Incidental Mutation 'R0117:Rapgef2'
ID 20867
Institutional Source Beutler Lab
Gene Symbol Rapgef2
Ensembl Gene ENSMUSG00000062232
Gene Name Rap guanine nucleotide exchange factor (GEF) 2
Synonyms CNRasGEF, nRapGEP, 5830453M24Rik, RA-GEF-1, Pdzgef1
MMRRC Submission 038403-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0117 (G1)
Quality Score 225
Status Validated (trace)
Chromosome 3
Chromosomal Location 78969823-79193824 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 78986484 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 1017 (S1017P)
Ref Sequence ENSEMBL: ENSMUSP00000113778 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000118100] [ENSMUST00000118340] [ENSMUST00000195708]
AlphaFold Q8CHG7
Predicted Effect probably benign
Transcript: ENSMUST00000118100
AA Change: S1019P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000114119
Gene: ENSMUSG00000062232
AA Change: S1019P

DomainStartEndE-ValueType
low complexity region 38 62 N/A INTRINSIC
low complexity region 84 95 N/A INTRINSIC
cNMP 135 253 2.48e-15 SMART
RasGEFN 267 380 1.3e-31 SMART
PDZ 395 467 1.28e-12 SMART
RA 606 692 7.59e-23 SMART
RasGEF 713 950 6.09e-100 SMART
low complexity region 1030 1046 N/A INTRINSIC
low complexity region 1110 1124 N/A INTRINSIC
low complexity region 1140 1161 N/A INTRINSIC
low complexity region 1392 1405 N/A INTRINSIC
low complexity region 1440 1455 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000118340
AA Change: S1017P

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000113778
Gene: ENSMUSG00000062232
AA Change: S1017P

DomainStartEndE-ValueType
low complexity region 36 60 N/A INTRINSIC
low complexity region 82 93 N/A INTRINSIC
cNMP 133 251 2.48e-15 SMART
RasGEFN 265 378 1.3e-31 SMART
PDZ 393 465 1.28e-12 SMART
RA 604 690 7.59e-23 SMART
RasGEF 711 948 6.09e-100 SMART
low complexity region 1028 1044 N/A INTRINSIC
low complexity region 1108 1122 N/A INTRINSIC
low complexity region 1138 1159 N/A INTRINSIC
low complexity region 1390 1403 N/A INTRINSIC
low complexity region 1438 1453 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000195708
AA Change: S1167P

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000141542
Gene: ENSMUSG00000062232
AA Change: S1167P

DomainStartEndE-ValueType
cNMP 24 131 3.9e-4 SMART
low complexity region 186 210 N/A INTRINSIC
low complexity region 232 243 N/A INTRINSIC
cNMP 283 401 1.2e-17 SMART
RasGEFN 415 528 6.4e-34 SMART
PDZ 543 615 6.4e-15 SMART
RA 754 840 4.8e-25 SMART
RasGEF 861 1098 3.8e-102 SMART
low complexity region 1178 1194 N/A INTRINSIC
low complexity region 1258 1272 N/A INTRINSIC
low complexity region 1288 1309 N/A INTRINSIC
low complexity region 1540 1553 N/A INTRINSIC
low complexity region 1588 1603 N/A INTRINSIC
Meta Mutation Damage Score 0.0594 question?
