Incidental Mutation 'R7315:Rapgef1'
ID 567857
Institutional Source Beutler Lab
Gene Symbol Rapgef1
Ensembl Gene ENSMUSG00000039844
Gene Name Rap guanine nucleotide exchange factor (GEF) 1
Synonyms C3G, Grf2, 4932418O06Rik
MMRRC Submission 045368-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7315 (G1)
Quality Score 225.009
Status Not validated
Chromosome 2
Chromosomal Location 29509732-29630376 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 29624504 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Lysine at position 1030 (T1030K)
Ref Sequence ENSEMBL: ENSMUSP00000092703 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000091146] [ENSMUST00000095087] [ENSMUST00000102872] [ENSMUST00000147755]
AlphaFold Q3UHC1
Predicted Effect probably damaging
Transcript: ENSMUST00000091146
AA Change: T1024K

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000088680
Gene: ENSMUSG00000039844
AA Change: T1024K

DomainStartEndE-ValueType
low complexity region 191 206 N/A INTRINSIC
low complexity region 309 324 N/A INTRINSIC
low complexity region 468 478 N/A INTRINSIC
low complexity region 510 521 N/A INTRINSIC
low complexity region 592 603 N/A INTRINSIC
low complexity region 664 682 N/A INTRINSIC
low complexity region 689 700 N/A INTRINSIC
low complexity region 727 741 N/A INTRINSIC
RasGEFN 828 970 8.04e-37 SMART
RasGEF 977 1206 5.85e-102 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000095087
AA Change: T1030K

PolyPhen 2 Score 0.975 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000092703
Gene: ENSMUSG00000039844
AA Change: T1030K

DomainStartEndE-ValueType
low complexity region 229 244 N/A INTRINSIC
low complexity region 347 362 N/A INTRINSIC
low complexity region 506 516 N/A INTRINSIC
low complexity region 548 559 N/A INTRINSIC
low complexity region 630 641 N/A INTRINSIC
low complexity region 702 720 N/A INTRINSIC
low complexity region 727 738 N/A INTRINSIC
RasGEFN 834 976 8.04e-37 SMART
RasGEF 983 1212 5.85e-102 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000102872
AA Change: T892K

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000099936
Gene: ENSMUSG00000039844
AA Change: T892K

DomainStartEndE-ValueType
low complexity region 229 244 N/A INTRINSIC
low complexity region 347 362 N/A INTRINSIC
low complexity region 506 516 N/A INTRINSIC
low complexity region 548 559 N/A INTRINSIC
RasGEFN 696 838 8.04e-37 SMART
RasGEF 845 1074 5.85e-102 SMART
Predicted Effect
SMART Domains Protein: ENSMUSP00000117631
Gene: ENSMUSG00000039844
AA Change: T448K

DomainStartEndE-ValueType
low complexity region 12 22 N/A INTRINSIC
low complexity region 54 65 N/A INTRINSIC
low complexity region 135 146 N/A INTRINSIC
RasGEFN 253 395 8.04e-37 SMART
RasGEF 402 631 5.85e-102 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000147755
SMART Domains Protein: ENSMUSP00000121615
Gene: ENSMUSG00000039844

