A INTRINSIC
cNMP 245 364 2.53e-12 SMART
RasGEFN 383 514 7.04e-10 SMART
Blast:RasGEF 547 644 6e-45 BLAST
RasGEF 661 918 2.11e-85 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000134371
SMART Domains Protein: ENSMUSP00000122746
Gene: ENSMUSG00000022469

DomainStartEndE-ValueType
Blast:cNMP 1 24 9e-8 BLAST
PDB:3CF6|E 1 67 5e-12 PDB
Blast:RasGEFN 36 67 2e-15 BLAST
Predicted Effect probably benign
Transcript: ENSMUST00000134885
SMART Domains Protein: ENSMUSP00000135317
Gene: ENSMUSG00000022469

DomainStartEndE-ValueType
RasGEF 1 216 2.91e-56 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000142196
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146214
Predicted Effect probably benign
Transcript: ENSMUST00000146620
SMART Domains Protein: ENSMUSP00000116673
Gene: ENSMUSG00000022469

DomainStartEndE-ValueType
DEP 69 144 2.05e-25 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000149373
Predicted Effect probably benign
Transcript: ENSMUST00000149419
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153241
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153464
Predicted Effect probably benign
Transcript: ENSMUST00000175894
Predicted Effect probably benign
Transcript: ENSMUST00000177352
AA Change: D276E

PolyPhen 2 Score 0.050 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000135238
Gene: ENSMUSG00000022469
AA Change: D276E

DomainStartEndE-ValueType
DEP 69 144 2.05e-25 SMART
low complexity region 155 166 N/A INTRINSIC
low complexity region 188 199 N/A INTRINSIC
cNMP 203 322 2.53e-12 SMART
RasGEFN 341 472 7.04e-10 SMART
Blast:RasGEF 505 602 3e-45 BLAST
RasGEF 619 884 7.98e-95 SMART
Meta Mutation Damage Score 0.6467 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 95.4%
Validation Efficiency
MGI Phenotype PHENOTYPE: Mice homozygous for a knock-out allele exhibit decreased induced neuron apoptosis. Mice homozygous for a different allele exhibit impaired glucose homeostasis with decreased insulin secretion, increased susceptibility to diet-induced obesity and streptozotocin-induced insulitis and hyperglycemia. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 92 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2010111I01Rik T C 13: 63,068,092 (GRCm38) S393P probably benign Het
Adam6a A T 12: 113,544,949 (GRCm38) D314V probably benign Het
Adamts18 C T 8: 113,773,168 (GRCm38) W371* probably null Het
Adamtsl2 T A 2: 27,093,585 (GRCm38) L331Q probably damaging Het
Akr1c13 G T 13: 4,197,870 (GRCm38) V214F probably damaging Het
Aldoart1 T C 4: 72,852,443 (GRCm38) T43A probably benign Het
Alkbh2 C T 5: 114,124,226 (GRCm38) E148K probably damaging Het
Ano7 T C 1: 93,375,185 (GRCm38) I15T probably benign Het
Aox3 A T 1: 58,125,035 (GRCm38) T155S probably damaging Het
Ap2a1 C T 7: 44,904,419 (GRCm38) V535M probably damaging Het
Apbb2 C T 5: 66,400,076 (GRCm38) probably null Het
Astn1 C A 1: 158,502,251 (GRCm38) H225Q possibly damaging Het
Atm A G 9: 53,456,506 (GRCm38) I2439T possibly damaging Het
