Incidental Mutation 'R0189:Rapgef6'
ID 23124
Institutional Source Beutler Lab
Gene Symbol Rapgef6
Ensembl Gene ENSMUSG00000037533
Gene Name Rap guanine nucleotide exchange factor (GEF) 6
Synonyms PDZ-GEF2, C030018K18Rik, Pdzgef2, RA-GEF-2
MMRRC Submission 038450-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R0189 (G1)
Quality Score 225
Status Validated (trace)
Chromosome 11
Chromosomal Location 54413673-54590111 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 54582075 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Leucine at position 1334 (S1334L)
Ref Sequence ENSEMBL: ENSMUSP00000147135 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000094536] [ENSMUST00000101206] [ENSMUST00000102743] [ENSMUST00000108894] [ENSMUST00000207429]
AlphaFold Q5NCJ1
Predicted Effect probably benign
Transcript: ENSMUST00000094536
SMART Domains Protein: ENSMUSP00000092114
Gene: ENSMUSG00000037533

DomainStartEndE-ValueType
cNMP 1 113 6.64e-7 SMART
RasGEFN 127 240 4.35e-33 SMART
PDZ 255 327 8.86e-16 SMART
low complexity region 409 420 N/A INTRINSIC
RA 464 550 1.47e-20 SMART
RasGEF 571 853 3.88e-84 SMART
low complexity region 944 957 N/A INTRINSIC
low complexity region 972 989 N/A INTRINSIC
low complexity region 1016 1061 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000101206
AA Change: S1337L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000098766
Gene: ENSMUSG00000037533
AA Change: S1337L

DomainStartEndE-ValueType
internal_repeat_1 10 82 1.45e-5 PROSPERO
low complexity region 187 205 N/A INTRINSIC
low complexity region 231 239 N/A INTRINSIC
cNMP 280 398 4.8e-13 SMART
RasGEFN 412 525 4.35e-33 SMART
PDZ 540 612 8.86e-16 SMART
low complexity region 694 705 N/A INTRINSIC
RA 749 835 1.47e-20 SMART
RasGEF 856 1095 5.35e-87 SMART
low complexity region 1237 1250 N/A INTRINSIC
low complexity region 1270 1293 N/A INTRINSIC
low complexity region 1345 1364 N/A INTRINSIC
low complexity region 1368 1380 N/A INTRINSIC
low complexity region 1444 1452 N/A INTRINSIC
low complexity region 1555 1568 N/A INTRINSIC
low complexity region 1591 1604 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000102743
AA Change: S1329L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000099804
Gene: ENSMUSG00000037533
AA Change: S1329L

DomainStartEndE-ValueType
internal_repeat_1 10 82 1.42e-5 PROSPERO
low complexity region 187 205 N/A INTRINSIC
low complexity region 231 239 N/A INTRINSIC
cNMP 280 398 4.8e-13 SMART
RasGEFN 412 525 4.35e-33 SMART
PDZ 540 612 8.86e-16 SMART
low complexity region 694 705 N/A INTRINSIC
RA 749 835 1.47e-20 SMART
RasGEF 856 1138 3.88e-84 SMART
low complexity region 1229 1242 N/A INTRINSIC
low complexity region 1262 1285 N/A INTRINSIC
low complexity region 1337 1356 N/A INTRINSIC
low complexity region 1360 1372 N/A INTRINSIC
low complexity region 1436 1444 N/A INTRINSIC
low complexity region 1547 1560 N/A INTRINSIC
