Incidental Mutation 'R1990:Rab3gap1'
ID 224809
Institutional Source Beutler Lab
Gene Symbol Rab3gap1
Ensembl Gene ENSMUSG00000036104
Gene Name RAB3 GTPase activating protein subunit 1
Synonyms 1700003B17Rik, 4732493F09Rik, p130
Accession Numbers
Essential gene? Probably non essential (E-score: 0.223) question?
Stock # R1990 (G1)
Quality Score 225
Status Not validated
Chromosome 1
Chromosomal Location 127796510-127871605 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 127870166 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 929 (E929G)
Ref Sequence ENSEMBL: ENSMUSP00000148357 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000037649] [ENSMUST00000212506]
AlphaFold Q80UJ7
Predicted Effect probably benign
Transcript: ENSMUST00000037649
AA Change: E922G

PolyPhen 2 Score 0.421 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000042070
Gene: ENSMUSG00000036104
AA Change: E922G

DomainStartEndE-ValueType
low complexity region 254 263 N/A INTRINSIC
low complexity region 574 587 N/A INTRINSIC
Pfam:Rab3-GTPase_cat 612 769 2.9e-67 PFAM
low complexity region 856 868 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000131884
Predicted Effect possibly damaging
Transcript: ENSMUST00000212506
AA Change: E929G

PolyPhen 2 Score 0.556 (Sensitivity: 0.88; Specificity: 0.91)
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.7%
  • 20x: 93.5%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes the catalytic subunit of a Rab GTPase activating protein. The encoded protein forms a heterodimer with a non-catalytic subunit to specifically regulate the activity of members of the Rab3 subfamily of small G proteins. This protein mediates the hydrolysis of GTP bound Rab3 to the GDP bound form. Mutations in this gene are associated with Warburg micro syndrome. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Feb 2010]
PHENOTYPE: Mice homozygous for a null mutation display abnormal synaptic transmission but have normal gross brain morphology. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 97 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1110002E22Rik C T 3: 137,771,419 (GRCm39) R203* probably null Het
Acp6 T C 3: 97,083,054 (GRCm39) L355P probably damaging Het
Aebp2 T C 6: 140,579,464 (GRCm39) S234P probably damaging Het
Anapc7 A G 5: 122,577,567 (GRCm39) D374G probably benign Het
Apob A T 12: 8,051,039 (GRCm39) I1088F probably damaging Het
Arid4b T C 13: 14,307,021 (GRCm39) V92A probably damaging Het
Armc3 T C 2: 19,297,953 (GRCm39) Y575H probably damaging Het
Asxl2 G T 12: 3,534,558 (GRCm39) G252* probably null Het
Atl1 A T 12: 70,010,102 (GRCm39) K556M probably damaging Het
AU018091 A G 7: 3,212,104 (GRCm39) V206A probably benign Het
Bcas1 A T 2: 170,212,397 (GRCm39) D383E possibly damaging Het
Bmx A G X: 163,015,192 (GRCm39) W257R probably benign Het
Bpifb6 T C 2: 153,747,270 (GRCm39) probably null Het
Cacna1b G A 2: 24,622,318 (GRCm39) P222L probably damaging Het