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.0%
  • 10x: 95.2%
  • 20x: 88.1%
Validation Efficiency 95% (59/62)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Members of the RAS (see HRAS; MIM 190020) subfamily of GTPases function in signal transduction as GTP/GDP-regulated switches that cycle between inactive GDP- and active GTP-bound states. Guanine nucleotide exchange factors (GEFs), such as RAPGEF2, serve as RAS activators by promoting acquisition of GTP to maintain the active GTP-bound state and are the key link between cell surface receptors and RAS activation (Rebhun et al., 2000 [PubMed 10934204]).[supplied by OMIM, Mar 2008]
PHENOTYPE: Homozygotes for a null allele die at mid-gestation exhibiting growth arrest and defects in vascular development, neural tube closure and embryo turning. Homozygotes for another null allele show yolk sac vascular defects, impaired cell physiology and heart, primitive gut, liver and brain formation. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 54 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Angptl4 A T 17: 33,999,776 (GRCm39) I141K probably damaging Het
Bbs10 T A 10: 111,135,194 (GRCm39) D102E possibly damaging Het
Btaf1 A G 19: 36,947,368 (GRCm39) T486A probably benign Het
Casp8ap2 A G 4: 32,640,817 (GRCm39) T624A probably benign Het
Cep192 T C 18: 67,983,808 (GRCm39) probably null Het
Cep76 T C 18: 67,759,744 (GRCm39) Y323C possibly damaging Het
CK137956 T A 4: 127,840,585 (GRCm39) T374S possibly damaging Het
Cyp2b23 A T 7: 26,372,539 (GRCm39) F359I probably benign Het
Cyp4f13 G T 17: 33,149,580 (GRCm39) H194Q probably damaging Het
Dach1 C T 14: 98,406,184 (GRCm39) G188R probably damaging Het
Def8 G A 8: 124,183,234 (GRCm39) A278T probably damaging Het
Dscam T C 16: 96,474,878 (GRCm39) H1228R probably benign Het
Eps15 T A 4: 109,240,016 (GRCm39) D667E probably damaging Het
Fig4 G A 10: 41,106,037 (GRCm39) R716* probably null Het
Fmnl3 G C 15: 99,220,619 (GRCm39) probably benign Het
Gmpr T A 13: 45,670,560 (GRCm39) probably null Het
Gsta5 C T 9: 78,211,700 (GRCm39) T154I probably damaging Het
Helz2 C A 2: 180,874,552 (GRCm39) G1981C probably damaging Het
Herc2 C A 7: 55,863,359 (GRCm39) probably benign Het
Htr2a G A 14: 74,882,533 (GRCm39) R173H probably damaging Het
Impg2 A G 16: 56,082,005 (GRCm39) N979S probably damaging Het
Kcna2 A G 3: 107,012,670 (GRCm39) Y417C probably damaging Het
Lmf1 G T 17: 25,874,965 (GRCm39) probably benign Het
Lmntd2 G A 7: 140,790,036 (GRCm39) R659C possibly damaging Het
Mcm9 A G 10: 53,413,832 (GRCm39) V416A possibly damaging Het
Mgarp G T 3: 51,304,133 (GRCm39) probably benign Het
Mpp3 G A 11: 101,891,399 (GRCm39) P580S probably damaging Het
Nfat5 C T 8: 108,065,707 (GRCm39) R156W probably damaging Het
Ninl G A 2: 150,779,593 (GRCm39) R269W probably damaging Het
Or7e170 T C 9: 19,795,595 (GRCm39) E2G probably damaging Het
Or8g19 T A 9: 39,056,146 (GRCm39) I250N probably damaging Het
Or8h8 T A 2: 86,753,214 (GRCm39) I221F probably damaging Het
Pcnt A T 10: 76,244,561 (GRCm39) L1173* probably null Het
Pde6c A G 19: 38,139,979 (GRCm39) E314G probably damaging Het
Peds1 A G 2: 167,486,678 (GRCm39) probably benign Het
Phldb1 T C 9: 44,623,003 (GRCm39) M1V probably null Het
Pkdrej T A 15: 85,700,300 (GRCm39) probably null Het
Plch2 T A 4: 155,069,815 (GRCm39) probably benign Het
Pld2 G A 11: 70,448,214 (GRCm39) R887Q probably benign Het
Plxnb1 A G 9: 108,934,286 (GRCm39) D838G possibly damaging Het
Postn C T 3: 54,290,902 (GRCm39) probably benign Het
Prl8a8 T A 13: 27,692,473 (GRCm39) I172F probably damaging Het
Psmc4 A T 7: 27,742,165 (GRCm39) probably benign Het
Rabgap1 T A 2: 37,451,897 (GRCm39) probably null Het