DomainStartEndE-ValueType
low complexity region 191 206 N/A INTRINSIC
low complexity region 309 324 N/A INTRINSIC
low complexity region 468 478 N/A INTRINSIC
low complexity region 510 521 N/A INTRINSIC
low complexity region 591 602 N/A INTRINSIC
low complexity region 663 681 N/A INTRINSIC
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.5%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a human guanine nucleotide exchange factor. It transduces signals from CRK by binding the SH3 domain of CRK, and activating several members of the Ras family of GTPases. This signaling cascade that may be involved in apoptosis, integrin-mediated signal transduction, and cell transformation. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some variants has not been determined. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a null allele die before E7.5. Mice homozygous for a hypomorphic gene trap allele show embryonic lethality during organogenesis, altered neuroepithelium morphology, vascular maturation defects, hemorrhage, and reduced cell migration and adhesion. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 74 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca14 A C 7: 119,893,341 (GRCm39) I1264L probably benign Het
Abcg8 C A 17: 85,004,142 (GRCm39) D484E probably damaging Het
Abhd13 T A 8: 10,037,970 (GRCm39) L189H probably damaging Het
Acox2 T C 14: 8,256,139 (GRCm38) D60G probably damaging Het
Acp3 A G 9: 104,193,423 (GRCm39) probably null Het
Agpat4 C T 17: 12,429,185 (GRCm39) R146C probably damaging Het
Antxrl T C 14: 33,793,504 (GRCm39) S411P unknown Het
B4galt5 A G 2: 167,143,296 (GRCm39) V376A probably damaging Het
Camk1d T C 2: 5,344,041 (GRCm39) Y198C probably damaging Het
Cd1d1 C T 3: 86,905,420 (GRCm39) R191H possibly damaging Het
Cd93 A G 2: 148,284,461 (GRCm39) V295A probably damaging Het
Cdc27 G A 11: 104,406,270 (GRCm39) T615I possibly damaging Het
Cfap74 T C 4: 155,547,476 (GRCm39) Y1221H unknown Het
Col24a1 G A 3: 145,137,625 (GRCm39) S896N possibly damaging Het
Crppa A G 12: 36,440,373 (GRCm39) T94A probably benign Het
Cst7 C A 2: 150,412,503 (GRCm39) P22Q probably benign Het
Dnah6 C T 6: 73,061,743 (GRCm39) A2781T probably damaging Het
Dscaml1 G A 9: 45,656,423 (GRCm39) A1588T probably benign Het
Dsg2 A T 18: 20,712,217 (GRCm39) I118F probably damaging Het
Eif1ad2 A G 12: 87,786,473 (GRCm39) E128G unknown Het
Eme2 G A 17: 25,113,840 (GRCm39) R62W probably damaging Het
Epha3 A T 16: 63,372,972 (GRCm39) D910E probably benign Het
Ext1 T C 15: 52,936,783 (GRCm39) D654G probably damaging Het
Fnip2 A G 3: 79,413,512 (GRCm39) probably null Het
Gon4l T A 3: 88,802,486 (GRCm39) H1032Q probably benign Het
Kitl G A 10: 99,851,974 (GRCm39) R31H unknown Het
Lcp2 G A 11: 34,019,906 (GRCm39) probably null Het
Lrp2 T C 2: 69,322,166 (GRCm39) H1921R probably damaging Het
Lvrn A G 18: 47,010,051 (GRCm39) T400A probably benign Het
Mak16 G A 8: 31,654,766 (GRCm39) R143* probably null Het
Mettl23 A G 11: 116,739,928 (GRCm39) I159V probably benign Het
Mr1 T C 1: 155,005,036 (GRCm39) N335D probably benign Het