low complexity region 1583 1596 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000108894
SMART Domains Protein: ENSMUSP00000104522
Gene: ENSMUSG00000037533

DomainStartEndE-ValueType
cNMP 1 113 6.64e-7 SMART
RasGEFN 127 240 4.35e-33 SMART
PDZ 255 327 8.86e-16 SMART
low complexity region 409 420 N/A INTRINSIC
RA 464 550 1.47e-20 SMART
RasGEF 571 810 5.35e-87 SMART
low complexity region 952 965 N/A INTRINSIC
low complexity region 980 997 N/A INTRINSIC
low complexity region 1024 1069 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000136494
SMART Domains Protein: ENSMUSP00000114574
Gene: ENSMUSG00000037533

DomainStartEndE-ValueType
low complexity region 47 55 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000207429
AA Change: S1334L

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.3%
  • 20x: 92.1%
Validation Efficiency 98% (96/98)
MGI Phenotype PHENOTYPE: Mice homozygous for a null allele exhibit an inlarged spleen, increased IgE and IgG levels and altered cytokine production. [provided by MGI curators]
Allele List at MGI

All alleles(16) : Targeted, knock-out(1) Targeted, other(2) Gene trapped(13)

Other mutations in this stock
Total: 83 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca9 A T 11: 109,999,479 (GRCm39) W1459R probably damaging Het
Abca9 A T 11: 110,032,488 (GRCm39) probably benign Het
Adam25 T A 8: 41,208,467 (GRCm39) C578S probably damaging Het
Adam32 T A 8: 25,412,353 (GRCm39) probably null Het
Add1 T C 5: 34,773,992 (GRCm39) V67A probably benign Het
Aggf1 A T 13: 95,492,988 (GRCm39) probably benign Het
Ahcyl2 A T 6: 29,891,242 (GRCm39) I449F probably benign Het
Ak6 A G 13: 100,791,650 (GRCm39) Y31C probably damaging Het
Akap6 T C 12: 53,188,037 (GRCm39) V1817A probably benign Het
Arhgef17 G T 7: 100,578,057 (GRCm39) P964T probably damaging Het
Atxn7l3b A T 10: 112,764,485 (GRCm39) L48Q possibly damaging Het
Bbs10 T G 10: 111,136,926 (GRCm39) S680A probably damaging Het
Bcl7c G A 7: 127,304,936 (GRCm39) T164I probably damaging Het
Btbd9 C T 17: 30,493,916 (GRCm39) D492N possibly damaging Het
Ccdc110 T A 8: 46,388,119 (GRCm39) D25E probably damaging Het
Ccdc83 T A 7: 89,875,891 (GRCm39) T327S possibly damaging Het
Coro1b T C 19: 4,203,250 (GRCm39) Y364H probably damaging Het
Cstf3 A G 2: 104,482,791 (GRCm39) D313G probably damaging Het
Dlgap5 T A 14: 47,650,432 (GRCm39) probably null Het
Dusp3 A T 11: 101,872,547 (GRCm39) I83N probably damaging Het
Eea1 A T 10: 95,831,444 (GRCm39) K178N possibly damaging Het
Efr3b T A 12: 4,032,925 (GRCm39) D144V probably damaging Het
Gfus C A 15: 75,798,827 (GRCm39) D127Y probably damaging Het
Gm1110 T A 9: 26,794,514 (GRCm39) E504V probably null Het
Got2 T C 8: 96,614,881 (GRCm39) H18R probably benign Het
Gprc5b T C 7: 118,582,856 (GRCm39) M338V probably benign Het
Has2 A T 15: 56,531,831 (GRCm39) F295I probably damaging Het
