Incidental Mutation 'R8751:Gapvd1'
ID 663821
Institutional Source Beutler Lab
Gene Symbol Gapvd1
Ensembl Gene ENSMUSG00000026867
Gene Name GTPase activating protein and VPS9 domains 1
Synonyms 2010005B09Rik, 4432404J10Rik
MMRRC Submission 068594-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R8751 (G1)
Quality Score 225.009
Status Not validated
Chromosome 2
Chromosomal Location 34566190-34645297 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to C at 34568078 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Valine at position 1429 (F1429V)
Ref Sequence ENSEMBL: ENSMUSP00000099864 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028224] [ENSMUST00000102800] [ENSMUST00000113099]
AlphaFold Q6PAR5
Predicted Effect probably damaging
Transcript: ENSMUST00000028224
AA Change: F1429V

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000028224
Gene: ENSMUSG00000026867
AA Change: F1429V

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 damaging
Transcript: ENSMUST00000102800
AA Change: F1429V

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000099864
Gene: ENSMUSG00000026867
AA Change: F1429V

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 damaging
Transcript: ENSMUST00000113099
AA Change: F1450V

PolyPhen 2 Score 0.963 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000108723
Gene: ENSMUSG00000026867
AA Change: F1450V

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
SMART Domains Protein: ENSMUSP00000108725
Gene: ENSMUSG00000026867
AA Change: F539V

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
SMART Domains Protein: ENSMUSP00000108735
Gene: ENSMUSG00000026867
AA Change: F887V