Cand1 A G 10: 119,045,972 (GRCm39) S978P probably damaging Het
Cap2 T A 13: 46,791,357 (GRCm39) Y175N possibly damaging Het
Caps2 G A 10: 112,036,591 (GRCm39) A384T probably benign Het
Catsperg2 A T 7: 29,420,470 (GRCm39) Y223* probably null Het
Cd81 G T 7: 142,620,938 (GRCm39) G206* probably null Het
Cd84 A G 1: 171,700,317 (GRCm39) T145A possibly damaging Het
Cdkn2aip G T 8: 48,165,211 (GRCm39) N167K probably benign Het
Ceacam14 T A 7: 17,549,290 (GRCm39) L227* probably null Het
Ceacam5 A T 7: 17,491,805 (GRCm39) D725V probably damaging Het
Cldn34a A T X: 151,346,841 (GRCm39) H171L probably benign Het
Col18a1 T C 10: 76,916,988 (GRCm39) I114V unknown Het
Cp A G 3: 20,033,177 (GRCm39) D667G probably damaging Het
Cr2 G A 1: 194,836,458 (GRCm39) P1278S possibly damaging Het
Crat A G 2: 30,295,060 (GRCm39) Y452H possibly damaging Het
Cyp4f13 T A 17: 33,144,542 (GRCm39) H318L probably damaging Het
Dab1 C T 4: 104,588,948 (GRCm39) A524V probably benign Het
Dmbt1 A G 7: 130,660,018 (GRCm39) N527S probably damaging Het
Fcgbpl1 A T 7: 27,853,785 (GRCm39) D1583V probably damaging Het
Fgb G T 3: 82,951,560 (GRCm39) Y256* probably null Het
Frmd3 T A 4: 74,105,676 (GRCm39) S441T probably damaging Het
Glp1r T A 17: 31,149,722 (GRCm39) C329S possibly damaging Het
Gm14190 G T 11: 99,581,431 (GRCm39) Q46K unknown Het
Golt1b T A 6: 142,338,080 (GRCm39) F17Y probably damaging Het
Gsdmc A G 15: 63,673,748 (GRCm39) I179T probably benign Het
Gsdmc2 T A 15: 63,700,086 (GRCm39) M229L probably benign Het
Gulp1 A C 1: 44,805,274 (GRCm39) N121T possibly damaging Het
Ift122 T A 6: 115,901,328 (GRCm39) F1037I probably damaging Het
Ildr1 A T 16: 36,536,568 (GRCm39) Y199F probably damaging Het
Ints2 T A 11: 86,139,760 (GRCm39) H278L possibly damaging Het
Invs T C 4: 48,392,599 (GRCm39) V271A possibly damaging Het
Kcnj2 T C 11: 110,963,709 (GRCm39) I367T probably benign Het
Kif21b T C 1: 136,089,508 (GRCm39) S1115P probably damaging Het
Lce1k A T 3: 92,714,125 (GRCm39) C20S unknown Het
Lcmt2 C A 2: 120,970,762 (GRCm39) R107L probably benign Het
Letm1 A AG 5: 33,926,859 (GRCm39) probably null Het
Lrrc9 A C 12: 72,544,635 (GRCm39) R71S probably damaging Het
Mcc C A 18: 44,624,382 (GRCm39) E213* probably null Het
Mis18bp1 T C 12: 65,205,468 (GRCm39) T235A probably benign Het
Mta2 C T 19: 8,919,696 (GRCm39) probably benign Het
Nebl T A 2: 17,457,321 (GRCm39) I80F probably damaging Het
Nek10 A G 14: 14,860,764 (GRCm38) T467A probably benign Het
Nexn A T 3: 151,958,576 (GRCm39) F106I probably damaging Het
Nrdc T A 4: 108,896,972 (GRCm39) Y282* probably null Het
Nxf3 G A X: 134,976,583 (GRCm39) P380S possibly damaging Het
Oma1 C T 4: 103,178,971 (GRCm39) T208I probably damaging Het
Or1a1 T C 11: 74,086,989 (GRCm39) V220A probably damaging Het
Or4c31 A G 2: 88,291,686 (GRCm39) M1V probably null Het
Or4d10c C A 19: 12,065,620 (GRCm39) V179F probably damaging Het
Or4p21 A G 2: 88,277,033 (GRCm39) L83P probably damaging Het
