Incidental Mutation 'R0282:Gapvd1'
ID 37593
Institutional Source Beutler Lab
Gene Symbol Gapvd1
Ensembl Gene ENSMUSG00000026867
Gene Name GTPase activating protein and VPS9 domains 1
Synonyms 2010005B09Rik, 4432404J10Rik
MMRRC Submission 038504-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0282 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 34566190-34645297 bp(-) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) T to A at 34578972 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Stop codon at position 654 (R654*)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028224] [ENSMUST00000102800] [ENSMUST00000113099]
AlphaFold Q6PAR5
Predicted Effect probably null
Transcript: ENSMUST00000028224
AA Change: R1196*
SMART Domains Protein: ENSMUSP00000028224
Gene: ENSMUSG00000026867
AA Change: R1196*

DomainStartEndE-ValueType
Pfam:RasGAP 152 353 2.3e-36 PFAM
internal_repeat_1 626 655 3.27e-5 PROSPERO
low complexity region 664 678 N/A INTRINSIC
internal_repeat_1 686 717 3.27e-5 PROSPERO
low complexity region 875 890 N/A INTRINSIC
low complexity region 909 920 N/A INTRINSIC
low complexity region 923 933 N/A INTRINSIC
low complexity region 936 952 N/A INTRINSIC
low complexity region 972 982 N/A INTRINSIC
VPS9 1332 1437 1.08e-24 SMART
Predicted Effect probably null
Transcript: ENSMUST00000102800
AA Change: R1196*
SMART Domains Protein: ENSMUSP00000099864
Gene: ENSMUSG00000026867
AA Change: R1196*

DomainStartEndE-ValueType
Pfam:RasGAP 152 353 2.3e-36 PFAM
internal_repeat_1 626 655 3.27e-5 PROSPERO
low complexity region 664 678 N/A INTRINSIC
internal_repeat_1 686 717 3.27e-5 PROSPERO
low complexity region 875 890 N/A INTRINSIC
low complexity region 909 920 N/A INTRINSIC
low complexity region 923 933 N/A INTRINSIC
low complexity region 936 952 N/A INTRINSIC
low complexity region 972 982 N/A INTRINSIC
VPS9 1332 1437 1.08e-24 SMART
Predicted Effect probably null
Transcript: ENSMUST00000113099
AA Change: R1217*
SMART Domains Protein: ENSMUSP00000108723
Gene: ENSMUSG00000026867
AA Change: R1217*

DomainStartEndE-ValueType
Pfam:RasGAP 152 353 2.8e-37 PFAM
internal_repeat_1 647 676 3.6e-5 PROSPERO
low complexity region 685 699 N/A INTRINSIC
internal_repeat_1 707 738 3.6e-5 PROSPERO
low complexity region 896 911 N/A INTRINSIC
low complexity region 930 941 N/A INTRINSIC
low complexity region 944 954 N/A INTRINSIC
low complexity region 957 973 N/A INTRINSIC
low complexity region 993 1003 N/A INTRINSIC
VPS9 1353 1458 1.08e-24 SMART
Predicted Effect probably null
Transcript: ENSMUST00000113101
AA Change: R306*
SMART Domains Protein: ENSMUSP00000108725
Gene: ENSMUSG00000026867
AA Change: R306*

DomainStartEndE-ValueType
low complexity region 13 28 N/A INTRINSIC
low complexity region 47 58 N/A INTRINSIC
low complexity region 61 71 N/A INTRINSIC
low complexity region 74 90 N/A INTRINSIC
