Incidental Mutation 'R4722:Rapgef2'
ID 354519
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 041987-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4722 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 78969823-79193824 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 78976480 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Threonine at position 1294 (M1294T)
Ref Sequence ENSEMBL: ENSMUSP00000114119 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000118100] [ENSMUST00000118340] [ENSMUST00000195708]
AlphaFold Q8CHG7
Predicted Effect probably benign
Transcript: ENSMUST00000118100
AA Change: M1294T

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)
SMART Domains Protein: ENSMUSP00000114119
Gene: ENSMUSG00000062232
AA Change: M1294T

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: M1292T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000113778
Gene: ENSMUSG00000062232
AA Change: M1292T

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: M1442T

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000141542
Gene: ENSMUSG00000062232
AA Change: M1442T

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 0.0580 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.9%
  • 20x: 94.2%
Validation Efficiency 99% (68/69)
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: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2700097O09Rik G T 12: 55,107,922 (GRCm39) D92E probably benign Het
Abca17 A G 17: 24,484,403 (GRCm39) F1620L probably damaging Het
Abcf1 T C 17: 36,268,933 (GRCm39) probably benign Het
Adtrp T C 13: 41,920,823 (GRCm39) H248R probably benign Het
Aldh1b1 T G 4: 45,803,472 (GRCm39) F337V probably damaging Het
Amz2 C T 11: 109,325,457 (GRCm39) L272F probably damaging Het
Asic2 A T 11: 81,859,009 (GRCm39) M1K probably null Het
Avpr1a T A 10: 122,284,906 (GRCm39) V66E possibly damaging Het
AW554918 C A 18: 25,307,772 (GRCm39) Y28* probably null Het
Cdc25b C T 2: 131,035,271 (GRCm39) P343L probably damaging Het
Chd7 T A 4: 8,822,445 (GRCm39) I846K probably damaging Het
Dnajc13 A T 9: 104,091,017 (GRCm39) M688K probably benign Het
Dock2 T A 11: 34,586,298 (GRCm39) I505F probably damaging Het
Dpy19l4 A G 4: 11,290,521 (GRCm39) V290A possibly damaging Het
Dtl G T 1: 191,288,953 (GRCm39) Q254K possibly damaging Het
Enpp2 T G 15: 54,750,985 (GRCm39) K265T probably damaging Het
Epm2aip1 TGTCGCCG TG 9: 111,101,152 (GRCm39) probably benign Het
Fam133b T A 5: 3,593,949 (GRCm39) probably null Het
Fuom A G 7: 139,679,480 (GRCm39) probably benign Het
Fut9 T C 4: 25,799,734 (GRCm39) probably benign Het
Gas8 T A 8: 124,252,374 (GRCm39) I171N possibly damaging Het
Gipc3 T G 10: 81,177,129 (GRCm39) D147A probably benign Het
Gkn3 C T 6: 87,360,507 (GRCm39) A163T probably damaging Het
Gm5591 T C 7: 38,218,572 (GRCm39) K767R probably damaging Het
Kctd8 G A 5: 69,498,544 (GRCm39) P34L possibly damaging Het
Kmt2b G A 7: 30,282,627 (GRCm39) R403C probably damaging Het
Krt84 A T 15: 101,436,846 (GRCm39) I396N probably damaging Het
Lrrk2 C A 15: 91,573,104 (GRCm39) F217L probably damaging Het
Med27 T A 2: 29,414,447 (GRCm39) D290E probably damaging Het
Mical3 T C 6: 121,015,486 (GRCm39) Q184R probably benign Het
Mlxip A T 5: 123,585,265 (GRCm39) K591M probably benign Het
Mutyh T A 4: 116,674,069 (GRCm39) L233H probably damaging Het
Naip6 G T 13: 100,443,580 (GRCm39) H253N possibly damaging Het
Nynrin A G 14: 56,091,852 (GRCm39) E56G probably damaging Het
Oip5 C T 2: 119,443,492 (GRCm39) probably null Het
Or10a4 T A 7: 106,696,777 (GRCm39) I35N possibly damaging Het
Or10ak12 T C 4: 118,666,146 (GRCm39) N305S probably damaging Het
Or4c104 T G 2: 88,586,356 (GRCm39) H221P possibly damaging Het
Or4c15 T C 2: 88,760,324 (GRCm39) I112V possibly damaging Het
Or5p61 T A 7: 107,758,445 (GRCm39) I212F probably benign Het
Oxr1 T C 15: 41,677,045 (GRCm39) S132P probably damaging Het
Pcdhac1 C T 18: 37,224,933 (GRCm39) T582I probably damaging Het
Prl7a2 A G 13: 27,844,858 (GRCm39) I176T probably damaging Het
Rabgap1l T C 1: 160,169,734 (GRCm39) T30A possibly damaging Het
Rbm22 G A 18: 60,697,463 (GRCm39) R56H probably damaging Het
Rnmt T A 18: 68,438,952 (GRCm39) N20K probably damaging Het
Scn7a T A 2: 66,531,228 (GRCm39) T550S possibly damaging Het
Shank1 T A 7: 43,962,638 (GRCm39) Y117* probably null Het
Skint5 T A 4: 113,751,052 (GRCm39) K331I unknown Het
Slc5a1 A G 5: 33,304,055 (GRCm39) Y290C possibly damaging Het
Slfn14 T C 11: 83,174,244 (GRCm39) E249G probably benign Het
Smarcal1 T C 1: 72,650,496 (GRCm39) S544P probably damaging Het
St6galnac3 A T 3: 153,117,166 (GRCm39) Y186N probably damaging Het
Tbc1d1 T C 5: 64,420,900 (GRCm39) F346S probably damaging Het
Tdrd5 A T 1: 156,129,945 (GRCm39) I75K probably benign Het
Tnrc6a T C 7: 122,791,313 (GRCm39) M1737T possibly damaging Het
Toe1 A T 4: 116,662,397 (GRCm39) Y283N probably damaging Het
Tubal3 G T 13: 3,978,185 (GRCm39) G34C probably damaging Het
Uxs1 A G 1: 43,814,006 (GRCm39) L77P probably damaging Het
Vmn1r212 T C 13: 23,068,078 (GRCm39) Y85C probably damaging Het
Yju2b A T 8: 84,985,439 (GRCm39) C277S probably benign Het
Zdhhc4 A G 5: 143,307,536 (GRCm39) S162P probably damaging Het
Zfp712 A G 13: 67,190,177 (GRCm39) S117P probably benign Het
Zic4 G T 9: 91,261,257 (GRCm39) G164C probably 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
R0117:Rapgef2 UTSW 3 78,986,484 (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
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'- ACAGGTTTGGCTTCCTCTGTAG -3'
(R):5'- AGCTTTCCCATGACCAAGG -3'

Sequencing Primer
(F):5'- CTCAGCGGAGACATCCTTC -3'
(R):5'- GACCGTGCTTCCCTCGATG -3'
Posted On 2015-10-21