Or51a42 A T 7: 103,708,335 (GRCm39) I158N possibly damaging Het
Or52l1 A T 7: 104,830,221 (GRCm39) C115S probably damaging Het
Or5p66 C A 7: 107,885,566 (GRCm39) G256* probably null Het
Or5p70 A G 7: 107,995,041 (GRCm39) Y238C probably benign Het
Panx2 A T 15: 88,953,941 (GRCm39) Y632F possibly damaging Het
Pdia4 T C 6: 47,773,589 (GRCm39) T587A probably benign Het
Piezo2 A T 18: 63,207,733 (GRCm39) L1426Q probably null Het
Pigk T A 3: 152,450,131 (GRCm39) Y212N probably damaging Het
Pramel22 T A 4: 143,380,838 (GRCm39) Y395F probably damaging Het
Prl3b1 C T 13: 27,429,775 (GRCm39) T71I possibly damaging Het
Rabl3 T C 16: 37,384,079 (GRCm39) I162T probably benign Het
Rasgrf2 T A 13: 92,172,473 (GRCm39) T188S probably damaging Het
Slc12a2 A G 18: 58,043,358 (GRCm39) I601V possibly damaging Het
Slc25a42 A T 8: 70,644,519 (GRCm39) I60N probably benign Het
Slc2a3 C T 6: 122,713,694 (GRCm39) G173S probably damaging Het
Slc46a3 G A 5: 147,823,404 (GRCm39) T146M probably damaging Het
Specc1 C A 11: 61,920,120 (GRCm39) P7T possibly damaging Het
Sptbn4 T C 7: 27,123,235 (GRCm39) D229G probably benign Het
Sspo T C 6: 48,427,984 (GRCm39) I154T probably benign Het
Stx5a T C 19: 8,726,254 (GRCm39) probably null Het
Stxbp6 A T 12: 44,902,640 (GRCm39) C210* probably null Het
Tagap1 C T 17: 7,224,285 (GRCm39) R137Q probably benign Het
Tbc1d9 A G 8: 83,997,932 (GRCm39) Y1163C probably damaging Het
Tex14 T G 11: 87,440,296 (GRCm39) L1367R probably damaging Het
Tnnt3 C T 7: 142,065,262 (GRCm39) R131C possibly damaging Het
Tpx2 T A 2: 152,732,544 (GRCm39) M606K probably benign Het
Trim46 A T 3: 89,145,008 (GRCm39) Y489N probably damaging Het
Ttc28 C T 5: 111,424,188 (GRCm39) S1485L probably benign Het
Txnl1 T C 18: 63,812,585 (GRCm39) T70A probably benign Het
Unc80 T C 1: 66,731,708 (GRCm39) L3053P probably damaging Het
Wars1 G T 12: 108,854,359 (GRCm39) N18K possibly damaging Het
Wnt8a A G 18: 34,677,937 (GRCm39) D115G probably damaging Het
Xndc1 T A 7: 101,722,398 (GRCm39) V21E probably damaging Het
Zfp493 T A 13: 67,934,388 (GRCm39) C114S probably damaging Het
Other mutations in Rab3gap1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01090:Rab3gap1 APN 1 127,858,124 (GRCm39) splice site probably benign
IGL01467:Rab3gap1 APN 1 127,858,121 (GRCm39) splice site probably null
IGL01554:Rab3gap1 APN 1 127,855,745 (GRCm39) missense possibly damaging 0.82
IGL01773:Rab3gap1 APN 1 127,845,958 (GRCm39) missense possibly damaging 0.64
IGL01866:Rab3gap1 APN 1 127,818,817 (GRCm39) missense probably damaging 1.00
IGL02078:Rab3gap1 APN 1 127,796,652 (GRCm39) splice site probably benign
IGL02251:Rab3gap1 APN 1 127,865,237 (GRCm39) missense probably benign 0.25
IGL02268:Rab3gap1 APN 1 127,796,695 (GRCm39) missense probably damaging 1.00
IGL02274:Rab3gap1 APN 1 127,866,817 (GRCm39) missense probably benign
IGL02372:Rab3gap1 APN 1 127,847,298 (GRCm39) splice site probably benign
IGL02399:Rab3gap1 APN 1 127,855,840 (GRCm39) missense possibly damaging 0.93
