Incidental Mutation 'IGL02620:Rabgef1'
ID 300833
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Rabgef1
Ensembl Gene ENSMUSG00000025340
Gene Name RAB guanine nucleotide exchange factor (GEF) 1
Synonyms Ras negative regulator Rabex-5
Accession Numbers
Essential gene? Probably essential (E-score: 0.853) question?
Stock # IGL02620
Quality Score
Status
Chromosome 5
Chromosomal Location 130200644-130243178 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 130219863 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 109 (S109P)
Ref Sequence ENSEMBL: ENSMUSP00000112537 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026390] [ENSMUST00000119027] [ENSMUST00000119797] [ENSMUST00000148264]
AlphaFold Q9JM13
Predicted Effect possibly damaging
Transcript: ENSMUST00000026390
AA Change: S109P

PolyPhen 2 Score 0.905 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000026390
Gene: ENSMUSG00000025340
AA Change: S109P

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: S109P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000112537
Gene: ENSMUSG00000025340
AA Change: S109P

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 possibly damaging
Transcript: ENSMUST00000119797
AA Change: S109P

PolyPhen 2 Score 0.905 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000114103
Gene: ENSMUSG00000025340
AA Change: S109P

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 benign
Transcript: ENSMUST00000148264
AA Change: S109P

PolyPhen 2 Score 0.032 (Sensitivity: 0.95; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000119245
Gene: ENSMUSG00000025340
AA Change: S109P

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
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: 34 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc12 A T 8: 87,231,943 (GRCm39) probably null Het
Bltp1 T C 3: 37,090,094 (GRCm39) V4174A possibly damaging Het
Ccdc150 T A 1: 54,302,704 (GRCm39) L108* probably null Het
Cdon C T 9: 35,364,095 (GRCm39) T71I probably benign Het
Chdh T C 14: 29,753,096 (GRCm39) W2R probably damaging Het
Ckap5 T G 2: 91,436,714 (GRCm39) L1605V probably benign Het
Cluh C T 11: 74,555,893 (GRCm39) Q819* probably null Het
Csgalnact1 C A 8: 68,854,144 (GRCm39) G219V probably damaging Het
Cwc27 C A 13: 104,938,714 (GRCm39) probably benign Het
Elk4 C A 1: 131,946,109 (GRCm39) A329D probably benign Het
Fbxo40 T C 16: 36,786,442 (GRCm39) H709R probably benign Het
Flna A G X: 73,273,582 (GRCm39) probably benign Het
Grip2 G T 6: 91,755,587 (GRCm39) D592E possibly damaging Het
H2-T24 T G 17: 36,328,183 (GRCm39) N100T probably damaging Het
Hepacam2 C A 6: 3,487,280 (GRCm39) probably benign Het
Ighv2-2 T A 12: 113,551,912 (GRCm39) T109S possibly damaging Het
Ipo11 T C 13: 107,012,789 (GRCm39) probably null Het
Kcnh8 T C 17: 53,205,525 (GRCm39) M540T probably damaging Het
Kifc3 A G 8: 95,836,582 (GRCm39) S82P probably damaging Het
Map4k5 T C 12: 69,939,476 (GRCm39) Y20C probably benign Het
Milr1 C A 11: 106,645,744 (GRCm39) S95R probably damaging Het
Mtnr1b A C 9: 15,785,617 (GRCm39) V47G possibly damaging Het
Nme1nme2 G T 11: 93,843,682 (GRCm39) R173S possibly damaging Het
Or6a2 T A 7: 106,600,825 (GRCm39) K81* probably null Het
Phactr2 T C 10: 13,167,632 (GRCm39) R100G probably damaging Het
Potefam1 C T 2: 111,041,970 (GRCm39) V322I probably benign Het
Ppargc1b A G 18: 61,431,810 (GRCm39) Y997H probably damaging Het
Pramel3a A G X: 134,211,158 (GRCm39) M397V probably benign Het
Ptprz1 A G 6: 22,959,739 (GRCm39) K79E probably damaging Het
Raf1 A T 6: 115,609,848 (GRCm39) probably benign Het
Rptor T C 11: 119,671,413 (GRCm39) L292P probably benign Het
Slc25a45 A G 19: 5,934,554 (GRCm39) D174G probably damaging Het
Tbcd C T 11: 121,352,081 (GRCm39) T146M probably damaging Het
Zfp458 T A 13: 67,406,058 (GRCm39) H127L 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
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
R2079:Rabgef1 UTSW 5 130,219,776 (GRCm39) missense probably damaging 0.99
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
Posted On 2015-04-16