Incidental Mutation 'R7857:Gapvd1'
ID 607260
Institutional Source Beutler Lab
Gene Symbol Gapvd1
Ensembl Gene ENSMUSG00000026867
Gene Name GTPase activating protein and VPS9 domains 1
Synonyms 2010005B09Rik, 4432404J10Rik
MMRRC Submission 045910-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7857 (G1)
Quality Score 225.009
Status Not validated
Chromosome 2
Chromosomal Location 34566190-34645297 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 34619079 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Valine at position 98 (E98V)
Ref Sequence ENSEMBL: ENSMUSP00000099864 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028224] [ENSMUST00000102800] [ENSMUST00000113099] [ENSMUST00000142436]
AlphaFold Q6PAR5
Predicted Effect probably benign
Transcript: ENSMUST00000028224
AA Change: E98V

PolyPhen 2 Score 0.065 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000028224
Gene: ENSMUSG00000026867
AA Change: E98V

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 benign
Transcript: ENSMUST00000102800
AA Change: E98V

PolyPhen 2 Score 0.065 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000099864
Gene: ENSMUSG00000026867
AA Change: E98V

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 benign
Transcript: ENSMUST00000113099
AA Change: E98V

PolyPhen 2 Score 0.039 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000108723
Gene: ENSMUSG00000026867
AA Change: E98V

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 benign
Transcript: ENSMUST00000113103
SMART Domains Protein: ENSMUSP00000108727
Gene: ENSMUSG00000026867

DomainStartEndE-ValueType
Pfam:RasGAP 1 184 4.9e-32 PFAM
internal_repeat_1 484 513 1.18e-5 PROSPERO
low complexity region 522 536 N/A INTRINSIC
internal_repeat_1 544 575 1.18e-5 PROSPERO
low complexity region 733 748 N/A INTRINSIC
low complexity region 767 778 N/A INTRINSIC
low complexity region 781 791 N/A INTRINSIC
low complexity region 794 810 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000137528
SMART Domains Protein: ENSMUSP00000120138
Gene: ENSMUSG00000026867

DomainStartEndE-ValueType
Pfam:RasGAP 15 216 1.2e-37 PFAM
internal_repeat_1 510 539 1.19e-5 PROSPERO
low complexity region 548 562 N/A INTRINSIC
internal_repeat_1 570 601 1.19e-5 PROSPERO
low complexity region 733 748 N/A INTRINSIC
low complexity region 767 778 N/A INTRINSIC
low complexity region 781 791 N/A INTRINSIC
low complexity region 794 810 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000142436
AA Change: E98V

PolyPhen 2 Score 0.039 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000126225
Gene: ENSMUSG00000026867
AA Change: E98V