Muc2 T C 7: 141,276,645 (GRCm39) C12R probably damaging Het
Myom1 T C 17: 71,387,892 (GRCm39) probably null Het
Nav2 A G 7: 49,198,037 (GRCm39) N33S possibly damaging Het
Ninl A G 2: 150,791,970 (GRCm39) V851A probably benign Het
Nmt1 A G 11: 102,951,009 (GRCm39) N367D probably benign Het
Noc2l T G 4: 156,325,817 (GRCm39) S354R probably damaging Het
Opn1sw A T 6: 29,379,362 (GRCm39) I214N probably damaging Het
Or12d14-ps1 G T 17: 37,673,551 (GRCm39) C181F probably damaging Het
Or13e8 T A 4: 43,696,961 (GRCm39) I71F probably damaging Het
Or14c40 T C 7: 86,313,445 (GRCm39) S192P probably damaging Het
Or4k52 T C 2: 111,611,004 (GRCm39) V113A probably damaging Het
Or5ac16 A G 16: 59,022,496 (GRCm39) F98L probably benign Het
Or7e169 G T 9: 19,757,131 (GRCm39) S261R probably damaging Het
Or8a1 T C 9: 37,641,872 (GRCm39) M136V probably benign Het
Or8b9 A T 9: 37,766,543 (GRCm39) Y143F probably benign Het
Papss2 T C 19: 32,616,625 (GRCm39) V217A possibly damaging Het
Pes1 A G 11: 3,926,085 (GRCm39) I291M probably benign Het
Ptprb T A 10: 116,198,284 (GRCm39) I1660N possibly damaging Het
Rassf8 A G 6: 145,761,477 (GRCm39) M268V probably benign Het
Rbl2 A T 8: 91,802,640 (GRCm39) T154S probably damaging Het
Rgs1 A G 1: 144,124,637 (GRCm39) probably null Het
Rpgrip1 C T 14: 52,358,458 (GRCm39) T188I not run Het
Rrp1b T A 17: 32,277,545 (GRCm39) F608L probably benign Het
Sbp C T 17: 24,164,280 (GRCm39) A154V probably benign Het
Scara3 C T 14: 66,168,889 (GRCm39) E243K probably damaging Het
Serpinb6b A T 13: 33,156,240 (GRCm39) D110V probably benign Het
Skic2 T A 17: 35,060,145 (GRCm39) D875V probably benign Het
Slc2a4 G C 11: 69,837,259 (GRCm39) T59R probably damaging Het
Slc4a1 A G 11: 102,247,310 (GRCm39) S462P probably damaging Het
Slc66a1 G A 4: 139,029,181 (GRCm39) T101M probably damaging Het
Snx33 C T 9: 56,833,151 (GRCm39) R306H probably damaging Het
Srf T C 17: 46,862,720 (GRCm39) probably null Het
Steap3 A G 1: 120,155,642 (GRCm39) V439A probably benign Het
Syt10 C T 15: 89,698,541 (GRCm39) D268N probably damaging Het
Tent5b C T 4: 133,214,395 (GRCm39) T422I probably damaging Het
Terf2 T C 8: 107,807,849 (GRCm39) N242S probably benign Het
Tex15 A G 8: 34,071,544 (GRCm39) T2364A probably benign Het
Tgfbr2 A T 9: 115,938,806 (GRCm39) H365Q possibly damaging Het
Tnrc6c T G 11: 117,614,354 (GRCm39) N837K probably benign Het
Trim67 T A 8: 125,521,069 (GRCm39) S144T probably benign Het
Zc3hav1l T G 6: 38,272,082 (GRCm39) D229A possibly damaging Het
Zmym4 A T 4: 126,776,385 (GRCm39) V1184E probably benign Het
Other mutations in Rapgef1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00156:Rapgef1 APN 2 29,612,281 (GRCm39) missense probably benign
IGL00917:Rapgef1 APN 2 29,592,535 (GRCm39) missense probably benign 0.00
IGL02618:Rapgef1 APN 2 29,627,955 (GRCm39) missense probably damaging 1.00
IGL02642:Rapgef1 APN 2 29,590,872 (GRCm39) splice site probably benign
IGL02974:Rapgef1 APN 2 29,600,228 (GRCm39) missense possibly damaging 0.64
R0034:Rapgef1 UTSW 2 29,614,780 (GRCm39) splice site probably benign
R0034:Rapgef1 UTSW 2 29,614,780 (GRCm39) splice site probably benign