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.1%
  • 20x: 96.2%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 73 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts12 T A 15: 11,215,813 (GRCm39) I278N probably damaging Het
Adcy9 A G 16: 4,129,492 (GRCm39) W702R probably damaging Het
Adgrf5 G A 17: 43,748,574 (GRCm39) V468I possibly damaging Het
Ahnak A C 19: 8,987,509 (GRCm39) K2931T probably damaging Het
Ank3 C T 10: 69,761,849 (GRCm39) probably benign Het
Birc6 G A 17: 74,955,135 (GRCm39) V3480I probably damaging Het
Bpifa5 A T 2: 154,007,432 (GRCm39) I125L probably benign Het
Catsperg2 T C 7: 29,404,744 (GRCm39) D773G possibly damaging Het
Ccm2l A T 2: 152,909,695 (GRCm39) I16F probably benign Het
Cep72 G A 13: 74,198,303 (GRCm39) S359F possibly damaging Het
Col1a1 A G 11: 94,838,100 (GRCm39) N844S unknown Het
Col7a1 C T 9: 108,796,730 (GRCm39) P1623S possibly damaging Het
Crybg1 T C 10: 43,880,838 (GRCm39) K117E probably benign Het
Csmd3 A G 15: 47,845,402 (GRCm39) C54R Het
Dlg1 A G 16: 31,600,648 (GRCm39) T211A probably benign Het
Emc1 C A 4: 139,097,279 (GRCm39) H724N possibly damaging Het
Epg5 A C 18: 78,008,223 (GRCm39) N784H probably benign Het
Epg5 T A 18: 78,008,225 (GRCm39) N784K probably benign Het
Epg5 A T 18: 78,008,224 (GRCm39) N784I possibly damaging Het
Erc2 A G 14: 27,802,145 (GRCm39) E771G possibly damaging Het
Exo1 T C 1: 175,719,678 (GRCm39) V241A probably benign Het
Fat4 A G 3: 38,946,002 (GRCm39) T1632A probably benign Het
Fbxo21 T A 5: 118,140,127 (GRCm39) M529K probably damaging Het
Fhad1 T C 4: 141,646,134 (GRCm39) E276G probably benign Het
Frem1 G A 4: 82,889,015 (GRCm39) T1069I probably damaging Het
Gbp9 T C 5: 105,229,117 (GRCm39) E510G possibly damaging Het
Gm17087 A T 17: 8,785,510 (GRCm39) H64Q probably damaging Het
Gm19965 A T 1: 116,749,867 (GRCm39) Y516F unknown Het
Hdac5 A T 11: 102,109,280 (GRCm39) I38N probably benign Het
Hectd4 T A 5: 121,501,838 (GRCm39) C4190* probably null Het
Helb A T 10: 119,925,412 (GRCm39) D988E probably benign Het
Herc6 C T 6: 57,639,359 (GRCm39) S909L probably damaging Het
Ice1 A T 13: 70,751,010 (GRCm39) V1692E probably damaging Het
Ino80 A G 2: 119,237,389 (GRCm39) Y1107H probably benign Het
Kif9 A T 9: 110,330,724 (GRCm39) Y350F probably benign Het
Lct T A 1: 128,221,534 (GRCm39) T1570S probably benign Het
Lias T A 5: 65,557,193 (GRCm39) N203K probably benign Het
Lrrtm4 A G 6: 79,999,092 (GRCm39) N168S probably damaging Het
Ltf A T 9: 110,860,192 (GRCm39) K538* probably null Het
Lysmd4 A G 7: 66,875,787 (GRCm39) D150G probably benign Het
Magi2 A G 5: 20,739,462 (GRCm39) D572G probably benign Het
Meiob T C 17: 25,047,008 (GRCm39) probably null Het
Ncor2 T C 5: 125,115,964 (GRCm39) Y130C Het
Ntmt2 T A 1: 163,544,738 (GRCm39) T82S probably benign Het
Ofcc1 A G 13: 40,409,072 (GRCm39) S118P probably benign Het
Or10g3 A G 14: 52,610,420 (GRCm39) F30S probably benign Het
Or2t45 A G 11: 58,669,213 (GRCm39) T87A probably benign Het
Or8b55 T A 9: 38,727,335 (GRCm39) C179S probably damaging Het
Parp14 A T 16: 35,677,181 (GRCm39) M929K probably benign Het
Pcdh8 T C 14: 80,006,229 (GRCm39) E778G probably benign Het
Pgls T C 8: 72,047,838 (GRCm39) V211A probably benign Het
Pkd2 T A 5: 104,637,151 (GRCm39) M588K probably damaging Het
Pms1 T C 1: 53,231,269 (GRCm39) N860S probably benign Het
Psg19 C T 7: 18,530,888 (GRCm39) V89M probably benign Het
Reln T C 5: 22,147,672 (GRCm39) H2426R probably benign Het
Ripor2 T A 13: 24,885,050 (GRCm39) N428K possibly damaging Het
Slc12a4 C T 8: 106,676,285 (GRCm39) probably null Het
Slc25a3 T C 10: 90,952,960 (GRCm39) I314V probably benign Het
Slc29a1 C A 17: 45,900,688 (GRCm39) V125F probably benign Het
Slc9a5 T A 8: 106,085,981 (GRCm39) C583S probably damaging Het
Slco2b1 G A 7: 99,309,259 (GRCm39) Q691* probably null Het
Smg7 T C 1: 152,719,129 (GRCm39) D874G probably damaging Het
Spef2 T A 15: 9,729,723 (GRCm39) K132* probably null Het
Tap1 A G 17: 34,412,133 (GRCm39) K446R probably benign Het
Tcam1 A T 11: 106,176,443 (GRCm39) T390S possibly damaging Het
Tnik A G 3: 28,666,057 (GRCm39) N687D probably damaging Het
Trim42 T C 9: 97,251,852 (GRCm39) R16G possibly damaging Het
Vcp A C 4: 42,984,658 (GRCm39) L411W probably damaging Het
Vma21-ps C A 4: 52,496,973 (GRCm39) G91V probably damaging Het
Vmn1r23 T C 6: 57,903,452 (GRCm39) T109A probably benign Het
Vmn2r67 C T 7: 84,801,450 (GRCm39) C162Y probably benign Het
Vmn2r-ps117 A G 17: 19,044,021 (GRCm39) T366A probably benign Het
Zfp804a A G 2: 82,066,190 (GRCm39) K54E 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
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
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
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'- TGCTTAGGAAGAGCCATGTG -3'
(R):5'- GATTGTTGTCCAGAGCCCTG -3'

Sequencing Primer
(F):5'- GCCATGTGGAAACGTCTGG -3'
(R):5'- TGGCAGCTCCAACAGATCATGG -3'
Posted On 2021-03-08