Incidental Mutation 'R1288:Rapgef3'
ID 150682
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 039354-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.186) question?
Stock # R1288 (G1)
Quality Score 225
Status Not validated
Chromosome 15
Chromosomal Location 97744770-97767972 bp(-) (GRCm38)
Type of Mutation missense
DNA Base Change (assembly) C to A at 97759342 bp (GRCm38)
Zygosity Heterozygous
Amino Acid Change Serine to Isoleucine at position 267 (S267I)
Ref Sequence ENSEMBL: ENSMUSP00000118148 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000126854] [ENSMUST00000128775] [ENSMUST00000129223] [ENSMUST00000134371] [ENSMUST00000134885] [ENSMUST00000146620] [ENSMUST00000149419] [ENSMUST00000177352] [ENSMUST00000175894]
AlphaFold Q8VCC8
Predicted Effect noncoding transcript
Transcript: ENSMUST00000123397
Predicted Effect probably benign
Transcript: ENSMUST00000126854
AA Change: S267I

PolyPhen 2 Score 0.306 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000116426
Gene: ENSMUSG00000022469
AA Change: S267I

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: S267I

PolyPhen 2 Score 0.194 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000120126
Gene: ENSMUSG00000022469
AA Change: S267I

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: S267I

PolyPhen 2 Score 0.306 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000118148
Gene: ENSMUSG00000022469
AA Change: S267I

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 probably benign
Transcript: ENSMUST00000177352
AA Change: S225I

PolyPhen 2 Score 0.194 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000135238
Gene: ENSMUSG00000022469
AA Change: S225I

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: ENSMUST00000153464
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153241
Predicted Effect probably benign
Transcript: ENSMUST00000175894
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 98.1%
  • 10x: 95.6%
  • 20x: 90.1%
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: 23 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgrd1 A T 5: 129,129,007 (GRCm38) D247V probably damaging Het
Ano5 A T 7: 51,546,872 (GRCm38) S184C probably damaging Het
Anpep C T 7: 79,838,256 (GRCm38) E518K probably benign Het
Atxn3 C T 12: 101,942,178 (GRCm38) probably null Het
BC005537 A T 13: 24,804,900 (GRCm38) E54V probably damaging Het
Ccdc150 A T 1: 54,364,458 (GRCm38) E881V probably damaging Het
Cep126 A T 9: 8,112,181 (GRCm38) N130K probably benign Het
Enoph1 A G 5: 100,040,279 (GRCm38) T21A possibly damaging Het
Fbxw28 A G 9: 109,337,293 (GRCm38) I165T probably damaging Het
Lrp12 A T 15: 39,878,403 (GRCm38) N305K probably damaging Het
Msl2 A G 9: 101,102,109 (GRCm38) T561A probably benign Het
Mup21 G T 4: 62,150,697 (GRCm38) A19E probably benign Het
Myh13 T C 11: 67,353,718 (GRCm38) I1027T probably benign Het
Nkg7 A G 7: 43,437,662 (GRCm38) probably null Het
Nme8 A G 13: 19,674,449 (GRCm38) V73A possibly damaging Het
Olfr1135 G A 2: 87,671,572 (GRCm38) A265V probably benign Het
Olfr123 T A 17: 37,795,693 (GRCm38) L83Q probably damaging Het
Olfr138 A G 17: 38,275,223 (GRCm38) T151A probably benign Het
Olfr68 A T 7: 103,778,042 (GRCm38) L101Q possibly damaging Het
Olfr822 A G 10: 130,075,285 (GRCm38) N292D probably damaging Het
Trhde T A 10: 114,801,290 (GRCm38) D4V probably benign Het
Vmn1r234 CTT CTTT 17: 21,229,251 (GRCm38) probably null Het
Zfp40 T A 17: 23,182,162 (GRCm38) I36L probably benign 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
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
R4627: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'- TGTCCACACGCAGAAAGTGACAG -3'
(R):5'- TGACCATAGCTCTATCCTCCAGTGC -3'

Sequencing Primer
(F):5'- GACAGTTGACATCTATCCCAGTGG -3'
(R):5'- AGTGCTGTCTTTGGATATACCC -3'
Posted On 2014-01-29