Incidental Mutation 'R1512:Rapgef3'
ID 168449
Institutional Source Beutler Lab
Gene Symbol Rapgef3
Ensembl Gene ENSMUSG00000022469
Gene Name Rap guanine nucleotide exchange factor (GEF) 3
Synonyms Epac1, 9330170P05Rik, 2310016P22Rik
MMRRC Submission 039559-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.268) question?
Stock # R1512 (G1)
Quality Score 161
Status Validated
Chromosome 15
Chromosomal Location 97642651-97665853 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 97655382 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Glutamic Acid at position 444 (V444E)
Ref Sequence ENSEMBL: ENSMUSP00000120126 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000126854] [ENSMUST00000128775] [ENSMUST00000129223] [ENSMUST00000134371] [ENSMUST00000134885] [ENSMUST00000177352] [ENSMUST00000149419] [ENSMUST00000146620] [ENSMUST00000175894]
AlphaFold Q8VCC8
Predicted Effect noncoding transcript
Transcript: ENSMUST00000123397
Predicted Effect probably benign
Transcript: ENSMUST00000126854
AA Change: V444E

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000116426
Gene: ENSMUSG00000022469
AA Change: V444E

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 probably benign
Transcript: ENSMUST00000128775
AA Change: V444E

PolyPhen 2 Score 0.239 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000120126
Gene: ENSMUSG00000022469
AA Change: V444E

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 benign
Transcript: ENSMUST00000129223
AA Change: V444E

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000118148
Gene: ENSMUSG00000022469
AA Change: V444E

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 probably benign
Transcript: ENSMUST00000177352
AA Change: V402E

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000135238
Gene: ENSMUSG00000022469
AA Change: V402E

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153241
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153464
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146214
Predicted Effect noncoding transcript
Transcript: ENSMUST00000149373
Predicted Effect probably benign
Transcript: ENSMUST00000149419
Predicted Effect probably benign
Transcript: ENSMUST00000146620
SMART Domains Protein: ENSMUSP00000116673
Gene: ENSMUSG00000022469