Atp1b2 T A 11: 69,601,334 (GRCm38) I263F probably damaging Het
Ccdc184 A T 15: 98,168,757 (GRCm38) N148Y probably benign Het
Cdca7 TGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA TGAAGAAGAAGAAGAAGAAGAAGAAGAAGA 2: 72,481,861 (GRCm38) probably benign Het
Cep192 C G 18: 67,812,369 (GRCm38) P180R probably benign Het
Cfap46 A T 7: 139,680,927 (GRCm38) L85Q probably damaging Het
Cfap46 T C 7: 139,657,281 (GRCm38) Y571C probably damaging Het
Chchd6 G A 6: 89,384,660 (GRCm38) L226F probably damaging Het
Cnot6l A G 5: 96,077,211 (GRCm38) V541A probably benign Het
Cobl T C 11: 12,251,093 (GRCm38) E1214G probably damaging Het
Cpsf2 G A 12: 101,989,895 (GRCm38) R319Q probably benign Het
Csdc2 T C 15: 81,949,123 (GRCm38) V107A probably benign Het
Csmd1 A G 8: 16,697,917 (GRCm38) W273R probably benign Het
Diexf T C 1: 193,107,695 (GRCm38) T719A probably benign Het
Dnah2 T A 11: 69,465,376 (GRCm38) N2156I probably damaging Het
Dsp A G 13: 38,168,641 (GRCm38) Y165C probably benign Het
Exoc1 T C 5: 76,542,228 (GRCm38) V205A probably benign Het
Fam98c T C 7: 29,155,268 (GRCm38) T49A possibly damaging Het
Fbln2 G T 6: 91,259,767 (GRCm38) V755L probably damaging Het
Fhad1 A T 4: 141,896,468 (GRCm38) V1371D possibly damaging Het
Folh1 A T 7: 86,773,252 (GRCm38) M59K probably benign Het
Foxf2 A T 13: 31,626,888 (GRCm38) H270L probably benign Het
Gm14401 G A 2: 177,086,316 (GRCm38) R65H probably benign Het
Gpn1 C A 5: 31,498,393 (GRCm38) Y592* probably null Het
Hmcn1 T G 1: 150,595,894 (GRCm38) D4903A probably benign Het
Hnf1a T C 5: 114,955,871 (GRCm38) R220G probably damaging Het
Hoxd10 G A 2: 74,692,292 (GRCm38) A105T probably benign Het
Kcnd3 C T 3: 105,658,766 (GRCm38) A421V probably damaging Het
Kidins220 C T 12: 25,057,042 (GRCm38) T1498I possibly damaging Het
Klhl2 G T 8: 64,758,191 (GRCm38) Y274* probably null Het
Lmbrd1 A G 1: 24,705,999 (GRCm38) Y140C probably damaging Het
Mapk8ip3 G A 17: 24,903,293 (GRCm38) T706I probably benign Het
Mast4 A C 13: 103,334,021 (GRCm38) S58A possibly damaging Het
Mcm6 T C 1: 128,351,548 (GRCm38) D167G probably benign Het
Mmachc A T 4: 116,703,471 (GRCm38) S276T probably damaging Het
Nfat5 A T 8: 107,369,276 (GRCm38) Q1289L probably damaging Het
Nlrc4 G T 17: 74,446,628 (GRCm38) F253L probably damaging Het
Nr1i3 C A 1: 171,216,445 (GRCm38) A112E probably benign Het
Olfr1367 T C 13: 21,347,464 (GRCm38) F179L probably damaging Het
Olfr45 T A 7: 140,691,378 (GRCm38) S158T probably benign Het
Olfr455 T A 6: 42,538,441 (GRCm38) T194S possibly damaging Het
Olfr853 G T 9: 19,537,673 (GRCm38) Q86K possibly damaging Het
Orc5 G T 5: 22,548,005 (GRCm38) F10L probably benign Het
Pde10a A C 17: 8,981,652 (GRCm38) D779A probably damaging Het
Pde4b T C 4: 102,601,605 (GRCm38) L486S probably damaging Het
Pex2 A T 3: 5,561,281 (GRCm38) I156N probably damaging Het
Phtf2 C T 5: 20,773,740 (GRCm38) R63Q probably damaging Het
Prag1 A G 8: 36,103,292 (GRCm38) Y343C probably damaging Het
Prdm16 A T 4: 154,367,240 (GRCm38) Y170N probably damaging Het