IGL02629:Rab3gap1 APN 1 127,837,600 (GRCm39) missense probably benign 0.01
IGL02700:Rab3gap1 APN 1 127,866,342 (GRCm39) missense probably benign 0.06
IGL02748:Rab3gap1 APN 1 127,865,198 (GRCm39) missense probably damaging 0.99
little_bighorn UTSW 1 127,818,835 (GRCm39) critical splice donor site probably null
IGL03048:Rab3gap1 UTSW 1 127,865,214 (GRCm39) missense probably damaging 1.00
R0828:Rab3gap1 UTSW 1 127,865,922 (GRCm39) splice site probably benign
R1382:Rab3gap1 UTSW 1 127,870,333 (GRCm39) missense probably damaging 0.97
R1729:Rab3gap1 UTSW 1 127,870,223 (GRCm39) missense probably damaging 1.00
R1809:Rab3gap1 UTSW 1 127,862,251 (GRCm39) missense probably damaging 0.99
R2001:Rab3gap1 UTSW 1 127,831,456 (GRCm39) missense possibly damaging 0.95
R2041:Rab3gap1 UTSW 1 127,865,727 (GRCm39) missense possibly damaging 0.78
R3955:Rab3gap1 UTSW 1 127,862,254 (GRCm39) missense probably damaging 1.00
R4192:Rab3gap1 UTSW 1 127,853,207 (GRCm39) intron probably benign
R4243:Rab3gap1 UTSW 1 127,865,304 (GRCm39) critical splice donor site probably null
R4244:Rab3gap1 UTSW 1 127,865,304 (GRCm39) critical splice donor site probably null
R4354:Rab3gap1 UTSW 1 127,843,378 (GRCm39) missense probably benign 0.02
R4592:Rab3gap1 UTSW 1 127,852,996 (GRCm39) intron probably benign
R4622:Rab3gap1 UTSW 1 127,870,156 (GRCm39) missense probably benign 0.00
R4738:Rab3gap1 UTSW 1 127,862,173 (GRCm39) missense probably damaging 0.99
R4917:Rab3gap1 UTSW 1 127,816,914 (GRCm39) missense possibly damaging 0.75
R4918:Rab3gap1 UTSW 1 127,816,914 (GRCm39) missense possibly damaging 0.75
R5090:Rab3gap1 UTSW 1 127,843,415 (GRCm39) missense probably benign 0.35
R5197:Rab3gap1 UTSW 1 127,816,931 (GRCm39) missense probably benign
R5310:Rab3gap1 UTSW 1 127,870,110 (GRCm39) critical splice acceptor site probably null
R5580:Rab3gap1 UTSW 1 127,858,727 (GRCm39) missense probably benign 0.01
R6670:Rab3gap1 UTSW 1 127,858,512 (GRCm39) missense probably benign
R6825:Rab3gap1 UTSW 1 127,858,158 (GRCm39) missense probably damaging 1.00
R7024:Rab3gap1 UTSW 1 127,818,835 (GRCm39) critical splice donor site probably null
R7274:Rab3gap1 UTSW 1 127,855,249 (GRCm39) missense probably benign
R7380:Rab3gap1 UTSW 1 127,865,727 (GRCm39) missense possibly damaging 0.78
R7583:Rab3gap1 UTSW 1 127,858,612 (GRCm39) missense probably benign 0.03
R7654:Rab3gap1 UTSW 1 127,837,652 (GRCm39) missense probably damaging 1.00
R8309:Rab3gap1 UTSW 1 127,837,655 (GRCm39) missense possibly damaging 0.82
R8392:Rab3gap1 UTSW 1 127,866,370 (GRCm39) missense probably benign 0.01
R8864:Rab3gap1 UTSW 1 127,837,630 (GRCm39) missense probably damaging 1.00
R9190:Rab3gap1 UTSW 1 127,858,495 (GRCm39) missense probably benign
R9799:Rab3gap1 UTSW 1 127,858,489 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- TAGTGCCCAAGCTCTTTCCAG -3'
(R):5'- TGTCTGAGGAAAAGGCACCC -3'

Sequencing Primer
(F):5'- TTGAGCAATCATAACACACAGTGG -3'
(R):5'- CGCGAGTCTGAAGTCCTCCTTG -3'
Posted On 2014-08-25