DomainStartEndE-ValueType
DEP 69 144 2.05e-25 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000175894
Meta Mutation Damage Score 0.0819 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.3%
  • 10x: 96.4%
  • 20x: 93.0%
Validation Efficiency 95% (79/83)
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: 83 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acaca T A 11: 84,086,295 (GRCm39) D40E probably benign Het
Acsf2 C T 11: 94,452,224 (GRCm39) probably benign Het
Adamts19 C T 18: 59,181,917 (GRCm39) H1119Y possibly damaging Het
Akap6 A G 12: 52,983,937 (GRCm39) D827G probably damaging Het
Ankrd33b T C 15: 31,367,375 (GRCm39) D55G probably damaging Het
Ano5 T A 7: 51,229,316 (GRCm39) H569Q probably benign Het
Aox1 A G 1: 58,346,510 (GRCm39) D548G probably benign Het
Baz2a A G 10: 127,960,021 (GRCm39) D1433G possibly damaging Het
BC031181 T G 18: 75,141,767 (GRCm39) V8G probably damaging Het
Bicdl2 A T 17: 23,887,083 (GRCm39) M457L probably damaging Het
C130074G19Rik T C 1: 184,615,103 (GRCm39) D29G probably damaging Het
Cd200r1 A T 16: 44,586,390 (GRCm39) T7S probably benign Het
Cdc37 A G 9: 21,053,712 (GRCm39) probably benign Het
Cmtr2 T C 8: 110,949,267 (GRCm39) S526P probably damaging Het
Cntn2 G T 1: 132,451,430 (GRCm39) A433D probably damaging Het
Cntnap5a T C 1: 115,828,680 (GRCm39) S35P probably benign Het
Csf3r A G 4: 125,923,777 (GRCm39) T96A possibly damaging Het
Ctbs A G 3: 146,160,720 (GRCm39) N96D probably benign Het
Cyp26b1 C A 6: 84,553,979 (GRCm39) V213L probably benign Het
Dach1 A G 14: 98,138,835 (GRCm39) L536P probably damaging Het
Dcaf6 T C 1: 165,179,589 (GRCm39) Q517R probably benign Het
Dnah1 G T 14: 31,014,994 (GRCm39) Q1733K probably damaging Het
Dnah17 A T 11: 117,985,841 (GRCm39) I1416N probably benign Het
Dock11 G A X: 35,283,688 (GRCm39) R1102H probably damaging Het
Dpp8 T C 9: 64,971,096 (GRCm39) probably benign Het
Emc1 G A 4: 139,087,495 (GRCm39) probably null Het
Emc8 A G 8: 121,384,983 (GRCm39) L76P possibly damaging Het
Emx2 T C 19: 59,448,035 (GRCm39) Y130H possibly damaging Het
Fbf1 C T 11: 116,038,753 (GRCm39) R815Q probably damaging Het
Foxb2 G A 19: 16,849,878 (GRCm39) P376L probably damaging Het
Gabrb1 C A 5: 72,266,047 (GRCm39) L202I probably damaging Het
Gabrb1 T A 5: 72,266,048 (GRCm39) L202Q probably damaging Het
Grin2c T A 11: 115,144,676 (GRCm39) I617F probably damaging Het
Gtf2h3 T A 5: 124,728,933 (GRCm39) V164E probably damaging Het
Gusb T C 5: 130,029,731 (GRCm39) Q88R probably damaging Het
Hormad2 T A 11: 4,374,788 (GRCm39) K75N probably damaging Het
Il33 A G 19: 29,929,390 (GRCm39) T38A possibly damaging Het
Ivns1abp A T 1: 151,236,687 (GRCm39) Q416L possibly damaging Het
Ivns1abp G C 1: 151,236,688 (GRCm39) Q416H probably benign Het
Kcnh5 T A 12: 75,166,711 (GRCm39) H178L probably benign Het
Kif21b A G 1: 136,080,543 (GRCm39) N579S probably benign Het
Kif26a G C 12: 112,113,389 (GRCm39) R95P possibly damaging Het
Kl A G 5: 150,912,062 (GRCm39) I604V probably benign Het
Klhl24 A G 16: 19,941,686 (GRCm39) K545E probably damaging Het
Mcm3ap A G 10: 76,306,347 (GRCm39) I153M probably damaging Het
Meis1 T G 11: 18,831,682 (GRCm39) D452A probably damaging Het