VPS9 443 548 1.08e-24 SMART
Predicted Effect probably null
Transcript: ENSMUST00000113111
AA Change: R654*
SMART Domains Protein: ENSMUSP00000108735
Gene: ENSMUSG00000026867
AA Change: R654*

DomainStartEndE-ValueType
internal_repeat_1 85 114 3.65e-6 PROSPERO
low complexity region 123 137 N/A INTRINSIC
internal_repeat_1 145 176 3.65e-6 PROSPERO
low complexity region 334 349 N/A INTRINSIC
low complexity region 368 379 N/A INTRINSIC
low complexity region 382 392 N/A INTRINSIC
low complexity region 395 411 N/A INTRINSIC
low complexity region 431 441 N/A INTRINSIC
VPS9 791 896 1.08e-24 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000138203
Predicted Effect noncoding transcript
Transcript: ENSMUST00000167251
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.4%
  • 10x: 96.6%
  • 20x: 93.7%
Validation Efficiency 100% (72/72)
Allele List at MGI
Other mutations in this stock
Total: 69 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acsbg3 T A 17: 57,192,169 (GRCm39) Y577* probably null Het
Afap1l2 A G 19: 56,904,653 (GRCm39) S549P possibly damaging Het
Alcam A T 16: 52,116,104 (GRCm39) C157S probably damaging Het
Aldh1a1 T C 19: 20,606,413 (GRCm39) probably benign Het
Ano8 G A 8: 71,933,258 (GRCm39) probably benign Het
Atr T C 9: 95,744,851 (GRCm39) V56A probably benign Het
Aurkc T A 7: 7,005,427 (GRCm39) probably null Het
Bnip3 T C 7: 138,499,759 (GRCm39) D76G probably damaging Het
Cbr1 A G 16: 93,407,022 (GRCm39) E246G possibly damaging Het
Ccdc157 G T 11: 4,096,708 (GRCm39) A449D probably damaging Het
Ces3b T A 8: 105,810,483 (GRCm39) V26D probably benign Het
Colgalt2 G T 1: 152,384,312 (GRCm39) A551S possibly damaging Het
Crk G T 11: 75,594,195 (GRCm39) G261C probably damaging Het
Ctbp1 A G 5: 33,408,200 (GRCm39) probably null Het
Ctnna1 G A 18: 35,377,175 (GRCm39) V572I possibly damaging Het
D430041D05Rik T C 2: 104,031,589 (GRCm39) Y1669C probably damaging Het
Dnah8 T C 17: 30,955,130 (GRCm39) F2053S probably damaging Het
Dner G A 1: 84,383,686 (GRCm39) T566M probably damaging Het
Dner A G 1: 84,423,101 (GRCm39) probably benign Het
Edrf1 T C 7: 133,245,751 (GRCm39) V223A probably benign Het
Fam169a A G 13: 97,234,223 (GRCm39) probably benign Het
Fbxl3 G A 14: 103,332,661 (GRCm39) H106Y probably damaging Het
Fiz1 A G 7: 5,012,200 (GRCm39) V106A probably benign Het
Gm7589 G A 9: 59,053,288 (GRCm39) noncoding transcript Het
Ifi202b A T 1: 173,804,926 (GRCm39) S9T probably benign Het
Ipmk G C 10: 71,208,661 (GRCm39) S149T probably benign Het
Irgm2 A G 11: 58,110,345 (GRCm39) E24G probably benign Het
Itga2b A C 11: 102,351,672 (GRCm39) V551G probably damaging Het
Itgad C T 7: 127,789,150 (GRCm39) probably benign Het
Kcnh8 T A 17: 53,032,879 (GRCm39) F55L probably damaging Het
Kdr G A 5: 76,110,760 (GRCm39) probably benign Het
