Incidental Mutation 'R6950:Gapvd1'
ID 541193
Institutional Source Beutler Lab
Gene Symbol Gapvd1
Ensembl Gene ENSMUSG00000026867
Gene Name GTPase activating protein and VPS9 domains 1
Synonyms 2010005B09Rik, 4432404J10Rik
MMRRC Submission 045062-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6950 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 34566190-34645297 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 34574257 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 1301 (V1301A)
Ref Sequence ENSEMBL: ENSMUSP00000108723 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028224] [ENSMUST00000102800] [ENSMUST00000113099]
AlphaFold Q6PAR5
Predicted Effect probably benign
Transcript: ENSMUST00000028224
AA Change: V1280A

PolyPhen 2 Score 0.037 (Sensitivity: 0.94; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000028224
Gene: ENSMUSG00000026867
AA Change: V1280A

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: V1280A

PolyPhen 2 Score 0.037 (Sensitivity: 0.94; Specificity: 0.82)
SMART Domains Protein: ENSMUSP00000099864
Gene: ENSMUSG00000026867
AA Change: V1280A

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: V1301A

PolyPhen 2 Score 0.040 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000108723
Gene: ENSMUSG00000026867
AA Change: V1301A

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: V390A

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: V738A

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.4%
  • 20x: 98.4%
Validation Efficiency 98% (59/60)
Allele List at MGI
Other mutations in this stock
Total: 59 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc1 T A 16: 14,229,480 (GRCm39) V404D probably damaging Het
Adcy2 A G 13: 69,036,184 (GRCm39) M159T possibly damaging Het
Agtpbp1 T C 13: 59,598,080 (GRCm39) K674R probably benign Het
Atxn7 C A 14: 14,095,511 (GRCm38) P403H probably damaging Het
Cav3 C T 6: 112,449,171 (GRCm39) T63I probably damaging Het
Ccr6 T C 17: 8,475,898 (GRCm39) *368Q probably null Het
Cdh8 A T 8: 99,757,395 (GRCm39) N734K probably benign Het
Ces5a G T 8: 94,257,402 (GRCm39) N134K probably benign Het
Cisd3 T G 11: 97,576,986 (GRCm39) probably null Het
Cyp4f39 T G 17: 32,711,280 (GRCm39) C476G probably damaging Het
Dffb A T 4: 154,054,549 (GRCm39) M180K probably benign Het
Dock4 A G 12: 40,783,313 (GRCm39) E749G possibly damaging Het
Eogt A G 6: 97,111,343 (GRCm39) F173L possibly damaging Het
Ephb1 T A 9: 102,072,108 (GRCm39) T224S probably benign Het
Fam114a1 A T 5: 65,137,322 (GRCm39) E88D possibly damaging Het
Fbn2 A C 18: 58,168,993 (GRCm39) M2262R probably null Het
Fsip2 A G 2: 82,816,332 (GRCm39) I4022V probably benign Het
Gch1 A T 14: 47,426,723 (GRCm39) M1K probably null Het
Hes1 T C 16: 29,886,089 (GRCm39) F231S probably damaging Het
Hoxb2 A G 11: 96,242,727 (GRCm39) T31A probably benign Het
Ifngr1 T A 10: 19,483,041 (GRCm39) V265D probably damaging Het
Ifnl3 A T 7: 28,222,432 (GRCm39) I58F probably benign Het
Igf2r T C 17: 12,937,605 (GRCm39) T561A probably benign Het
Igfbpl1 T A 4: 45,815,494 (GRCm39) H214L probably damaging Het
Irf8 A G 8: 121,481,864 (GRCm39) T318A probably benign Het
Kmt2d T C 15: 98,737,901 (GRCm39) probably benign Het
Lratd2 T C 15: 60,695,563 (GRCm39) D61G probably benign Het
Lrrc36 G T 8: 106,152,021 (GRCm39) probably null Het
Msl2 C T 9: 100,979,174 (GRCm39) P516L possibly damaging Het
Naaladl1 A T 19: 6,156,011 (GRCm39) I62F probably damaging Het
Neto2 G T 8: 86,397,072 (GRCm39) P60Q probably damaging Het
Nipsnap3b A T 4: 53,015,136 (GRCm39) H61L possibly damaging Het
Npb T C 11: 120,499,473 (GRCm39) F47L probably benign Het
Nutm1 T A 2: 112,078,904 (GRCm39) T1004S probably benign Het
Or4a78 T A 2: 89,497,895 (GRCm39) I112F probably benign Het
Or4z4 A G 19: 12,076,754 (GRCm39) V83A probably benign Het
Or8c17 A T 9: 38,179,842 (GRCm39) N3I probably damaging Het
Oxr1 C A 15: 41,683,951 (GRCm39) A439E probably benign Het
Phf14 A T 6: 12,006,854 (GRCm39) K835N probably damaging Het
Prkdc T A 16: 15,633,850 (GRCm39) V3518E probably damaging Het
Ptpru T A 4: 131,503,663 (GRCm39) E1132D probably damaging Het
Rapgef6 T A 11: 54,567,206 (GRCm39) M1129K probably benign Het
Rgmb T C 17: 16,028,048 (GRCm39) K224E probably damaging Het
Ryr3 T C 2: 112,517,170 (GRCm39) I3318V possibly damaging Het
Slc9a4 A G 1: 40,642,045 (GRCm39) Y338C probably damaging Het
Smg5 T C 3: 88,256,576 (GRCm39) probably null Het
Tenm3 A T 8: 48,693,514 (GRCm39) Y1789* probably null Het
Tgm7 T C 2: 120,924,128 (GRCm39) E598G probably damaging Het
Tiam1 C T 16: 89,657,092 (GRCm39) probably null Het
Tmem175 A G 5: 108,790,948 (GRCm39) N166S probably benign Het
Trp73 G T 4: 154,146,510 (GRCm39) N368K probably benign Het
Trpc3 C T 3: 36,692,739 (GRCm39) R751H probably damaging Het
Trpm4 C A 7: 44,968,704 (GRCm39) A410S probably damaging Het
Ube2t T G 1: 134,899,095 (GRCm39) probably null Het
Vmn2r114 C T 17: 23,529,137 (GRCm39) A322T probably benign Het
Xylt2 C T 11: 94,558,455 (GRCm39) R567H probably benign Het
Zfp119b T C 17: 56,246,137 (GRCm39) K318E probably damaging Het
Zfp626 T G 7: 27,518,339 (GRCm39) L440R probably damaging Het
Zfp850 A G 7: 27,689,939 (GRCm39) S90P possibly 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
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'- CATCCACTCTGACCGTGAATGTG -3'
(R):5'- AGGAGGTTGACTGTAATTCCCC -3'

Sequencing Primer
(F):5'- CTCTGACCGTGAATGTGAATGGTAAC -3'
(R):5'- AGGTTGACTGTAATTCCCCTTTAG -3'
Posted On 2018-11-28