Msantd4 C T 9: 4,384,138 (GRCm39) P153L probably benign Het
Myot A G 18: 44,475,422 (GRCm39) E181G probably damaging Het
Nf1 T C 11: 79,281,195 (GRCm39) F150S probably damaging Het
Nyap2 T A 1: 81,219,566 (GRCm39) S529R probably damaging Het
Or10d3 T C 9: 39,461,390 (GRCm39) Y259C probably damaging Het
Or12e10 A T 2: 87,640,988 (GRCm39) T275S probably benign Het
Or2y1c A G 11: 49,361,286 (GRCm39) I103V probably benign Het
Or8b56 T A 9: 38,739,660 (GRCm39) Y224* probably null Het
Pcnt C T 10: 76,240,496 (GRCm39) probably null Het
Pik3c3 T C 18: 30,455,289 (GRCm39) probably null Het
Pkdcc A T 17: 83,527,473 (GRCm39) Y217F possibly damaging Het
Pnpla6 C A 8: 3,585,459 (GRCm39) probably benign Het
Polr3gl T C 3: 96,488,190 (GRCm39) M26V probably benign Het
Ppp1r13b T C 12: 111,838,842 (GRCm39) N12S possibly damaging Het
Ppp1r26 G A 2: 28,341,528 (GRCm39) R386K probably benign Het
Prdm10 A G 9: 31,248,697 (GRCm39) E355G probably damaging Het
Prex2 T C 1: 11,131,554 (GRCm39) F41S possibly damaging Het
Prkar1b G T 5: 139,036,428 (GRCm39) Y231* probably null Het
Prkdc A T 16: 15,505,268 (GRCm39) I857L probably benign Het
Psg21 A T 7: 18,390,425 (GRCm39) N10K probably benign Het
Rnf17 A T 14: 56,705,243 (GRCm39) T716S probably benign Het
Rps6ka1 C T 4: 133,578,315 (GRCm39) R577H probably damaging Het
Scn1a A C 2: 66,161,629 (GRCm39) N306K possibly damaging Het
Skint6 A G 4: 113,095,329 (GRCm39) I110T probably damaging Het
Ssu2 A G 6: 112,364,959 (GRCm39) M1T probably null Het
Stag3 A T 5: 138,296,247 (GRCm39) T437S probably benign Het
Tal2 A G 4: 53,786,107 (GRCm39) Y96C probably benign Het
Thoc3 A T 13: 54,613,991 (GRCm39) probably null Het
Tle1 T C 4: 72,059,495 (GRCm39) D19G probably damaging Het
Trpm4 A G 7: 44,964,468 (GRCm39) I690T probably benign Het
Trpm6 A T 19: 18,853,295 (GRCm39) M1772L probably benign Het
Unc5b G A 10: 60,667,254 (GRCm39) probably benign Het
Usf3 G T 16: 44,041,561 (GRCm39) V2014F probably damaging Het
Utp18 C T 11: 93,776,390 (GRCm39) A32T probably benign Het
Wdfy4 A G 14: 32,682,765 (GRCm39) V2981A probably damaging Het
Zfp608 A G 18: 55,079,738 (GRCm39) V349A probably damaging Het
Znfx1 A C 2: 166,898,237 (GRCm39) I229S probably benign Het
Other mutations in Rapgef3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01314:Rapgef3 APN 15 97,646,104 (GRCm39) missense probably damaging 1.00
IGL01339:Rapgef3 APN 15 97,655,940 (GRCm39) missense probably damaging 1.00
IGL01670:Rapgef3 APN 15 97,647,543 (GRCm39) missense probably benign 0.15
IGL01902:Rapgef3 APN 15 97,648,181 (GRCm39) missense probably benign 0.32
IGL02137:Rapgef3 APN 15 97,648,025 (GRCm39) missense probably benign 0.08
IGL02419:Rapgef3 APN 15 97,648,171 (GRCm39) missense probably benign 0.33
IGL02427:Rapgef3 APN 15 97,645,017 (GRCm39) splice site probably null
IGL02648:Rapgef3 APN 15 97,656,273 (GRCm39) missense probably damaging 1.00
IGL02834:Rapgef3 APN 15 97,646,146 (GRCm39) missense probably damaging 0.98
IGL03389:Rapgef3 APN 15 97,647,397 (GRCm39) missense probably damaging 1.00
IGL03055:Rapgef3 UTSW 15 97,647,370 (GRCm39) splice site probably benign
R0394:Rapgef3 UTSW 15 97,655,700 (GRCm39) intron probably benign