R0241:Rapgef1 UTSW 2 29,592,682 (GRCm39) missense possibly damaging 0.53
R0241:Rapgef1 UTSW 2 29,592,682 (GRCm39) missense possibly damaging 0.53
R0279:Rapgef1 UTSW 2 29,616,239 (GRCm39) missense probably damaging 1.00
R0432:Rapgef1 UTSW 2 29,569,828 (GRCm39) missense possibly damaging 0.86
R1817:Rapgef1 UTSW 2 29,576,268 (GRCm39) missense probably damaging 1.00
R1837:Rapgef1 UTSW 2 29,627,438 (GRCm39) missense probably damaging 1.00
R1970:Rapgef1 UTSW 2 29,623,723 (GRCm39) missense probably damaging 1.00
R1980:Rapgef1 UTSW 2 29,612,239 (GRCm39) missense probably benign
R2076:Rapgef1 UTSW 2 29,592,520 (GRCm39) missense probably benign 0.00
R2363:Rapgef1 UTSW 2 29,626,608 (GRCm39) missense possibly damaging 0.63
R3016:Rapgef1 UTSW 2 29,597,405 (GRCm39) missense probably damaging 1.00
R3053:Rapgef1 UTSW 2 29,614,868 (GRCm39) missense probably damaging 1.00
R3777:Rapgef1 UTSW 2 29,609,701 (GRCm39) missense possibly damaging 0.67
R3980:Rapgef1 UTSW 2 29,609,662 (GRCm39) missense probably benign 0.33
R4491:Rapgef1 UTSW 2 29,609,668 (GRCm39) missense possibly damaging 0.93
R4524:Rapgef1 UTSW 2 29,569,258 (GRCm39) missense probably benign 0.00
R4732:Rapgef1 UTSW 2 29,579,172 (GRCm39) missense probably damaging 1.00
R4733:Rapgef1 UTSW 2 29,579,172 (GRCm39) missense probably damaging 1.00
R5391:Rapgef1 UTSW 2 29,627,977 (GRCm39) missense probably damaging 1.00
R5395:Rapgef1 UTSW 2 29,627,977 (GRCm39) missense probably damaging 1.00
R5611:Rapgef1 UTSW 2 29,592,448 (GRCm39) missense probably damaging 0.96
R6062:Rapgef1 UTSW 2 29,590,744 (GRCm39) missense probably damaging 0.96
R6145:Rapgef1 UTSW 2 29,626,678 (GRCm39) missense probably damaging 1.00
R6580:Rapgef1 UTSW 2 29,620,621 (GRCm39) missense possibly damaging 0.95
R6892:Rapgef1 UTSW 2 29,589,852 (GRCm39) critical splice donor site probably null
R6897:Rapgef1 UTSW 2 29,592,514 (GRCm39) missense probably damaging 1.00
R6957:Rapgef1 UTSW 2 29,623,710 (GRCm39) missense possibly damaging 0.62
R7039:Rapgef1 UTSW 2 29,616,226 (GRCm39) missense probably damaging 0.97
R7149:Rapgef1 UTSW 2 29,610,712 (GRCm39) missense probably damaging 0.98
R7253:Rapgef1 UTSW 2 29,589,733 (GRCm39) missense possibly damaging 0.72
R7956:Rapgef1 UTSW 2 29,589,027 (GRCm39) missense probably benign 0.03
R8161:Rapgef1 UTSW 2 29,569,210 (GRCm39) missense probably benign 0.08
R8162:Rapgef1 UTSW 2 29,626,011 (GRCm39) missense probably damaging 0.99
R8372:Rapgef1 UTSW 2 29,600,243 (GRCm39) missense probably damaging 0.99
R8373:Rapgef1 UTSW 2 29,600,243 (GRCm39) missense probably damaging 0.99
R8485:Rapgef1 UTSW 2 29,600,186 (GRCm39) missense probably damaging 1.00
R8838:Rapgef1 UTSW 2 29,627,458 (GRCm39) missense possibly damaging 0.77
R9484:Rapgef1 UTSW 2 29,625,821 (GRCm39) missense possibly damaging 0.95
R9521:Rapgef1 UTSW 2 29,624,291 (GRCm39) missense probably benign 0.16
RF005:Rapgef1 UTSW 2 29,597,207 (GRCm39) splice site probably null
Predicted Primers PCR Primer
(F):5'- AACACTCTGCCTGGAAGCTG -3'
(R):5'- CAGACATTACTAATCAATCCTGGC -3'

Sequencing Primer
(F):5'- GCTGCTGCTGCTGGCTG -3'
(R):5'- AGAGCCTATGGTGCCACCTC -3'
Posted On 2019-06-26