Prpf6 A C 2: 181,601,474 (GRCm38) K5T probably damaging Het
Ptpn1 A G 2: 167,967,781 (GRCm38) K103R probably benign Het
Ralgapa2 A G 2: 146,361,453 (GRCm38) S1159P possibly damaging Het
Ripk4 A T 16: 97,744,026 (GRCm38) S474T probably damaging Het
Rmi1 A G 13: 58,409,136 (GRCm38) R400G probably benign Het
Sec16a A G 2: 26,429,393 (GRCm38) V1491A probably damaging Het
Sec16a C T 2: 26,431,068 (GRCm38) probably null Het
Setd7 G T 3: 51,542,665 (GRCm38) N113K probably damaging Het
Shank2 C T 7: 144,411,424 (GRCm38) T1502M probably damaging Het
Skor1 A T 9: 63,145,476 (GRCm38) C376S probably damaging Het
Slc12a3 A T 8: 94,329,384 (GRCm38) L49F probably benign Het
Slc35d3 C T 10: 19,849,331 (GRCm38) V260M probably damaging Het
Slc46a1 T A 11: 78,466,889 (GRCm38) V256E probably benign Het
Slc6a1 T C 6: 114,308,106 (GRCm38) S127P probably benign Het
Syngr4 A G 7: 45,887,028 (GRCm38) L190P probably damaging Het
Tagap G A 17: 7,926,941 (GRCm38) probably null Het
Tamm41 A T 6: 115,035,002 (GRCm38) N89K probably benign Het
Tbc1d31 T A 15: 57,967,912 (GRCm38) M922K probably benign Het
Tbk1 T C 10: 121,568,080 (GRCm38) N254S possibly damaging Het
Tfec A G 6: 16,840,479 (GRCm38) S140P probably damaging Het
Tnrc18 T C 5: 142,740,128 (GRCm38) E1802G unknown Het
Tom1l2 C T 11: 60,242,707 (GRCm38) probably null Het
Tonsl T G 15: 76,637,224 (GRCm38) K323Q probably damaging Het
Tsnaxip1 A T 8: 105,841,407 (GRCm38) E268D probably damaging Het
Ttf1 C A 2: 29,065,160 (GRCm38) H179N possibly damaging Het
Ttn T C 2: 76,726,173 (GRCm38) S30163G probably damaging Het
Ube2c A G 2: 164,772,173 (GRCm38) N143S possibly damaging Het
Ugt1a10 G A 1: 88,218,390 (GRCm38) R519Q probably damaging Het
Vmn2r9 T C 5: 108,847,597 (GRCm38) Y395C probably damaging Het
Vwa8 G A 14: 79,103,697 (GRCm38) probably null Het
Zfp9 A G 6: 118,464,976 (GRCm38) Y242H probably damaging Het
Other mutations in Rapgef3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01314:Rapgef3 APN 15 97,748,223 (GRCm38) missense probably damaging 1.00
IGL01339:Rapgef3 APN 15 97,758,059 (GRCm38) missense probably damaging 1.00
IGL01670:Rapgef3 APN 15 97,749,662 (GRCm38) missense probably benign 0.15
IGL01902:Rapgef3 APN 15 97,750,300 (GRCm38) missense probably benign 0.32
IGL02137:Rapgef3 APN 15 97,750,144 (GRCm38) missense probably benign 0.08
IGL02419:Rapgef3 APN 15 97,750,290 (GRCm38) missense probably benign 0.33
IGL02427:Rapgef3 APN 15 97,747,136 (GRCm38) splice site probably null
IGL02648:Rapgef3 APN 15 97,758,392 (GRCm38) missense probably damaging 1.00
IGL02834:Rapgef3 APN 15 97,748,265 (GRCm38) missense probably damaging 0.98
IGL03389:Rapgef3 APN 15 97,749,516 (GRCm38) missense probably damaging 1.00
IGL03055:Rapgef3 UTSW 15 97,749,489 (GRCm38) splice site probably benign
R0394:Rapgef3 UTSW 15 97,757,819 (GRCm38) intron probably benign
R0538:Rapgef3 UTSW 15 97,757,817 (GRCm38) intron probably benign
R0744:Rapgef3 UTSW 15 97,761,585 (GRCm38) splice site probably benign