Hcn3 T C 3: 89,056,107 (GRCm39) D519G probably damaging Het
Ino80 T A 2: 119,210,160 (GRCm39) D1377V probably benign Het
Iqsec3 A T 6: 121,390,521 (GRCm39) probably benign Het
Kif3c T A 12: 3,415,989 (GRCm39) S3R probably benign Het
Krt17 A G 11: 100,151,445 (GRCm39) I116T possibly damaging Het
Lrba T C 3: 86,275,816 (GRCm39) V1728A probably damaging Het
Map3k6 G T 4: 132,974,252 (GRCm39) V550L possibly damaging Het
Mcph1 T C 8: 18,838,487 (GRCm39) V803A probably damaging Het
Med13 A G 11: 86,210,702 (GRCm39) V480A probably benign Het
Ms4a20 A G 19: 11,074,311 (GRCm39) V207A possibly damaging Het
Msh5 T C 17: 35,248,630 (GRCm39) E772G probably null Het
Nanos3 C T 8: 84,902,763 (GRCm39) R133Q probably damaging Het
Ndfip2 T C 14: 105,542,174 (GRCm39) L308P probably damaging Het
Ndufb10 T C 17: 24,943,209 (GRCm39) T34A probably benign Het
Nipal3 A T 4: 135,195,829 (GRCm39) I258N possibly damaging Het
Nup54 A G 5: 92,570,423 (GRCm39) V328A probably damaging Het
Oprm1 T C 10: 6,739,071 (GRCm39) V66A possibly damaging Het
Or10p21 T A 10: 128,847,191 (GRCm39) F12L possibly damaging Het
Or51ah3 G T 7: 103,210,289 (GRCm39) V202F probably benign Het
Or5b105 G A 19: 13,080,642 (GRCm39) R3C possibly damaging Het
Or8b56 T A 9: 38,739,111 (GRCm39) Y41* probably null Het
Or9s14 T C 1: 92,535,615 (GRCm39) F19L probably damaging Het
Peg12 G A 7: 62,113,296 (GRCm39) T267I unknown Het
Phf20 A G 2: 156,145,061 (GRCm39) S890G probably benign Het
Plk2 C T 13: 110,535,997 (GRCm39) T567M probably damaging Het
Pola2 A T 19: 5,992,370 (GRCm39) probably benign Het
Ppp1r12b A G 1: 134,793,514 (GRCm39) probably null Het
Prickle1 A T 15: 93,400,900 (GRCm39) L528* probably null Het
Prpf6 T A 2: 181,297,250 (GRCm39) N903K probably benign Het
Ptprc G A 1: 138,010,453 (GRCm39) A601V probably benign Het
Ranbp1 A T 16: 18,059,607 (GRCm39) probably null Het
Rgs2 T C 1: 143,878,022 (GRCm39) probably null Het
Ripk2 A T 4: 16,129,125 (GRCm39) probably null Het
Rnf17 A G 14: 56,719,650 (GRCm39) S967G probably null Het
Rock2 T A 12: 17,009,517 (GRCm39) probably benign Het
Rpusd3 C T 6: 113,392,514 (GRCm39) probably null Het
Scgb1b20 G T 7: 33,072,935 (GRCm39) V48L probably benign Het
Sec16a T A 2: 26,314,426 (GRCm39) probably null Het
Serpina5 T A 12: 104,069,589 (GRCm39) L267H probably damaging Het
Slc12a3 C T 8: 95,082,986 (GRCm39) H875Y probably benign Het
Slc45a4 A G 15: 73,453,763 (GRCm39) S745P probably benign Het
Sucla2 T C 14: 73,830,088 (GRCm39) V375A probably damaging Het
Sun2 C A 15: 79,621,277 (GRCm39) V213F probably damaging Het
Taar2 G A 10: 23,817,393 (GRCm39) R311H probably benign Het
Tac1 C T 6: 7,562,424 (GRCm39) R129C probably damaging Het
Taf6 T C 5: 138,180,975 (GRCm39) E202G probably benign Het
Tex21 T A 12: 76,286,307 (GRCm39) H64L probably benign Het
Tgs1 A G 4: 3,593,620 (GRCm39) S503G probably benign Het
Tmem184c C T 8: 78,324,441 (GRCm39) V350I possibly damaging Het
