Incidental Mutation 'R8113:Gapvd1'
ID 630978
Institutional Source Beutler Lab
Gene Symbol Gapvd1
Ensembl Gene ENSMUSG00000026867
Gene Name GTPase activating protein and VPS9 domains 1
Synonyms 2010005B09Rik, 4432404J10Rik
MMRRC Submission 067542-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R8113 (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 34594330 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 886 (S886P)
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: S886P

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000028224
Gene: ENSMUSG00000026867
AA Change: S886P

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: S886P

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000099864
Gene: ENSMUSG00000026867
AA Change: S886P

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: S907P

PolyPhen 2 Score 0.966 (Sensitivity: 0.77; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000108723
Gene: ENSMUSG00000026867
AA Change: S907P

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: S23P

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: ENSMUSP00000108727
Gene: ENSMUSG00000026867
AA Change: S743P

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
SMART Domains Protein: ENSMUSP00000108735
Gene: ENSMUSG00000026867
AA Change: S344P

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
SMART Domains Protein: ENSMUSP00000120138
Gene: ENSMUSG00000026867
AA Change: S743P

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.7%
Validation Efficiency 96% (72/75)
Allele List at MGI
Other mutations in this stock
Total: 74 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adcy7 T C 8: 89,048,431 (GRCm39) S625P probably damaging Het
Agpat1 T C 17: 34,830,586 (GRCm39) V170A probably damaging Het
Alg9 C T 9: 50,720,080 (GRCm39) Q519* probably null Het
Apol8 C T 15: 77,634,336 (GRCm39) R80H probably benign Het
Arhgap25 G T 6: 87,465,287 (GRCm39) S118* probably null Het
Arhgap30 T A 1: 171,225,086 (GRCm39) Y47* probably null Het
Arhgap42 C T 9: 9,011,434 (GRCm39) D451N probably damaging Het
Cabp2 T A 19: 4,135,582 (GRCm39) F91I probably damaging Het
Ccdc30 T C 4: 119,230,943 (GRCm39) E108G probably benign Het
Cfap99 T C 5: 34,458,763 (GRCm39) S53P probably damaging Het
Clec5a C T 6: 40,556,361 (GRCm39) R135H possibly damaging Het
Cops8 T G 1: 90,531,325 (GRCm39) D18E probably benign Het
Cped1 A T 6: 22,233,480 (GRCm39) M779L possibly damaging Het
Cyp4x1 G A 4: 114,967,263 (GRCm39) H438Y probably damaging Het
Disc1 A T 8: 125,815,014 (GRCm39) T293S probably benign Het
Ercc1 T C 7: 19,084,102 (GRCm39) L113S probably damaging Het
Ermp1 G T 19: 29,593,196 (GRCm39) N765K probably benign Het
Fam83c A G 2: 155,676,740 (GRCm39) I10T probably benign Het
Farp1 T C 14: 121,513,008 (GRCm39) V788A probably benign Het
Fbn1 C G 2: 125,319,489 (GRCm39) G92R probably damaging Het
Fsd1 T A 17: 56,302,881 (GRCm39) M328K probably benign Het
Fzd3 C A 14: 65,440,262 (GRCm39) S636I probably benign Het
Gatad2b T A 3: 90,249,029 (GRCm39) D22E probably benign Het
Gm7168 A T 17: 14,169,238 (GRCm39) K202* probably null Het
Gmps T C 3: 63,887,690 (GRCm39) I54T probably damaging Het