DomainStartEndE-ValueType
SCOP:d1wer__ 95 135 6e-4 SMART
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.2%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 61 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam6b A T 12: 113,454,104 (GRCm39) N307I probably benign Het
Ahnak G A 19: 8,984,832 (GRCm39) V2039M probably damaging Het
Arhgef40 T A 14: 52,226,212 (GRCm39) H85Q probably damaging Het
Ash1l T A 3: 88,891,616 (GRCm39) L1165* probably null Het
Cck A G 9: 121,322,514 (GRCm39) W100R probably damaging Het
Cdon A G 9: 35,367,908 (GRCm39) R268G possibly damaging Het
Cldn12 T C 5: 5,558,209 (GRCm39) T73A probably benign Het
Cnot1 ACG A 8: 96,472,275 (GRCm39) probably null Het
Ctnnd2 A T 15: 30,620,076 (GRCm39) T143S probably benign Het
Cyp2b13 T A 7: 25,788,153 (GRCm39) L427Q possibly damaging Het
Dnah3 A T 7: 119,550,927 (GRCm39) Y152N probably damaging Het
Dsg1b A T 18: 20,529,520 (GRCm39) M322L probably benign Het
Efhc1 T C 1: 21,045,226 (GRCm39) M414T probably benign Het
Elp3 G A 14: 65,800,759 (GRCm39) T302M probably benign Het
Entpd6 T C 2: 150,607,473 (GRCm39) probably null Het
Epb41l4a G T 18: 34,139,098 (GRCm39) C13* probably null Het
Ephb6 T C 6: 41,590,331 (GRCm39) S28P probably benign Het
Fbxo21 T C 5: 118,126,878 (GRCm39) S210P probably benign Het
Gcdh A G 8: 85,619,093 (GRCm39) V157A probably damaging Het
Gm10638 G T 8: 87,472,891 (GRCm39) R188L unknown Het
Grk3 T C 5: 113,109,427 (GRCm39) T177A unknown Het
Gsc T G 12: 104,438,424 (GRCm39) E148A probably damaging Het
Hacd4 C T 4: 88,355,702 (GRCm39) G61E probably damaging Het
Herc3 G A 6: 58,820,637 (GRCm39) W7* probably null Het
Il1rl2 T C 1: 40,366,642 (GRCm39) Y59H probably benign Het
Irag1 T A 7: 110,522,742 (GRCm39) K234* probably null Het
Kif1c A G 11: 70,619,103 (GRCm39) T913A probably benign Het
Lipg C T 18: 75,078,891 (GRCm39) G454R probably damaging Het
Lrrc74a A G 12: 86,788,485 (GRCm39) D155G probably benign Het
Ltf A T 9: 110,851,444 (GRCm39) I137F probably benign Het
Med19 T A 2: 84,515,969 (GRCm39) M166K probably damaging Het
Mei1 A T 15: 81,976,918 (GRCm39) Y167F not run Het
Ncaph A C 2: 126,946,165 (GRCm39) D724E probably damaging Het
Neb T A 2: 52,112,996 (GRCm39) D4266V probably damaging Het
Npffr1 G T 10: 61,449,765 (GRCm39) W13L probably benign Het
Or51b6 A T 7: 103,555,817 (GRCm39) H54L Het
Pcdha12 A T 18: 37,155,468 (GRCm39) D729V probably benign Het
Pcdha7 A T 18: 37,108,892 (GRCm39) E639V probably damaging Het
Pcdhb18 A T 18: 37,624,364 (GRCm39) M565L probably benign Het
Plcd3 A T 11: 102,968,760 (GRCm39) D310E probably benign Het
Pmm2 C G 16: 8,460,632 (GRCm39) Q29E probably benign Het
Poli T G 18: 70,642,225 (GRCm39) E658D probably benign Het
Prss22 G A 17: 24,212,853 (GRCm39) R295C probably damaging Het
Psg26 A G 7: 18,212,215 (GRCm39) I380T possibly damaging Het
Reep5 A T 18: 34,505,521 (GRCm39) V50E possibly damaging Het
Rfx7 A G 9: 72,500,605 (GRCm39) T122A possibly damaging Het
Robo1 A G 16: 72,767,099 (GRCm39) N424D probably damaging Het
Slc4a7 T C 14: 14,772,624 (GRCm38) V711A probably benign Het
Smc4 T C 3: 68,940,552 (GRCm39) V1162A possibly damaging Het
Snta1 A T 2: 154,225,817 (GRCm39) L189H probably benign Het
Tmem121 C T 12: 113,152,696 (GRCm39) R305C possibly damaging Het
Tmem68 A G 4: 3,551,825 (GRCm39) V271A probably damaging Het
Tmx4 T G 2: 134,481,582 (GRCm39) M114L probably benign Het
Trps1 T A 15: 50,524,401 (GRCm39) R1176S probably damaging Het
Usp21 A G 1: 171,114,335 (GRCm39) L63P probably benign Het
Vmn2r84 T A 10: 130,226,738 (GRCm39) M367L probably benign Het
Wbp2nl A G 15: 82,190,273 (GRCm39) N67S probably benign Het
Wdr35 T C 12: 9,058,113 (GRCm39) probably null Het
Zfp236 G A 18: 82,686,726 (GRCm39) Q271* probably null Het
Zfp831 T C 2: 174,547,035 (GRCm39) V1406A probably benign Het
Zfp934 G A 13: 62,665,361 (GRCm39) H459Y 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
R0282:Gapvd1 UTSW 2 34,578,972 (GRCm39) nonsense probably null
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
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'- CTGAAGGCACAAGTTCCTCTC -3'
(R):5'- CTGTTGGCACAGTAATGAACTC -3'

Sequencing Primer
(F):5'- AGTTCCTCTCCTCAAAAGGCG -3'
(R):5'- TTCCAGTGCTGAAGCTT -3'
Posted On 2019-12-20