Incidental Mutation 'R7154:Gapvd1'
ID 557122
Institutional Source Beutler Lab
Gene Symbol Gapvd1
Ensembl Gene ENSMUSG00000026867
Gene Name GTPase activating protein and VPS9 domains 1
Synonyms 2010005B09Rik, 4432404J10Rik
MMRRC Submission 045256-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7154 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 34566190-34645297 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 34615075 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Arginine at position 474 (K474R)
Ref Sequence ENSEMBL: ENSMUSP00000099864 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028224] [ENSMUST00000102800] [ENSMUST00000113099] [ENSMUST00000142436]
AlphaFold Q6PAR5
Predicted Effect probably damaging
Transcript: ENSMUST00000028224
AA Change: K474R

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000028224
Gene: ENSMUSG00000026867
AA Change: K474R

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: K474R

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000099864
Gene: ENSMUSG00000026867
AA Change: K474R

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: K474R

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000108723
Gene: ENSMUSG00000026867
AA Change: K474R

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: ENSMUSP00000108727
Gene: ENSMUSG00000026867
AA Change: K304R

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: ENSMUSP00000120138
Gene: ENSMUSG00000026867
AA Change: K336R

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
SMART Domains Protein: ENSMUSP00000126225
Gene: ENSMUSG00000026867