Tnks1bp1 A G 2: 84,901,273 (GRCm39) S960G possibly damaging Het
Trbc2 T C 6: 41,525,083 (GRCm39) probably benign Het
Tubgcp2 A T 7: 139,581,518 (GRCm39) probably benign Het
Vmn1r39 T A 6: 66,782,181 (GRCm39) T46S probably benign Het
Vmn1r61 T C 7: 5,613,699 (GRCm39) H205R probably benign Het
Zdhhc14 T C 17: 5,775,539 (GRCm39) S264P possibly damaging Het
Zfp101 T A 17: 33,601,213 (GRCm39) H181L possibly damaging Het
Other mutations in Rapgef6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00436:Rapgef6 APN 11 54,570,091 (GRCm39) missense probably benign 0.00
IGL00507:Rapgef6 APN 11 54,554,935 (GRCm39) nonsense probably null
IGL00809:Rapgef6 APN 11 54,540,126 (GRCm39) missense probably damaging 1.00
IGL00843:Rapgef6 APN 11 54,582,099 (GRCm39) missense probably benign 0.03
IGL00899:Rapgef6 APN 11 54,510,844 (GRCm39) nonsense probably null
IGL01372:Rapgef6 APN 11 54,559,437 (GRCm39) splice site probably benign
IGL01604:Rapgef6 APN 11 54,585,389 (GRCm39) missense probably damaging 0.99
IGL01935:Rapgef6 APN 11 54,501,668 (GRCm39) missense possibly damaging 0.78
IGL01991:Rapgef6 APN 11 54,443,695 (GRCm39) missense probably benign 0.37
IGL02243:Rapgef6 APN 11 54,567,226 (GRCm39) missense probably damaging 1.00
IGL02407:Rapgef6 APN 11 54,567,181 (GRCm39) missense possibly damaging 0.91
IGL02676:Rapgef6 APN 11 54,540,172 (GRCm39) unclassified probably benign
IGL02934:Rapgef6 APN 11 54,516,690 (GRCm39) missense probably damaging 1.00
IGL03076:Rapgef6 APN 11 54,516,793 (GRCm39) missense probably damaging 1.00
IGL03110:Rapgef6 APN 11 54,586,915 (GRCm39) missense probably damaging 0.97
IGL03256:Rapgef6 APN 11 54,548,255 (GRCm39) missense probably damaging 1.00
shocker UTSW 11 54,510,842 (GRCm39) missense probably damaging 1.00
D4216:Rapgef6 UTSW 11 54,559,572 (GRCm39) splice site probably benign
PIT4305001:Rapgef6 UTSW 11 54,570,203 (GRCm39) missense probably damaging 1.00
PIT4366001:Rapgef6 UTSW 11 54,582,446 (GRCm39) missense probably damaging 0.98
R0047:Rapgef6 UTSW 11 54,437,204 (GRCm39) missense possibly damaging 0.65
R0047:Rapgef6 UTSW 11 54,437,204 (GRCm39) missense possibly damaging 0.65
R0125:Rapgef6 UTSW 11 54,516,701 (GRCm39) nonsense probably null
R0201:Rapgef6 UTSW 11 54,510,767 (GRCm39) missense probably damaging 1.00
R0505:Rapgef6 UTSW 11 54,516,789 (GRCm39) missense probably benign 0.00
R0524:Rapgef6 UTSW 11 54,581,110 (GRCm39) missense probably benign 0.32
R0853:Rapgef6 UTSW 11 54,559,503 (GRCm39) missense probably damaging 1.00
R1203:Rapgef6 UTSW 11 54,582,525 (GRCm39) missense probably benign 0.09
R1440:Rapgef6 UTSW 11 54,517,534 (GRCm39) missense probably damaging 1.00
R1453:Rapgef6 UTSW 11 54,530,553 (GRCm39) splice site probably null
R1530:Rapgef6 UTSW 11 54,552,009 (GRCm39) missense probably damaging 1.00
R1593:Rapgef6 UTSW 11 54,437,223 (GRCm39) frame shift probably null
