Incidental Mutation 'R6897:Rapgef1'
ID 538363
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 044991-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6897 (G1)
Quality Score 184.009
Status Validated
Chromosome 2
Chromosomal Location 29509732-29630376 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 29592514 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 502 (D502G)
Ref Sequence ENSEMBL: ENSMUSP00000099936 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000091146] [ENSMUST00000095087] [ENSMUST00000102872] [ENSMUST00000147755]
AlphaFold Q3UHC1
Predicted Effect probably damaging
Transcript: ENSMUST00000091146
AA Change: D464G

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000088680
Gene: ENSMUSG00000039844
AA Change: D464G

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 possibly damaging
Transcript: ENSMUST00000095087
AA Change: D502G

PolyPhen 2 Score 0.845 (Sensitivity: 0.83; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000092703
Gene: ENSMUSG00000039844
AA Change: D502G

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: D502G

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000099936
Gene: ENSMUSG00000039844
AA Change: D502G

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 probably benign
Transcript: ENSMUST00000147488
AA Change: D7G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000117631
Gene: ENSMUSG00000039844
AA Change: D7G

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 possibly damaging
Transcript: ENSMUST00000147755
AA Change: D464G

PolyPhen 2 Score 0.904 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000121615
Gene: ENSMUSG00000039844
AA Change: D464G