Rbak G T 5: 143,159,387 (GRCm39) Y555* probably null Het
Serpina1c T G 12: 103,861,271 (GRCm39) *414C probably null Het
Sntb1 A G 15: 55,769,749 (GRCm39) V80A probably benign Het
Sorl1 A G 9: 41,944,873 (GRCm39) V884A probably benign Het
Stmnd1 C A 13: 46,438,962 (GRCm39) Q65K possibly damaging Het
Tgm5 C T 2: 120,905,583 (GRCm39) probably null Het
Tubb1 T C 2: 174,299,577 (GRCm39) S420P probably benign Het
Tvp23b T C 11: 62,770,430 (GRCm39) probably benign Het
Xirp2 C T 2: 67,347,464 (GRCm39) A3235V possibly damaging Het
Zc3h15 T C 2: 83,488,427 (GRCm39) S122P possibly damaging Het
Other mutations in Rapgef2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00488:Rapgef2 APN 3 78,999,332 (GRCm39) missense possibly damaging 0.89
IGL01024:Rapgef2 APN 3 78,977,445 (GRCm39) missense probably benign 0.43
IGL01448:Rapgef2 APN 3 79,011,269 (GRCm39) critical splice donor site probably null
IGL01448:Rapgef2 APN 3 78,976,244 (GRCm39) missense probably benign
IGL01928:Rapgef2 APN 3 79,011,270 (GRCm39) missense probably damaging 1.00
IGL01973:Rapgef2 APN 3 78,999,116 (GRCm39) splice site probably null
IGL02015:Rapgef2 APN 3 78,999,371 (GRCm39) splice site probably benign
IGL02498:Rapgef2 APN 3 78,974,060 (GRCm39) missense probably damaging 0.97
IGL02631:Rapgef2 APN 3 78,990,533 (GRCm39) missense possibly damaging 0.77
IGL02835:Rapgef2 APN 3 79,000,293 (GRCm39) splice site probably benign
IGL02887:Rapgef2 APN 3 78,976,187 (GRCm39) splice site probably benign
IGL03030:Rapgef2 APN 3 78,981,614 (GRCm39) critical splice donor site probably null
IGL03035:Rapgef2 APN 3 79,001,731 (GRCm39) missense probably damaging 1.00
IGL03222:Rapgef2 APN 3 78,995,302 (GRCm39) missense probably damaging 1.00
IGL03227:Rapgef2 APN 3 78,999,920 (GRCm39) splice site probably benign
IGL03326:Rapgef2 APN 3 78,999,140 (GRCm39) missense probably damaging 0.96
IGL03335:Rapgef2 APN 3 79,006,492 (GRCm39) missense probably damaging 1.00
IGL03384:Rapgef2 APN 3 78,990,853 (GRCm39) missense probably damaging 1.00
Bulge UTSW 3 78,986,439 (GRCm39) missense probably benign 0.01
Hai_phat UTSW 3 78,993,266 (GRCm39) missense probably damaging 1.00
R0022:Rapgef2 UTSW 3 78,995,207 (GRCm39) missense probably damaging 1.00
R0022:Rapgef2 UTSW 3 78,995,207 (GRCm39) missense probably damaging 1.00
R0038:Rapgef2 UTSW 3 78,976,703 (GRCm39) missense probably benign 0.00
R0225:Rapgef2 UTSW 3 79,011,412 (GRCm39) missense probably damaging 0.99
R0723:Rapgef2 UTSW 3 78,986,481 (GRCm39) missense probably benign 0.20
R0788:Rapgef2 UTSW 3 79,006,502 (GRCm39) missense possibly damaging 0.59
R1311:Rapgef2 UTSW 3 78,990,854 (GRCm39) missense probably benign 0.12
R1374:Rapgef2 UTSW 3 78,995,275 (GRCm39) missense probably benign 0.08
R1507:Rapgef2 UTSW 3 78,988,600 (GRCm39) splice site probably benign
R1523:Rapgef2 UTSW 3 79,000,056 (GRCm39) missense probably damaging 1.00
R1753:Rapgef2 UTSW 3 78,996,098 (GRCm39) missense possibly damaging 0.65
R1759:Rapgef2 UTSW 3 78,974,038 (GRCm39) missense possibly damaging 0.89
R1766:Rapgef2 UTSW 3 79,000,010 (GRCm39) missense probably damaging 1.00
R2436:Rapgef2 UTSW 3 78,996,079 (GRCm39) missense possibly damaging 0.95
R3033:Rapgef2 UTSW 3 78,981,613 (GRCm39) critical splice donor site probably null
R3766:Rapgef2 UTSW 3 78,996,057 (GRCm39) missense probably benign 0.01
R4118:Rapgef2 UTSW 3 78,976,194 (GRCm39) critical splice donor site probably null
R4416:Rapgef2 UTSW 3 78,976,364 (GRCm39) nonsense probably null
R4722:Rapgef2 UTSW 3 78,976,480 (GRCm39) missense probably benign 0.00
R4743:Rapgef2 UTSW 3 79,080,375 (GRCm39) missense probably damaging 0.99
R4780:Rapgef2 UTSW 3 79,077,076 (GRCm39) splice site probably benign
