Incidental Mutation 'R2079:Rabgef1'
ID 229334
Institutional Source Beutler Lab
Gene Symbol Rabgef1
Ensembl Gene ENSMUSG00000025340
Gene Name RAB guanine nucleotide exchange factor (GEF) 1
Synonyms Ras negative regulator Rabex-5
MMRRC Submission 040084-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.850) question?
Stock # R2079 (G1)
Quality Score 225
Status Not validated
Chromosome 5
Chromosomal Location 130200644-130243178 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 130219776 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 80 (S80P)
Ref Sequence ENSEMBL: ENSMUSP00000112537 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026390] [ENSMUST00000119027] [ENSMUST00000119797] [ENSMUST00000148264]
AlphaFold Q9JM13
Predicted Effect probably benign
Transcript: ENSMUST00000026390
AA Change: S80P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000026390
Gene: ENSMUSG00000025340
AA Change: S80P

DomainStartEndE-ValueType
ZnF_A20 16 40 1.5e-12 SMART
low complexity region 56 80 N/A INTRINSIC
low complexity region 82 106 N/A INTRINSIC
VPS9 262 383 1.8e-29 SMART
coiled coil region 411 445 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000118998
Predicted Effect probably damaging
Transcript: ENSMUST00000119027
AA Change: S80P

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000112537
Gene: ENSMUSG00000025340
AA Change: S80P

DomainStartEndE-ValueType
ZnF_A20 16 40 2.35e-10 SMART
low complexity region 56 80 N/A INTRINSIC
low complexity region 82 106 N/A INTRINSIC
PDB:1TXU|A 132 221 7e-51 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000119797
AA Change: S80P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000114103
Gene: ENSMUSG00000025340
AA Change: S80P

DomainStartEndE-ValueType
ZnF_A20 16 40 1.4e-12 SMART
low complexity region 56 80 N/A INTRINSIC
low complexity region 82 106 N/A INTRINSIC
VPS9 262 383 1.8e-29 SMART
coiled coil region 411 445 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000143727
Predicted Effect probably damaging
Transcript: ENSMUST00000148264
AA Change: S80P

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000119245
Gene: ENSMUSG00000025340
AA Change: S80P