Krt35 T C 11: 99,986,573 (GRCm39) Y147C probably damaging Het
Lamc1 A G 1: 153,131,058 (GRCm39) F298L probably benign Het
Lrrk2 T C 15: 91,662,617 (GRCm39) probably benign Het
Matn1 T C 4: 130,673,238 (GRCm39) S69P probably damaging Het
Micall1 G T 15: 79,016,101 (GRCm39) probably benign Het
Msto1 A G 3: 88,818,884 (GRCm39) V257A possibly damaging Het
Mybpc3 G C 2: 90,954,369 (GRCm39) probably benign Het
Mycn A G 12: 12,987,314 (GRCm39) V361A probably benign Het
Myo10 A G 15: 25,793,253 (GRCm39) T1277A probably damaging Het
Myo3a T C 2: 22,250,409 (GRCm39) I92T probably benign Het
Nup50l T C 6: 96,141,797 (GRCm39) T416A probably benign Het
Or10g1 A G 14: 52,647,720 (GRCm39) V203A possibly damaging Het
Or2k2 A G 4: 58,785,344 (GRCm39) I126T probably damaging Het
Or4c104 G A 2: 88,586,800 (GRCm39) T73I probably damaging Het
Or56b1b T A 7: 108,164,684 (GRCm39) Q106L probably damaging Het
Otog C T 7: 45,926,917 (GRCm39) T1222I possibly damaging Het
P4ha1 C T 10: 59,172,970 (GRCm39) T23M probably damaging Het
Pld1 A T 3: 28,132,422 (GRCm39) I537F probably benign Het
Plekhn1 A G 4: 156,312,780 (GRCm39) probably benign Het
Pxdn C A 12: 30,034,439 (GRCm39) S8* probably null Het
Rnf135 A T 11: 80,084,784 (GRCm39) I186F probably damaging Het
Rock2 T C 12: 17,027,887 (GRCm39) probably benign Het
Rph3a C A 5: 121,101,973 (GRCm39) G88* probably null Het
Sarm1 G A 11: 78,365,806 (GRCm39) Q740* probably null Het
Setd1b C A 5: 123,299,080 (GRCm39) probably benign Het
Sidt1 A G 16: 44,102,249 (GRCm39) S304P possibly damaging Het
Slc2a4 A T 11: 69,837,181 (GRCm39) V85E probably damaging Het
Swi5 A G 2: 32,170,766 (GRCm39) Y54H probably damaging Het
Sycp1 A G 3: 102,823,111 (GRCm39) probably benign Het
Tarm1 T C 7: 3,546,006 (GRCm39) Y87C probably damaging Het
Tmem67 G A 4: 12,087,930 (GRCm39) T72M probably damaging Het
Tor1a A G 2: 30,857,737 (GRCm39) Y44H possibly damaging Het
Ttll5 T C 12: 86,042,827 (GRCm39) Y1128H probably benign Het
Usp40 G A 1: 87,908,680 (GRCm39) probably benign Het
Vmn2r18 A T 5: 151,508,668 (GRCm39) M152K probably benign Het
Xirp2 T A 2: 67,343,724 (GRCm39) D1988E probably damaging Het
Zfp420 A G 7: 29,575,105 (GRCm39) I442V probably benign Het
Zyx A G 6: 42,332,939 (GRCm39) E363G probably damaging Het
Other mutations in Gapvd1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00799:Gapvd1 APN 2 34,589,872 (GRCm39) missense probably benign 0.00
IGL00985:Gapvd1 APN 2 34,585,575 (GRCm39) missense probably damaging 0.99
IGL01133:Gapvd1 APN 2 34,615,410 (GRCm39) missense probably damaging 0.98
IGL01347:Gapvd1 APN 2 34,596,708 (GRCm39) critical splice donor site probably null
IGL01830:Gapvd1 APN 2 34,578,968 (GRCm39) missense probably benign 0.44
IGL01865:Gapvd1 APN 2 34,585,515 (GRCm39) missense probably null
IGL02009:Gapvd1 APN 2 34,594,203 (GRCm39) missense probably damaging 1.00