R4825:Rapgef2 UTSW 3 78,990,534 (GRCm39) missense probably benign 0.03
R4861:Rapgef2 UTSW 3 78,981,743 (GRCm39) missense probably benign 0.01
R4861:Rapgef2 UTSW 3 78,981,743 (GRCm39) missense probably benign 0.01
R4900:Rapgef2 UTSW 3 78,981,670 (GRCm39) missense probably benign 0.02
R4943:Rapgef2 UTSW 3 78,971,854 (GRCm39) missense probably benign 0.00
R5291:Rapgef2 UTSW 3 78,977,366 (GRCm39) missense possibly damaging 0.64
R5369:Rapgef2 UTSW 3 78,976,739 (GRCm39) missense probably benign 0.00
R5413:Rapgef2 UTSW 3 78,995,173 (GRCm39) missense probably damaging 1.00
R5561:Rapgef2 UTSW 3 78,995,950 (GRCm39) critical splice donor site probably null
R5568:Rapgef2 UTSW 3 79,011,308 (GRCm39) missense probably damaging 1.00
R5642:Rapgef2 UTSW 3 79,002,157 (GRCm39) missense probably damaging 1.00
R5783:Rapgef2 UTSW 3 78,995,300 (GRCm39) missense probably benign 0.00
R6041:Rapgef2 UTSW 3 78,976,469 (GRCm39) missense probably benign 0.00
R6193:Rapgef2 UTSW 3 78,976,751 (GRCm39) missense possibly damaging 0.48
R6324:Rapgef2 UTSW 3 78,986,439 (GRCm39) missense probably benign 0.01
R6551:Rapgef2 UTSW 3 79,122,342 (GRCm39) splice site probably null
R6688:Rapgef2 UTSW 3 78,976,435 (GRCm39) missense probably benign 0.03
R6908:Rapgef2 UTSW 3 79,011,370 (GRCm39) missense probably benign 0.01
R6913:Rapgef2 UTSW 3 78,993,281 (GRCm39) missense probably damaging 1.00
R6933:Rapgef2 UTSW 3 78,993,266 (GRCm39) missense probably damaging 1.00
R7086:Rapgef2 UTSW 3 78,993,353 (GRCm39) missense probably benign 0.08
R7106:Rapgef2 UTSW 3 78,973,915 (GRCm39) missense probably benign
R7228:Rapgef2 UTSW 3 78,976,525 (GRCm39) missense probably benign 0.03
R7242:Rapgef2 UTSW 3 78,995,210 (GRCm39) nonsense probably null
R7257:Rapgef2 UTSW 3 78,989,934 (GRCm39) missense probably damaging 0.99
R7322:Rapgef2 UTSW 3 79,053,130 (GRCm39) start codon destroyed probably null 0.02
R7443:Rapgef2 UTSW 3 78,988,531 (GRCm39) missense probably damaging 1.00
R7450:Rapgef2 UTSW 3 79,080,366 (GRCm39) missense probably benign 0.01
R7472:Rapgef2 UTSW 3 78,976,580 (GRCm39) missense probably benign 0.45
R7884:Rapgef2 UTSW 3 78,973,933 (GRCm39) missense possibly damaging 0.49
R7954:Rapgef2 UTSW 3 78,977,454 (GRCm39) nonsense probably null
R7957:Rapgef2 UTSW 3 79,122,276 (GRCm39) missense probably benign 0.27
R8071:Rapgef2 UTSW 3 79,000,343 (GRCm39) missense probably damaging 1.00
R8261:Rapgef2 UTSW 3 78,993,325 (GRCm39) missense probably benign 0.34
R8268:Rapgef2 UTSW 3 78,993,263 (GRCm39) missense probably benign 0.12
R8309:Rapgef2 UTSW 3 78,990,509 (GRCm39) missense possibly damaging 0.65
R8505:Rapgef2 UTSW 3 78,986,349 (GRCm39) nonsense probably null
R8783:Rapgef2 UTSW 3 79,005,651 (GRCm39) missense probably damaging 1.00
R8897:Rapgef2 UTSW 3 79,019,566 (GRCm39) missense probably damaging 1.00
R8965:Rapgef2 UTSW 3 78,999,851 (GRCm39) missense probably damaging 1.00
R9028:Rapgef2 UTSW 3 78,981,651 (GRCm39) missense probably damaging 1.00
R9284:Rapgef2 UTSW 3 79,000,010 (GRCm39) missense probably damaging 1.00
R9371:Rapgef2 UTSW 3 79,082,300 (GRCm39) missense probably damaging 1.00
R9479:Rapgef2 UTSW 3 79,019,495 (GRCm39) missense probably damaging 1.00
R9493:Rapgef2 UTSW 3 79,019,495 (GRCm39) missense probably damaging 1.00
R9494:Rapgef2 UTSW 3 79,019,495 (GRCm39) missense probably damaging 1.00
R9500:Rapgef2 UTSW 3 78,974,093 (GRCm39) missense probably benign
R9657:Rapgef2 UTSW 3 78,999,191 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- CTTACCAAAAGGAGGCAGATCCTTCAC -3'
(R):5'- TCGTGTGTTTAACTTCCATGCACATTG -3'

Sequencing Primer
(F):5'- GATCCTTCACCGGCACC -3'
(R):5'- GGCAAATAAATACCCTTGTCCTG -3'
Posted On 2013-04-11