DomainStartEndE-ValueType
SCOP:d1wer__ 95 135 6e-4 SMART
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 100% (67/67)
Allele List at MGI
Other mutations in this stock
Total: 67 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
8030423J24Rik T C 13: 71,032,344 (GRCm39) F139L unknown Het
Adgre1 G A 17: 57,751,087 (GRCm39) probably null Het
Agap2 A G 10: 126,927,524 (GRCm39) D1135G probably benign Het
Akp3 T C 1: 87,052,946 (GRCm39) L45P probably damaging Het
Arfgap3 A T 15: 83,220,905 (GRCm39) W71R probably damaging Het
Asic3 G A 5: 24,618,660 (GRCm39) probably benign Het
Asph A T 4: 9,630,930 (GRCm39) N139K possibly damaging Het
Atr T A 9: 95,747,098 (GRCm39) C127S probably benign Het
Auts2 A T 5: 131,480,731 (GRCm39) S255T Het
Bcl6 G A 16: 23,784,976 (GRCm39) R675* probably null Het
Cacnb1 A G 11: 97,895,959 (GRCm39) L443P probably damaging Het
Cbfa2t3 G A 8: 123,364,883 (GRCm39) Q300* probably null Het
Ccer1 A T 10: 97,530,201 (GRCm39) D288V unknown Het
Col18a1 G A 10: 76,908,799 (GRCm39) P611S probably benign Het
Cpa6 T A 1: 10,407,694 (GRCm39) D281V possibly damaging Het
Cyp2e1 A G 7: 140,350,050 (GRCm39) Y245C probably damaging Het
Cyp4a31 T C 4: 115,431,963 (GRCm39) probably null Het
Efcab3 T A 11: 104,589,966 (GRCm39) probably null Het
Entpd1 T C 19: 40,713,430 (GRCm39) Y188H probably damaging Het
Epb42 T C 2: 120,863,843 (GRCm39) D111G probably benign Het
Espl1 A G 15: 102,232,484 (GRCm39) D2064G probably damaging Het
Fat3 A C 9: 15,908,160 (GRCm39) V2614G probably damaging Het
Fos A T 12: 85,520,931 (GRCm39) M40L probably benign Het
Frmd4b T A 6: 97,283,707 (GRCm39) E434V probably damaging Het
Galnt6 A T 15: 100,591,345 (GRCm39) D586E probably benign Het
Gimap8 T A 6: 48,633,122 (GRCm39) F314I probably damaging Het
Gm14393 T G 2: 174,903,576 (GRCm39) K110N probably damaging Het
Gm4131 C A 14: 62,718,382 (GRCm39) A75S probably damaging Het
Heatr6 G A 11: 83,668,067 (GRCm39) V854I probably benign Het
Hic2 T A 16: 17,076,806 (GRCm39) M545K possibly damaging Het
Ift70b C T 2: 75,768,405 (GRCm39) R116H possibly damaging Het
Ip6k1 A G 9: 107,922,861 (GRCm39) Y331C probably damaging Het
Kalrn C T 16: 34,032,527 (GRCm39) probably null Het
Kxd1 T C 8: 70,968,084 (GRCm39) K88E probably damaging Het
Lrrc37a A C 11: 103,393,682 (GRCm39) V581G probably benign Het
Mex3d A T 10: 80,222,584 (GRCm39) V224E Het
Mtx2 T A 2: 74,706,762 (GRCm39) C246S probably damaging Het
Mybbp1a A G 11: 72,338,468 (GRCm39) probably null Het
Myh6 A G 14: 55,197,764 (GRCm39) I458T probably benign Het
Ndufs6 A G 13: 73,468,411 (GRCm39) V96A possibly damaging Het
Nemf A T 12: 69,363,515 (GRCm39) probably null Het
Notch1 T C 2: 26,349,950 (GRCm39) S2397G probably benign Het
Or4c15b A G 2: 89,113,204 (GRCm39) I91T probably damaging Het
Or6ae1 T C 7: 139,741,997 (GRCm39) I289V probably benign Het
Osbpl1a T C 18: 12,901,649 (GRCm39) E619G probably benign Het
Pfkl T C 10: 77,837,289 (GRCm39) R95G probably benign Het
Plat T A 8: 23,268,521 (GRCm39) I391K possibly damaging Het
Ppp1r21 A G 17: 88,862,314 (GRCm39) H244R probably damaging Het
Rapgef3 G C 15: 97,651,758 (GRCm39) H578Q probably benign Het
Rnf145 C A 11: 44,415,822 (GRCm39) N12K probably damaging Het
Sfxn5 C T 6: 85,309,405 (GRCm39) C100Y unknown Het
Sh3rf1 T A 8: 61,825,748 (GRCm39) L581Q possibly damaging Het
Sipa1l2 T C 8: 126,195,078 (GRCm39) K887E probably benign Het
Spopfm2 A G 3: 94,083,526 (GRCm39) I95T probably benign Het
Stard9 C A 2: 120,531,795 (GRCm39) T2684N probably benign Het
Stard9 A C 2: 120,535,023 (GRCm39) Q3760P probably benign Het
Stpg2 A G 3: 138,921,056 (GRCm39) E87G probably benign Het
Syne2 A G 12: 76,106,231 (GRCm39) Q792R possibly damaging Het
Taf7 T C 18: 37,775,601 (GRCm39) D322G possibly damaging Het
Tbc1d1 A G 5: 64,331,156 (GRCm39) S112G possibly damaging Het
Tbx3 A G 5: 119,810,093 (GRCm39) M5V possibly damaging Het
Tmem45b A T 9: 31,339,328 (GRCm39) I215N possibly damaging Het
Tpd52 G A 3: 9,028,916 (GRCm39) Q43* probably null Het
Trpa1 T A 1: 14,952,457 (GRCm39) N858I possibly damaging Het
Ttll5 A G 12: 85,972,538 (GRCm39) D767G probably damaging Het
Vmn2r3 G A 3: 64,194,732 (GRCm39) T62I probably benign Het
Wdr59 A T 8: 112,185,367 (GRCm39) N874K 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
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'- CAAAGACTCAGTGAGTAAAGCC -3'
(R):5'- TTGGCAGGTCACAGATGAATACG -3'

Sequencing Primer
(F):5'- CACCATCTGGATGCTGGTATTACAG -3'
(R):5'- GGTCACAGATGAATACGTACTATAAG -3'
Posted On 2019-06-26