IGL02014:Gapvd1 APN 2 34,594,203 (GRCm39) missense probably damaging 1.00
IGL02189:Gapvd1 APN 2 34,618,556 (GRCm39) missense probably damaging 1.00
IGL02418:Gapvd1 APN 2 34,620,530 (GRCm39) missense probably benign 0.00
IGL02632:Gapvd1 APN 2 34,574,186 (GRCm39) splice site probably benign
IGL02636:Gapvd1 APN 2 34,615,416 (GRCm39) missense probably benign 0.01
IGL02643:Gapvd1 APN 2 34,594,192 (GRCm39) missense probably damaging 1.00
IGL03271:Gapvd1 APN 2 34,617,219 (GRCm39) unclassified probably benign
P0023:Gapvd1 UTSW 2 34,596,700 (GRCm39) splice site probably benign
R0016:Gapvd1 UTSW 2 34,589,925 (GRCm39) splice site probably benign
R0016:Gapvd1 UTSW 2 34,589,925 (GRCm39) splice site probably benign
R0029:Gapvd1 UTSW 2 34,568,153 (GRCm39) missense probably damaging 1.00
R0029:Gapvd1 UTSW 2 34,568,153 (GRCm39) missense probably damaging 1.00
R0414:Gapvd1 UTSW 2 34,583,439 (GRCm39) missense probably benign 0.14
R0443:Gapvd1 UTSW 2 34,594,633 (GRCm39) intron probably benign
R0542:Gapvd1 UTSW 2 34,615,048 (GRCm39) unclassified probably benign
R0570:Gapvd1 UTSW 2 34,618,552 (GRCm39) missense probably damaging 1.00
R0840:Gapvd1 UTSW 2 34,619,125 (GRCm39) missense probably benign 0.29
R0866:Gapvd1 UTSW 2 34,599,229 (GRCm39) missense probably damaging 1.00
R0890:Gapvd1 UTSW 2 34,602,329 (GRCm39) missense probably damaging 1.00
R0926:Gapvd1 UTSW 2 34,602,337 (GRCm39) missense probably damaging 1.00
R0970:Gapvd1 UTSW 2 34,620,625 (GRCm39) splice site probably null
R1168:Gapvd1 UTSW 2 34,594,481 (GRCm39) missense probably damaging 1.00
R1391:Gapvd1 UTSW 2 34,596,814 (GRCm39) missense probably damaging 1.00
R1577:Gapvd1 UTSW 2 34,599,240 (GRCm39) missense probably damaging 1.00
R1585:Gapvd1 UTSW 2 34,602,207 (GRCm39) missense possibly damaging 0.93
R1669:Gapvd1 UTSW 2 34,620,694 (GRCm39) critical splice acceptor site probably null
R1677:Gapvd1 UTSW 2 34,590,773 (GRCm39) critical splice donor site probably null
R1812:Gapvd1 UTSW 2 34,615,076 (GRCm39) nonsense probably null
R1874:Gapvd1 UTSW 2 34,596,033 (GRCm39) missense probably damaging 1.00
R1878:Gapvd1 UTSW 2 34,615,212 (GRCm39) missense probably benign 0.00
R1974:Gapvd1 UTSW 2 34,590,853 (GRCm39) missense probably damaging 0.99
R2111:Gapvd1 UTSW 2 34,574,329 (GRCm39) missense probably benign 0.08
R2921:Gapvd1 UTSW 2 34,578,875 (GRCm39) missense probably damaging 0.97
R2923:Gapvd1 UTSW 2 34,578,875 (GRCm39) missense probably damaging 0.97
R3846:Gapvd1 UTSW 2 34,619,084 (GRCm39) nonsense probably null
R3894:Gapvd1 UTSW 2 34,618,488 (GRCm39) missense probably benign 0.23
R4405:Gapvd1 UTSW 2 34,618,747 (GRCm39) missense probably damaging 1.00
R4605:Gapvd1 UTSW 2 34,618,549 (GRCm39) missense probably damaging 1.00
R4770:Gapvd1 UTSW 2 34,581,193 (GRCm39) missense probably damaging 0.98
R4935:Gapvd1 UTSW 2 34,594,504 (GRCm39) nonsense probably null