DomainStartEndE-ValueType
ZnF_A20 16 40 2.35e-10 SMART
low complexity region 56 80 N/A INTRINSIC
low complexity region 82 106 N/A INTRINSIC
PDB:1TXU|A 132 250 1e-72 PDB
Predicted Effect noncoding transcript
Transcript: ENSMUST00000202729
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.4%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] RABGEF1 forms a complex with rabaptin-5 (RABPT5; MIM 603616) that is required for endocytic membrane fusion, and it serves as a specific guanine nucleotide exchange factor (GEF) for RAB5 (RAB5A; MIM 179512) (Horiuchi et al., 1997 [PubMed 9323142]).[supplied by OMIM, Mar 2010]
PHENOTYPE: Nullizygous mutations can cause neonatal or postnatal lethality associated with severe skin inflammation, high mast cell numbers and serum levels of IgE and histamine, and enhanced mast cell degranulation and release of mediators and cytokines in response to high affinity IgE receptor aggregation. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts6 A T 13: 104,598,746 (GRCm39) R862S probably benign Het
Aldoa T C 7: 126,396,076 (GRCm39) D164G probably null Het
Ankle2 T C 5: 110,392,371 (GRCm39) V459A probably damaging Het
Atp11a A G 8: 12,907,902 (GRCm39) Y482C probably damaging Het
BC035947 A G 1: 78,488,561 (GRCm39) probably benign Het
Cfap65 G A 1: 74,956,358 (GRCm39) R1074C probably benign Het
Ciart G T 3: 95,786,350 (GRCm39) H242N probably damaging Het
Cidec T A 6: 113,402,615 (GRCm39) M220L probably benign Het
Clca3a1 A G 3: 144,713,534 (GRCm39) I699T possibly damaging Het
Csf2rb2 T C 15: 78,172,207 (GRCm39) D401G probably benign Het
Cyp2j6 C A 4: 96,419,962 (GRCm39) L256F possibly damaging Het
Ddr2 A T 1: 169,832,345 (GRCm39) Y148* probably null Het
Depdc5 T A 5: 33,104,018 (GRCm39) I373N possibly damaging Het
Dpp10 A T 1: 123,360,721 (GRCm39) M268K probably damaging Het
Fam118b C A 9: 35,134,960 (GRCm39) V216F possibly damaging Het
Fancd2 T C 6: 113,532,148 (GRCm39) V487A probably damaging Het
Fhad1 T A 4: 141,718,513 (GRCm39) R147* probably null Het
Flt3 A G 5: 147,291,893 (GRCm39) S544P probably damaging Het
Frem3 C A 8: 81,341,732 (GRCm39) Q1342K probably benign Het
Garin3 T G 11: 46,295,934 (GRCm39) V102G probably benign Het
Gimap4 T C 6: 48,667,881 (GRCm39) M84T possibly damaging Het
Gm20481 T C 17: 35,189,196 (GRCm39) K569R probably benign Het
Gm4871 A C 5: 144,966,741 (GRCm39) D247E possibly damaging Het
Gm5141 A T 13: 62,922,424 (GRCm39) N248K probably benign Het
Gulo A G 14: 66,227,832 (GRCm39) Y367H probably damaging Het
Hap1 T C 11: 100,244,572 (GRCm39) E120G probably damaging Het
Heatr3 T A 8: 88,868,404 (GRCm39) N51K probably damaging Het
Hipk2 T C 6: 38,795,720 (GRCm39) D183G probably damaging Het
Hnrnpll T A 17: 80,342,806 (GRCm39) T439S probably benign Het
Hoxd3 A C 2: 74,574,610 (GRCm39) E85D probably damaging Het
Ipo8 A T 6: 148,690,660 (GRCm39) M694K probably damaging Het
Jag2 A G 12: 112,883,997 (GRCm39) I194T probably damaging Het
Jrkl A T 9: 13,244,864 (GRCm39) F266I probably damaging Het
Kcnt1 A G 2: 25,790,260 (GRCm39) I436V possibly damaging Het
Kdm3b A T 18: 34,936,570 (GRCm39) D284V probably damaging Het
Khdrbs2 A G 1: 32,506,955 (GRCm39) T200A probably benign Het
Kmt2c T C 5: 25,557,278 (GRCm39) D1143G possibly damaging Het
Kremen1 G GGGGT 11: 5,151,794 (GRCm39) probably null Het
Lama2 A C 10: 27,245,049 (GRCm39) I244S probably damaging Het
Lama5 G A 2: 179,867,301 (GRCm39) P99S possibly damaging Het
Lrrc30 A T 17: 67,938,875 (GRCm39) L235Q possibly damaging Het
Man2b2 C T 5: 36,971,716 (GRCm39) V667M possibly damaging Het
Mmp2 T A 8: 93,576,817 (GRCm39) N77K probably damaging Het
Myo1a A G 10: 127,556,482 (GRCm39) E1009G probably benign Het
Ndst1 A G 18: 60,828,581 (GRCm39) Y658H probably damaging Het
Nlrp10 A G 7: 108,524,835 (GRCm39) L215P possibly damaging Het
