Incidental Mutation 'R4935:Gapvd1'
ID 380272
Institutional Source Beutler Lab
Gene Symbol Gapvd1
Ensembl Gene ENSMUSG00000026867
Gene Name GTPase activating protein and VPS9 domains 1
Synonyms 2010005B09Rik, 4432404J10Rik
MMRRC Submission 042535-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4935 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 34566190-34645297 bp(-) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) G to A at 34594504 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Arginine to Stop codon at position 685 (R685*)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028224] [ENSMUST00000102800] [ENSMUST00000113099]
AlphaFold Q6PAR5
Predicted Effect probably null
Transcript: ENSMUST00000028224
AA Change: R828*
SMART Domains Protein: ENSMUSP00000028224
Gene: ENSMUSG00000026867
AA Change: R828*

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: R828*
SMART Domains Protein: ENSMUSP00000099864
Gene: ENSMUSG00000026867
AA Change: R828*

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: R849*
SMART Domains Protein: ENSMUSP00000108723
Gene: ENSMUSG00000026867
AA Change: R849*

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: ENSMUST00000113101
SMART Domains Protein: ENSMUSP00000108725
Gene: ENSMUSG00000026867

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: ENSMUST00000113103
AA Change: R685*
SMART Domains Protein: ENSMUSP00000108727
Gene: ENSMUSG00000026867
AA Change: R685*

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 null
Transcript: ENSMUST00000113111
AA Change: R286*
SMART Domains Protein: ENSMUSP00000108735
Gene: ENSMUSG00000026867
AA Change: R286*

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: ENSMUST00000128855
SMART Domains Protein: ENSMUSP00000129138
Gene: ENSMUSG00000026867

DomainStartEndE-ValueType
low complexity region 26 40 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000167251
Predicted Effect probably null
Transcript: ENSMUST00000137528
AA Change: R685*
SMART Domains Protein: ENSMUSP00000120138
Gene: ENSMUSG00000026867
AA Change: R685*

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 noncoding transcript
Transcript: ENSMUST00000201772
Predicted Effect noncoding transcript
Transcript: ENSMUST00000150859
Predicted Effect noncoding transcript
Transcript: ENSMUST00000156098
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 97.9%
  • 10x: 94.8%
  • 20x: 86.9%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 56 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A730071L15Rik A G 11: 6,150,442 (GRCm39) *138W probably null Het
Abcb1a T A 5: 8,787,773 (GRCm39) probably null Het
Acp6 T C 3: 97,079,060 (GRCm39) probably null Het
Adcyap1 A T 17: 93,511,541 (GRCm39) I172L probably benign Het
Adgrf1 A C 17: 43,606,130 (GRCm39) I85L probably benign Het
Afdn A T 17: 14,111,228 (GRCm39) T1604S probably benign Het
Angpt2 T C 8: 18,742,131 (GRCm39) Y475C probably damaging Het
Ank2 A G 3: 126,749,713 (GRCm39) S439P probably damaging Het
Ank3 T A 10: 69,812,033 (GRCm39) N366K probably damaging Het
Ankrd11 A G 8: 123,626,922 (GRCm39) S87P probably benign Het
Ano7 T A 1: 93,323,036 (GRCm39) S459T possibly damaging Het
Asxl3 G A 18: 22,656,369 (GRCm39) V1460M probably benign Het
Atg16l1 A C 1: 87,694,764 (GRCm39) N147T possibly damaging Het
Atp10a T C 7: 58,463,512 (GRCm39) V1015A probably damaging Het
Atxn7 T A 14: 14,100,401 (GRCm38) S696T probably benign Het
Babam1 C T 8: 71,852,446 (GRCm39) T184I probably benign Het
Blk A G 14: 63,618,711 (GRCm39) S175P possibly damaging Het
Col5a1 T A 2: 27,914,754 (GRCm39) F123L probably damaging Het
Csmd3 T C 15: 48,024,480 (GRCm39) Y496C probably damaging Het
Dnah3 A T 7: 119,615,700 (GRCm39) Y1676* probably null Het
Fdxacb1 T A 9: 50,683,243 (GRCm39) M402K probably benign Het
Frmd5 A G 2: 121,393,405 (GRCm39) V141A possibly damaging Het
Grik2 A G 10: 49,116,826 (GRCm39) L645P probably damaging Het
H2aj T A 6: 136,785,681 (GRCm39) V115E possibly damaging Het
Hrh3 T C 2: 179,743,061 (GRCm39) Y189C probably damaging Het
Kcnc2 A G 10: 112,108,133 (GRCm39) T175A probably benign Het
Kcnv2 A G 19: 27,300,332 (GRCm39) Y61C probably damaging Het
Kif24 T C 4: 41,394,939 (GRCm39) R645G probably damaging Het
Knl1 A G 2: 118,899,438 (GRCm39) I380V possibly damaging Het
Lamb2 A G 9: 108,364,700 (GRCm39) I1151M possibly damaging Het
Leo1 A G 9: 75,353,159 (GRCm39) D234G probably benign Het
Lrp1b T G 2: 41,388,405 (GRCm39) N407H probably benign Het
Matn2 T C 15: 34,428,831 (GRCm39) S732P probably damaging Het
Mrps30 A T 13: 118,523,431 (GRCm39) F114I possibly damaging Het
Or1l8 T C 2: 36,817,713 (GRCm39) N138D probably benign Het
Or4f17-ps1 G A 2: 111,357,793 (GRCm39) V45I probably damaging Het
Or5b123 T C 19: 13,597,066 (GRCm39) I180T probably benign Het
Oxr1 T C 15: 41,676,980 (GRCm39) V179A probably benign Het
Plaur A T 7: 24,166,141 (GRCm39) S71C possibly damaging Het
Plbd2 T C 5: 120,624,786 (GRCm39) N461D possibly damaging Het
Plcb2 T A 2: 118,549,396 (GRCm39) Y322F probably damaging Het
Prkab2 T C 3: 97,569,671 (GRCm39) V79A probably damaging Het
Ptpn3 A T 4: 57,197,568 (GRCm39) C774S probably damaging Het
Ring1 A C 17: 34,242,016 (GRCm39) L131R probably benign Het
Rxfp2 G A 5: 149,975,097 (GRCm39) probably null Het
Selenbp1 A T 3: 94,845,269 (GRCm39) I122F probably benign Het
Septin7 A G 9: 25,217,468 (GRCm39) H394R probably benign Het
Slc1a7 G A 4: 107,864,758 (GRCm39) V266I probably damaging Het
Slc2a10 A G 2: 165,359,578 (GRCm39) T481A probably benign Het
Spmap2l T C 5: 77,185,200 (GRCm39) probably null Het
Tapbp A G 17: 34,144,596 (GRCm39) M231V probably benign Het
Tbxas1 A T 6: 38,999,981 (GRCm39) N256I probably benign Het
Uimc1 A G 13: 55,240,998 (GRCm39) I30T probably damaging Het
Usp48 C A 4: 137,377,669 (GRCm39) N231K probably benign Het
Zfhx3 T G 8: 109,674,482 (GRCm39) V1844G possibly damaging Het
Znrf3 A T 11: 5,233,422 (GRCm39) C212S 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
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'- GGAAGTTCTTCATTCCCTGGAC -3'
(R):5'- CAGAGTCTCTGCTTGCCATG -3'

Sequencing Primer
(F):5'- TTCCAGCTGGGGTCACTCATG -3'
(R):5'- GTTTGATCCACTGTCCTCACATGAAG -3'
Posted On 2016-04-15