R5218:Gapvd1 UTSW 2 34,618,488 (GRCm39) missense probably benign 0.23
R5490:Gapvd1 UTSW 2 34,583,445 (GRCm39) missense probably benign 0.23
R5571:Gapvd1 UTSW 2 34,605,265 (GRCm39) missense probably damaging 1.00
R5588:Gapvd1 UTSW 2 34,599,166 (GRCm39) missense probably damaging 1.00
R5933:Gapvd1 UTSW 2 34,574,303 (GRCm39) missense probably benign 0.27
R6117:Gapvd1 UTSW 2 34,580,471 (GRCm39) splice site probably null
R6661:Gapvd1 UTSW 2 34,618,450 (GRCm39) missense probably damaging 1.00
R6857:Gapvd1 UTSW 2 34,618,389 (GRCm39) missense probably damaging 1.00
R6950:Gapvd1 UTSW 2 34,574,257 (GRCm39) missense probably benign 0.04
R7009:Gapvd1 UTSW 2 34,590,829 (GRCm39) missense probably damaging 1.00
R7125:Gapvd1 UTSW 2 34,585,612 (GRCm39) missense probably benign
R7154:Gapvd1 UTSW 2 34,615,075 (GRCm39) missense probably damaging 1.00
R7316:Gapvd1 UTSW 2 34,594,681 (GRCm39) missense probably damaging 1.00
R7358:Gapvd1 UTSW 2 34,580,473 (GRCm39) critical splice donor site probably null
R7363:Gapvd1 UTSW 2 34,602,207 (GRCm39) missense probably benign 0.01
R7371:Gapvd1 UTSW 2 34,607,385 (GRCm39) missense probably benign
R7418:Gapvd1 UTSW 2 34,615,130 (GRCm39) missense probably benign 0.12
R7690:Gapvd1 UTSW 2 34,619,134 (GRCm39) missense possibly damaging 0.68
R7740:Gapvd1 UTSW 2 34,590,834 (GRCm39) missense probably damaging 1.00
R7742:Gapvd1 UTSW 2 34,568,635 (GRCm39) missense probably damaging 1.00
R7857:Gapvd1 UTSW 2 34,619,079 (GRCm39) missense probably benign 0.06
R8062:Gapvd1 UTSW 2 34,568,126 (GRCm39) missense probably benign 0.37
R8113:Gapvd1 UTSW 2 34,594,330 (GRCm39) missense probably damaging 0.98
R8303:Gapvd1 UTSW 2 34,602,212 (GRCm39) missense probably damaging 1.00
R8558:Gapvd1 UTSW 2 34,594,493 (GRCm39) missense probably damaging 1.00
R8751:Gapvd1 UTSW 2 34,568,078 (GRCm39) missense probably damaging 0.96
R8781:Gapvd1 UTSW 2 34,610,698 (GRCm39) missense probably benign 0.37
R8794:Gapvd1 UTSW 2 34,594,330 (GRCm39) missense possibly damaging 0.49
R8876:Gapvd1 UTSW 2 34,568,560 (GRCm39) missense possibly damaging 0.95
R8942:Gapvd1 UTSW 2 34,619,134 (GRCm39) missense probably benign 0.06
R8954:Gapvd1 UTSW 2 34,568,110 (GRCm39) missense probably damaging 1.00
R9066:Gapvd1 UTSW 2 34,617,297 (GRCm39) missense probably damaging 1.00
R9428:Gapvd1 UTSW 2 34,607,318 (GRCm39) missense probably damaging 1.00
R9470:Gapvd1 UTSW 2 34,602,280 (GRCm39) missense possibly damaging 0.78
R9505:Gapvd1 UTSW 2 34,613,026 (GRCm39) missense
R9690:Gapvd1 UTSW 2 34,618,492 (GRCm39) missense probably damaging 1.00
Z1177:Gapvd1 UTSW 2 34,589,876 (GRCm39) missense possibly damaging 0.78
Predicted Primers PCR Primer
(F):5'- GGCTGGCAGGGTAATTTAAGGAACT -3'
(R):5'- GCTTATCTACAGCCTCTCGTGCCAA -3'

Sequencing Primer
(F):5'- TTAAGGAACTGCTGTAAGACATGC -3'
(R):5'- GCCAACTAGTAAAACCAAAGTCTGTG -3'
Posted On 2013-05-23