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: 99.9%
  • 10x: 99.3%
  • 20x: 97.7%
Validation Efficiency 97% (72/74)
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: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930579F01Rik T C 3: 137,889,534 (GRCm39) I28V possibly damaging Het
Adamts2 A T 11: 50,627,991 (GRCm39) probably null Het
Adgrg1 T C 8: 95,729,126 (GRCm39) F17L probably benign Het
Aldob A G 4: 49,539,789 (GRCm39) L183P probably damaging Het
Alg5 T C 3: 54,656,063 (GRCm39) C270R probably benign Het
Anxa4 T A 6: 86,720,160 (GRCm39) probably null Het
Armc2 C A 10: 41,869,225 (GRCm39) probably null Het
Atrnl1 A G 19: 58,030,800 (GRCm39) N1314S probably benign Het
Bbs7 T A 3: 36,652,460 (GRCm39) E331V probably benign Het
Bmper T A 9: 23,285,225 (GRCm39) V258E probably benign Het
Catspere2 A T 1: 177,939,139 (GRCm39) I671F possibly damaging Het
Cd101 A G 3: 100,920,376 (GRCm39) S508P probably damaging Het
Cd177 C T 7: 24,444,499 (GRCm39) R694H probably benign Het
Clptm1 C A 7: 19,369,751 (GRCm39) Q386H possibly damaging Het
Cnrip1 A G 11: 17,004,705 (GRCm39) Y85C probably damaging Het
Dclk2 A T 3: 86,739,070 (GRCm39) F310I probably benign Het
Dmxl1 A G 18: 49,984,562 (GRCm39) K186R probably null Het
Dmxl1 C A 18: 49,996,124 (GRCm39) Q417K possibly damaging Het
Eloa T C 4: 135,740,220 (GRCm39) D67G possibly damaging Het
Elovl4 T C 9: 83,665,278 (GRCm39) I103V probably benign Het
Gabpa C G 16: 84,657,361 (GRCm39) A412G probably benign Het
Gldn T A 9: 54,242,158 (GRCm39) probably null Het
Ino80d A T 1: 63,104,993 (GRCm39) I361N probably damaging Het
Kalrn G A 16: 33,796,073 (GRCm39) T1234M probably damaging Het
Kcnk13 T A 12: 100,028,026 (GRCm39) M367K probably benign Het
Klrd1 G A 6: 129,570,468 (GRCm39) R8Q possibly damaging Het
Kmt2a T C 9: 44,758,942 (GRCm39) N969S probably benign Het
Lgi4 A G 7: 30,768,315 (GRCm39) D438G probably benign Het
Lig1 T C 7: 13,039,840 (GRCm39) L684P probably damaging Het
Lrp2 T C 2: 69,340,846 (GRCm39) M1010V probably benign Het
Magi3 C A 3: 103,996,873 (GRCm39) R224I probably damaging Het
Mier2 T C 10: 79,380,573 (GRCm39) N277S probably damaging Het
Morn1 A G 4: 155,171,112 (GRCm39) H17R probably benign Het
Nf2 A T 11: 4,749,878 (GRCm39) S265T probably damaging Het
Or5m11b A G 2: 85,805,700 (GRCm39) T38A possibly damaging Het
Or8k24 G A 2: 86,216,024 (GRCm39) T246I possibly damaging Het
Palb2 A G 7: 121,726,270 (GRCm39) probably null Het
Pdzd2 C T 15: 12,385,951 (GRCm39) V940M probably damaging Het
Phldb2 T C 16: 45,598,138 (GRCm39) K850E probably damaging Het
Pitx1 G A 13: 55,976,335 (GRCm39) T108M probably damaging Het
Polr2a C T 11: 69,626,787 (GRCm39) A1516T probably benign Het
Pomp T A 5: 147,812,313 (GRCm39) M133K possibly damaging Het
Prex1 T C 2: 166,423,913 (GRCm39) E993G probably damaging Het
Prrc2c C A 1: 162,533,075 (GRCm39) probably benign Het
Pwp2 C A 10: 78,007,917 (GRCm39) Q879H probably damaging Het
Rab26 G A 17: 24,748,766 (GRCm39) T245I probably damaging Het
Rsf1 GGCG GGCGACGGCCGCG 7: 97,229,113 (GRCm39) probably benign Het
Sema5a T A 15: 32,550,421 (GRCm39) D153E probably benign Het
Sez6 C G 11: 77,844,385 (GRCm39) H69Q probably damaging Het
Sgsm3 A T 15: 80,893,095 (GRCm39) T391S probably benign Het
Sh3rf2 T C 18: 42,234,670 (GRCm39) V151A possibly damaging Het
Socs1 G T 16: 10,602,266 (GRCm39) A157E probably benign Het
Spmip4 T A 6: 50,566,145 (GRCm39) Q110L possibly damaging Het
Sptbn4 C A 7: 27,071,375 (GRCm39) V346L possibly damaging Het
Srgap1 T A 10: 121,621,523 (GRCm39) H990L probably damaging Het
Tbc1d9 G T 8: 83,892,809 (GRCm39) G36W probably damaging Het
Tbk1 T C 10: 121,395,782 (GRCm39) E437G probably benign Het
Tns3 A G 11: 8,481,743 (GRCm39) L203P probably damaging Het
Tspoap1 A T 11: 87,656,638 (GRCm39) K283M probably damaging Het
Ttyh1 C T 7: 4,127,649 (GRCm39) probably benign Het
Ufd1 T A 16: 18,645,850 (GRCm39) I254N probably benign Het
Ugdh T G 5: 65,584,776 (GRCm39) T49P probably benign Het
Vav3 T C 3: 109,434,810 (GRCm39) L447P probably damaging Het
Vmn1r216 A T 13: 23,283,445 (GRCm39) K43* probably null Het
Vmn2r111 T C 17: 22,778,032 (GRCm39) N549S possibly damaging Het
Vmn2r13 A G 5: 109,306,015 (GRCm39) I521T possibly damaging Het
Wdfy3 T C 5: 101,991,932 (GRCm39) T3470A probably benign Het
Wdhd1 T A 14: 47,485,587 (GRCm39) K791N probably damaging Het
Xirp2 A G 2: 67,338,911 (GRCm39) D384G probably damaging Het
Zfp512b C T 2: 181,232,273 (GRCm39) R86Q probably damaging Het
Zfp735 A C 11: 73,601,880 (GRCm39) I275L probably benign Het
Zfp957 A T 14: 79,451,344 (GRCm39) S152T probably damaging 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
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
R7315:Rapgef1 UTSW 2 29,624,504 (GRCm39) missense probably damaging 0.98
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'- GGAATCTGGGCCTCCATTTC -3'
(R):5'- CACAGTGTGCTCACAGAGAG -3'

Sequencing Primer
(F):5'- GGCCACCCTTTCCAGCTG -3'
(R):5'- CAGAGAACTTACTGTGCTTGTTC -3'
Posted On 2018-11-06