Nrbp1 T C 5: 31,408,417 (GRCm39) F526L probably benign Het
Or10p21 T C 10: 128,847,898 (GRCm39) V248A probably damaging Het
Or51t4 T A 7: 102,598,702 (GRCm39) F333L probably benign Het
Padi2 T C 4: 140,660,507 (GRCm39) L329P probably damaging Het
Pcdhb20 A G 18: 37,638,224 (GRCm39) Q250R probably benign Het
Pcdhb3 T A 18: 37,436,362 (GRCm39) L776Q possibly damaging Het
Pik3cb A T 9: 98,942,257 (GRCm39) M700K probably benign Het
Pla2g6 C T 15: 79,197,194 (GRCm39) V127M probably damaging Het
Sema3a C T 5: 13,501,098 (GRCm39) T47I possibly damaging Het
Sik2 C T 9: 50,818,706 (GRCm39) probably null Het
Sin3a T C 9: 56,996,807 (GRCm39) V112A probably benign Het
Slc26a6 G A 9: 108,736,257 (GRCm39) A472T probably damaging Het
Syne1 A G 10: 5,311,502 (GRCm39) V561A probably benign Het
Syt16 C T 12: 74,285,073 (GRCm39) T422I probably damaging Het
Tlr11 A T 14: 50,598,437 (GRCm39) H141L probably damaging Het
Tmem252 A T 19: 24,655,017 (GRCm39) E131D probably benign Het
Trim55 T G 3: 19,698,830 (GRCm39) L20V probably damaging Het
Uqcrfs1 A T 13: 30,725,291 (GRCm39) V83D probably benign Het
Utf1 C T 7: 139,524,808 (GRCm39) R309* probably null Het
Uxs1 T C 1: 43,804,133 (GRCm39) T261A probably damaging Het
Vmn1r24 T C 6: 57,932,655 (GRCm39) I288V probably benign Het
Vmn1r80 A T 7: 11,927,121 (GRCm39) D77V probably damaging Het
Vmn2r74 T G 7: 85,606,383 (GRCm39) H321P probably benign Het
Zfp638 T C 6: 83,930,371 (GRCm39) probably null Het
Zwilch T A 9: 64,060,856 (GRCm39) Q332L probably damaging Het
Zwilch G T 9: 64,060,857 (GRCm39) Q332K probably damaging Het
Other mutations in Rabgef1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00432:Rabgef1 APN 5 130,237,565 (GRCm39) nonsense probably null
IGL00964:Rabgef1 APN 5 130,219,863 (GRCm39) missense probably damaging 1.00
IGL01830:Rabgef1 APN 5 130,240,907 (GRCm39) missense possibly damaging 0.88
IGL02161:Rabgef1 APN 5 130,235,940 (GRCm39) splice site probably benign
IGL02231:Rabgef1 APN 5 130,240,816 (GRCm39) missense probably damaging 1.00
IGL02429:Rabgef1 APN 5 130,239,329 (GRCm39) missense possibly damaging 0.48
IGL02620:Rabgef1 APN 5 130,219,863 (GRCm39) missense probably damaging 1.00
IGL03005:Rabgef1 APN 5 130,237,638 (GRCm39) missense probably damaging 1.00
LCD18:Rabgef1 UTSW 5 130,187,586 (GRCm38) frame shift probably null
R0227:Rabgef1 UTSW 5 130,219,831 (GRCm39) missense probably damaging 1.00
R1028:Rabgef1 UTSW 5 130,241,703 (GRCm39) nonsense probably null
R1838:Rabgef1 UTSW 5 130,241,862 (GRCm39) missense probably benign 0.01
R2027:Rabgef1 UTSW 5 130,237,620 (GRCm39) missense possibly damaging 0.69
R2074:Rabgef1 UTSW 5 130,216,402 (GRCm39) missense probably benign 0.21
R2355:Rabgef1 UTSW 5 130,240,928 (GRCm39) missense probably benign 0.29
R3625:Rabgef1 UTSW 5 130,240,961 (GRCm39) critical splice donor site probably null
R3892:Rabgef1 UTSW 5 130,237,520 (GRCm39) splice site probably benign
R5060:Rabgef1 UTSW 5 130,240,844 (GRCm39) missense probably damaging 1.00
R5249:Rabgef1 UTSW 5 130,241,841 (GRCm39) missense probably benign 0.00
R6597:Rabgef1 UTSW 5 130,219,885 (GRCm39) critical splice donor site probably null
R7223:Rabgef1 UTSW 5 130,219,801 (GRCm39) missense probably benign 0.14
R7326:Rabgef1 UTSW 5 130,216,192 (GRCm39) intron probably benign
R8762:Rabgef1 UTSW 5 130,237,557 (GRCm39) missense possibly damaging 0.67
R9086:Rabgef1 UTSW 5 130,240,792 (GRCm39) missense probably benign 0.05
R9142:Rabgef1 UTSW 5 130,237,554 (GRCm39) missense possibly damaging 0.78
R9697:Rabgef1 UTSW 5 130,241,781 (GRCm39) missense probably benign
Predicted Primers PCR Primer
(F):5'- TGAGATCTCAGACCCACTTGG -3'
(R):5'- TCTTGGGCTTACAGAAGTGAG -3'

Sequencing Primer
(F):5'- GGACCCAGATCATTCACA -3'
(R):5'- CTTACAGAAGTGAGAGGCTGAGC -3'
Posted On 2014-09-17