R0538:Rapgef3 UTSW 15 97,655,698 (GRCm39) intron probably benign
R0744:Rapgef3 UTSW 15 97,659,466 (GRCm39) splice site probably benign
R1288:Rapgef3 UTSW 15 97,657,223 (GRCm39) missense probably benign 0.31
R1676:Rapgef3 UTSW 15 97,659,063 (GRCm39) missense probably benign 0.35
R1745:Rapgef3 UTSW 15 97,648,059 (GRCm39) missense probably benign 0.22
R1928:Rapgef3 UTSW 15 97,647,914 (GRCm39) missense probably damaging 1.00
R2063:Rapgef3 UTSW 15 97,664,842 (GRCm39) missense probably damaging 1.00
R2067:Rapgef3 UTSW 15 97,664,842 (GRCm39) missense probably damaging 1.00
R2092:Rapgef3 UTSW 15 97,658,604 (GRCm39) missense probably damaging 1.00
R4358:Rapgef3 UTSW 15 97,646,529 (GRCm39) missense probably benign 0.05
R4624:Rapgef3 UTSW 15 97,656,810 (GRCm39) missense probably damaging 1.00
R4627:Rapgef3 UTSW 15 97,656,810 (GRCm39) missense probably damaging 1.00
R4727:Rapgef3 UTSW 15 97,658,481 (GRCm39) missense probably damaging 1.00
R4812:Rapgef3 UTSW 15 97,651,684 (GRCm39) missense probably benign 0.21
R4928:Rapgef3 UTSW 15 97,655,256 (GRCm39) missense probably damaging 1.00
R5161:Rapgef3 UTSW 15 97,655,606 (GRCm39) missense probably damaging 1.00
R5442:Rapgef3 UTSW 15 97,656,742 (GRCm39) missense probably damaging 0.99
R5652:Rapgef3 UTSW 15 97,656,318 (GRCm39) missense probably benign 0.00
R5837:Rapgef3 UTSW 15 97,655,223 (GRCm39) splice site probably benign
R6056:Rapgef3 UTSW 15 97,656,742 (GRCm39) missense probably damaging 0.99
R6167:Rapgef3 UTSW 15 97,665,292 (GRCm39) unclassified probably benign
R6694:Rapgef3 UTSW 15 97,657,865 (GRCm39) missense probably benign 0.03
R7039:Rapgef3 UTSW 15 97,659,449 (GRCm39) missense probably benign 0.01
R7154:Rapgef3 UTSW 15 97,651,758 (GRCm39) missense probably benign
R7380:Rapgef3 UTSW 15 97,664,672 (GRCm39) missense probably benign 0.00
R7655:Rapgef3 UTSW 15 97,659,090 (GRCm39) missense probably damaging 1.00
R7656:Rapgef3 UTSW 15 97,659,090 (GRCm39) missense probably damaging 1.00
R7754:Rapgef3 UTSW 15 97,655,627 (GRCm39) missense probably damaging 1.00
R7849:Rapgef3 UTSW 15 97,656,271 (GRCm39) critical splice donor site probably null
R8061:Rapgef3 UTSW 15 97,659,401 (GRCm39) missense probably benign
R8117:Rapgef3 UTSW 15 97,648,747 (GRCm39) missense probably benign 0.01
R8179:Rapgef3 UTSW 15 97,658,621 (GRCm39) missense probably benign 0.06
R8819:Rapgef3 UTSW 15 97,646,538 (GRCm39) missense probably benign 0.39
R8820:Rapgef3 UTSW 15 97,646,538 (GRCm39) missense probably benign 0.39
R8824:Rapgef3 UTSW 15 97,664,789 (GRCm39) missense probably benign 0.39
R9779:Rapgef3 UTSW 15 97,643,479 (GRCm39) missense probably damaging 0.99
R9781:Rapgef3 UTSW 15 97,643,479 (GRCm39) missense probably damaging 0.99
R9782:Rapgef3 UTSW 15 97,643,479 (GRCm39) missense probably damaging 0.99
RF024:Rapgef3 UTSW 15 97,658,621 (GRCm39) missense probably benign 0.06
X0011:Rapgef3 UTSW 15 97,659,354 (GRCm39) critical splice donor site probably null
Predicted Primers PCR Primer
(F):5'- AGCAAGTTGCTAAGTCGGGCATC -3'
(R):5'- GTGAGCTATGACTCGGGCTGAAATC -3'

Sequencing Primer
(F):5'- CAAGAGTCAGCCCCTGAGATG -3'
(R):5'- AGAGACGTTCCTCAGTGACTTC -3'
Posted On 2014-04-13