R1620:Rapgef6 UTSW 11 54,517,420 (GRCm39) missense possibly damaging 0.88
R1628:Rapgef6 UTSW 11 54,437,223 (GRCm39) frame shift probably null
R1629:Rapgef6 UTSW 11 54,437,223 (GRCm39) frame shift probably null
R1630:Rapgef6 UTSW 11 54,437,223 (GRCm39) frame shift probably null
R1634:Rapgef6 UTSW 11 54,437,223 (GRCm39) frame shift probably null
R1640:Rapgef6 UTSW 11 54,548,231 (GRCm39) missense probably damaging 1.00
R1686:Rapgef6 UTSW 11 54,582,458 (GRCm39) missense possibly damaging 0.81
R1722:Rapgef6 UTSW 11 54,437,223 (GRCm39) frame shift probably null
R1743:Rapgef6 UTSW 11 54,567,110 (GRCm39) missense probably damaging 1.00
R1816:Rapgef6 UTSW 11 54,585,314 (GRCm39) missense probably benign
R1851:Rapgef6 UTSW 11 54,533,637 (GRCm39) missense probably benign 0.01
R1852:Rapgef6 UTSW 11 54,533,637 (GRCm39) missense probably benign 0.01
R1868:Rapgef6 UTSW 11 54,437,223 (GRCm39) frame shift probably null
R1888:Rapgef6 UTSW 11 54,551,654 (GRCm39) missense probably damaging 1.00
R1888:Rapgef6 UTSW 11 54,551,654 (GRCm39) missense probably damaging 1.00
R1942:Rapgef6 UTSW 11 54,548,089 (GRCm39) missense possibly damaging 0.95
R1943:Rapgef6 UTSW 11 54,548,089 (GRCm39) missense possibly damaging 0.95
R2031:Rapgef6 UTSW 11 54,443,684 (GRCm39) missense probably benign 0.30
R2087:Rapgef6 UTSW 11 54,522,075 (GRCm39) missense probably damaging 1.00
R2106:Rapgef6 UTSW 11 54,559,512 (GRCm39) missense probably benign 0.17
R2362:Rapgef6 UTSW 11 54,585,098 (GRCm39) missense probably damaging 1.00
R2484:Rapgef6 UTSW 11 54,533,582 (GRCm39) missense possibly damaging 0.48
R2566:Rapgef6 UTSW 11 54,578,537 (GRCm39) missense possibly damaging 0.66
R2872:Rapgef6 UTSW 11 54,552,001 (GRCm39) missense probably damaging 1.00
R2872:Rapgef6 UTSW 11 54,552,001 (GRCm39) missense probably damaging 1.00
R3744:Rapgef6 UTSW 11 54,516,760 (GRCm39) missense probably benign 0.40
R3848:Rapgef6 UTSW 11 54,582,134 (GRCm39) missense probably damaging 0.97
R4823:Rapgef6 UTSW 11 54,585,326 (GRCm39) missense probably benign 0.08
R4859:Rapgef6 UTSW 11 54,526,989 (GRCm39) missense probably benign
R4906:Rapgef6 UTSW 11 54,443,662 (GRCm39) missense probably damaging 1.00
R4911:Rapgef6 UTSW 11 54,513,143 (GRCm39) missense probably damaging 0.97
R4937:Rapgef6 UTSW 11 54,548,143 (GRCm39) missense probably damaging 1.00
R5033:Rapgef6 UTSW 11 54,582,207 (GRCm39) missense possibly damaging 0.92
R5249:Rapgef6 UTSW 11 54,413,943 (GRCm39) missense probably benign 0.19
R5304:Rapgef6 UTSW 11 54,548,200 (GRCm39) missense probably benign 0.01
R5656:Rapgef6 UTSW 11 54,526,962 (GRCm39) missense possibly damaging 0.95
R5701:Rapgef6 UTSW 11 54,567,220 (GRCm39) missense possibly damaging 0.76
R5758:Rapgef6 UTSW 11 54,559,470 (GRCm39) missense probably damaging 1.00
R5973:Rapgef6 UTSW 11 54,530,609 (GRCm39) missense probably damaging 1.00
R6177:Rapgef6 UTSW 11 54,510,842 (GRCm39) missense probably damaging 1.00