R1288:Rapgef3 UTSW 15 97,759,342 (GRCm38) missense probably benign 0.31
R1512:Rapgef3 UTSW 15 97,757,501 (GRCm38) missense probably benign 0.24
R1676:Rapgef3 UTSW 15 97,761,182 (GRCm38) missense probably benign 0.35
R1745:Rapgef3 UTSW 15 97,750,178 (GRCm38) missense probably benign 0.22
R1928:Rapgef3 UTSW 15 97,750,033 (GRCm38) missense probably damaging 1.00
R2063:Rapgef3 UTSW 15 97,766,961 (GRCm38) missense probably damaging 1.00
R2067:Rapgef3 UTSW 15 97,766,961 (GRCm38) missense probably damaging 1.00
R2092:Rapgef3 UTSW 15 97,760,723 (GRCm38) missense probably damaging 1.00
R4358:Rapgef3 UTSW 15 97,748,648 (GRCm38) missense probably benign 0.05
R4624:Rapgef3 UTSW 15 97,758,929 (GRCm38) missense probably damaging 1.00
R4727:Rapgef3 UTSW 15 97,760,600 (GRCm38) missense probably damaging 1.00
R4812:Rapgef3 UTSW 15 97,753,803 (GRCm38) missense probably benign 0.21
R4928:Rapgef3 UTSW 15 97,757,375 (GRCm38) missense probably damaging 1.00
R5161:Rapgef3 UTSW 15 97,757,725 (GRCm38) missense probably damaging 1.00
R5442:Rapgef3 UTSW 15 97,758,861 (GRCm38) missense probably damaging 0.99
R5652:Rapgef3 UTSW 15 97,758,437 (GRCm38) missense probably benign 0.00
R5837:Rapgef3 UTSW 15 97,757,342 (GRCm38) splice site probably benign
R6056:Rapgef3 UTSW 15 97,758,861 (GRCm38) missense probably damaging 0.99
R6167:Rapgef3 UTSW 15 97,767,411 (GRCm38) unclassified probably benign
R6694:Rapgef3 UTSW 15 97,759,984 (GRCm38) missense probably benign 0.03
R7039:Rapgef3 UTSW 15 97,761,568 (GRCm38) missense probably benign 0.01
R7154:Rapgef3 UTSW 15 97,753,877 (GRCm38) missense probably benign
R7380:Rapgef3 UTSW 15 97,766,791 (GRCm38) missense probably benign 0.00
R7655:Rapgef3 UTSW 15 97,761,209 (GRCm38) missense probably damaging 1.00
R7656:Rapgef3 UTSW 15 97,761,209 (GRCm38) missense probably damaging 1.00
R7754:Rapgef3 UTSW 15 97,757,746 (GRCm38) missense probably damaging 1.00
R7849:Rapgef3 UTSW 15 97,758,390 (GRCm38) critical splice donor site probably null
R8061:Rapgef3 UTSW 15 97,761,520 (GRCm38) missense probably benign
R8117:Rapgef3 UTSW 15 97,750,866 (GRCm38) missense probably benign 0.01
R8179:Rapgef3 UTSW 15 97,760,740 (GRCm38) missense probably benign 0.06
R8819:Rapgef3 UTSW 15 97,748,657 (GRCm38) missense probably benign 0.39
R8820:Rapgef3 UTSW 15 97,748,657 (GRCm38) missense probably benign 0.39
R8824:Rapgef3 UTSW 15 97,766,908 (GRCm38) missense probably benign 0.39
R9779:Rapgef3 UTSW 15 97,745,598 (GRCm38) missense probably damaging 0.99
R9781:Rapgef3 UTSW 15 97,745,598 (GRCm38) missense probably damaging 0.99
R9782:Rapgef3 UTSW 15 97,745,598 (GRCm38) missense probably damaging 0.99
RF024:Rapgef3 UTSW 15 97,760,740 (GRCm38) missense probably benign 0.06
X0011:Rapgef3 UTSW 15 97,761,473 (GRCm38) critical splice donor site probably null
Predicted Primers PCR Primer
(F):5'- TGTTCTCTCACGCCAAACTG -3'
(R):5'- TGGACACTCCCTTTGATAGCC -3'

Sequencing Primer
(F):5'- GATCCCAAGTGTCCTTACAAATTC -3'
(R):5'- CCCTTTGATAGCCCCAAGG -3'
Posted On 2015-10-08