Gp6 A G 7: 4,397,114 (GRCm39) I107T probably benign Het
Gpat2 T C 2: 127,273,267 (GRCm39) V217A possibly damaging Het
Hdlbp T A 1: 93,344,917 (GRCm39) I863F probably damaging Het
Hmcn1 A C 1: 150,624,841 (GRCm39) I1021M possibly damaging Het
Igkv6-14 C T 6: 70,412,087 (GRCm39) A66T probably benign Het
Ippk C T 13: 49,599,818 (GRCm39) P226S Het
Iqch A G 9: 63,361,855 (GRCm39) I925T probably benign Het
Kcnt1 A G 2: 25,791,223 (GRCm39) E522G possibly damaging Het
Kremen2 C G 17: 23,962,776 (GRCm39) E103D probably damaging Het
Lig4 G T 8: 10,023,485 (GRCm39) N98K probably benign Het
Lrrc3b T G 14: 15,358,232 (GRCm38) I125L probably benign Het
Lrrc4 T C 6: 28,829,902 (GRCm39) D148G probably damaging Het
Lrsam1 A G 2: 32,837,901 (GRCm39) Y218H possibly damaging Het
Mmrn2 G A 14: 34,119,593 (GRCm39) V191I probably benign Het
Nadk T A 4: 155,655,127 (GRCm39) probably null Het
Napb C A 2: 148,551,351 (GRCm39) A61S possibly damaging Het
Ncan T A 8: 70,561,221 (GRCm39) D582V possibly damaging Het
Ncl T C 1: 86,284,364 (GRCm39) D244G possibly damaging Het
Nlrp14 A G 7: 106,791,715 (GRCm39) N800S possibly damaging Het
Nlrp9b C T 7: 19,753,260 (GRCm39) T55M probably benign Het
Nobox G A 6: 43,282,951 (GRCm39) T228I probably benign Het
Npffr1 C A 10: 61,449,750 (GRCm39) P8H possibly damaging Het
Nrg2 T C 18: 36,154,156 (GRCm39) Y587C probably damaging Het
Nsd1 T G 13: 55,393,434 (GRCm39) V448G probably benign Het
Or2w1 T A 13: 21,317,371 (GRCm39) V142D probably benign Het
Or5e1 G T 7: 108,354,438 (GRCm39) C125F probably damaging Het
Or8k41 T G 2: 86,313,412 (GRCm39) I225L probably damaging Het
Or9g20 A G 2: 85,630,011 (GRCm39) L201P probably damaging Het
Peg10 T TCCC 6: 4,756,451 (GRCm39) probably benign Het
Ppp5c T C 7: 16,742,932 (GRCm39) T229A probably benign Het
Pramel51 T C 12: 88,143,850 (GRCm39) Y329C probably benign Het
Prr5 C T 15: 84,577,993 (GRCm39) R101C probably damaging Het
Psg22 T C 7: 18,456,987 (GRCm39) M290T probably benign Het
Pzp C T 6: 128,490,694 (GRCm39) probably null Het
Rapgef6 T C 11: 54,516,784 (GRCm39) V347A probably benign Het
Rttn A T 18: 89,029,040 (GRCm39) H586L probably damaging Het
Sema3f A T 9: 107,565,275 (GRCm39) I259K possibly damaging Het
Sgpp1 A T 12: 75,763,374 (GRCm39) L269Q probably damaging Het
Slc22a8 A C 19: 8,582,903 (GRCm39) I195L probably benign Het
Slc35a5 T C 16: 44,962,551 (GRCm39) T425A unknown Het
Spata31e1 G A 13: 49,939,548 (GRCm39) R721C probably benign Het
Stard13 G A 5: 150,986,970 (GRCm39) T180I probably damaging Het
Stard9 G A 2: 120,534,911 (GRCm39) G3723S probably benign Het
Svil A T 18: 5,062,385 (GRCm39) T902S probably damaging Het
Tnfaip8l3 T A 9: 53,934,421 (GRCm39) R185W probably damaging Het
Ttn A T 2: 76,590,393 (GRCm39) D21105E probably benign Het
Vmn2r109 T A 17: 20,774,729 (GRCm39) M209L probably benign Het
Vmn2r125 A G 4: 156,703,642 (GRCm39) H340R probably damaging Het
Zfp946 T C 17: 22,674,481 (GRCm39) C412R 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
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'- ATTCTACATGGCTGTGTCCC -3'
(R):5'- TTCTGTGTTACAGGGGCCTC -3'

Sequencing Primer
(F):5'- ACATGGCTGTGTCCCATACC -3'
(R):5'- GTAAGGCCAAAGGTTCACTATGCC -3'
Posted On 2020-06-30