R6268:Rapgef6 UTSW 11 54,540,073 (GRCm39) missense probably damaging 1.00
R6287:Rapgef6 UTSW 11 54,517,164 (GRCm39) splice site probably null
R6293:Rapgef6 UTSW 11 54,525,607 (GRCm39) missense probably damaging 1.00
R6471:Rapgef6 UTSW 11 54,582,563 (GRCm39) missense probably damaging 0.99
R6863:Rapgef6 UTSW 11 54,437,206 (GRCm39) missense probably benign 0.00
R6950:Rapgef6 UTSW 11 54,567,206 (GRCm39) missense probably benign 0.09
R7144:Rapgef6 UTSW 11 54,548,191 (GRCm39) missense possibly damaging 0.78
R7171:Rapgef6 UTSW 11 54,567,189 (GRCm39) missense possibly damaging 0.94
R7199:Rapgef6 UTSW 11 54,437,252 (GRCm39) missense probably benign 0.00
R7291:Rapgef6 UTSW 11 54,582,065 (GRCm39) missense probably benign 0.05
R7436:Rapgef6 UTSW 11 54,501,747 (GRCm39) critical splice donor site probably null
R7498:Rapgef6 UTSW 11 54,510,830 (GRCm39) missense probably damaging 1.00
R7506:Rapgef6 UTSW 11 54,526,997 (GRCm39) missense probably benign 0.00
R7527:Rapgef6 UTSW 11 54,525,787 (GRCm39) missense unknown
R7646:Rapgef6 UTSW 11 54,516,780 (GRCm39) missense probably benign 0.00
R7655:Rapgef6 UTSW 11 54,585,279 (GRCm39) missense probably benign 0.10
R7656:Rapgef6 UTSW 11 54,585,279 (GRCm39) missense probably benign 0.10
R7687:Rapgef6 UTSW 11 54,551,901 (GRCm39) missense possibly damaging 0.93
R7768:Rapgef6 UTSW 11 54,517,414 (GRCm39) missense probably damaging 1.00
R7788:Rapgef6 UTSW 11 54,585,225 (GRCm39) missense probably damaging 1.00
R7890:Rapgef6 UTSW 11 54,517,549 (GRCm39) missense probably damaging 1.00
R8113:Rapgef6 UTSW 11 54,516,784 (GRCm39) missense probably benign 0.03
R8337:Rapgef6 UTSW 11 54,522,127 (GRCm39) nonsense probably null
R8393:Rapgef6 UTSW 11 54,578,487 (GRCm39) missense probably benign
R8465:Rapgef6 UTSW 11 54,582,308 (GRCm39) missense probably benign 0.00
R8492:Rapgef6 UTSW 11 54,581,063 (GRCm39) missense probably damaging 0.99
R8791:Rapgef6 UTSW 11 54,459,295 (GRCm39) missense probably benign 0.15
R8866:Rapgef6 UTSW 11 54,443,700 (GRCm39) critical splice donor site probably null
R8917:Rapgef6 UTSW 11 54,582,392 (GRCm39) nonsense probably null
R8921:Rapgef6 UTSW 11 54,570,065 (GRCm39) missense probably benign 0.09
R9031:Rapgef6 UTSW 11 54,578,667 (GRCm39) missense probably benign 0.00
R9093:Rapgef6 UTSW 11 54,487,912 (GRCm39) nonsense probably null
R9354:Rapgef6 UTSW 11 54,510,749 (GRCm39) missense possibly damaging 0.66
R9514:Rapgef6 UTSW 11 54,443,684 (GRCm39) missense probably benign 0.14
R9516:Rapgef6 UTSW 11 54,582,169 (GRCm39) missense probably damaging 1.00
R9739:Rapgef6 UTSW 11 54,513,189 (GRCm39) missense probably benign 0.03
R9789:Rapgef6 UTSW 11 54,540,097 (GRCm39) missense probably benign 0.03
Predicted Primers PCR Primer
(F):5'- TTCACCGTACAGCAGACTTCCAGG -3'
(R):5'- TTGAGCAGCCTTTAGGACAGGCAC -3'

Sequencing Primer
(F):5'- GCATGTCTGTCCAGCACAATG -3'
(R):5'- GGCTCAACTTCTGCAATAGGG -3'
Posted On 2013-04-16