Incidental Mutation 'R5490:Gapvd1'
ID 432023
Institutional Source Beutler Lab
Gene Symbol Gapvd1
Ensembl Gene ENSMUSG00000026867
Gene Name GTPase activating protein and VPS9 domains 1
Synonyms 2010005B09Rik, 4432404J10Rik
MMRRC Submission 043051-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5490 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 34566190-34645297 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 34583445 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 1057 (D1057G)
Ref Sequence ENSEMBL: ENSMUSP00000099864 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028224] [ENSMUST00000102800] [ENSMUST00000113099]
AlphaFold Q6PAR5
Predicted Effect probably benign
Transcript: ENSMUST00000028224
AA Change: D1057G

PolyPhen 2 Score 0.226 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000028224
Gene: ENSMUSG00000026867
AA Change: D1057G

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: D1057G

PolyPhen 2 Score 0.226 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000099864
Gene: ENSMUSG00000026867
AA Change: D1057G

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: D1078G

PolyPhen 2 Score 0.087 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000108723
Gene: ENSMUSG00000026867
AA Change: D1078G

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 unknown
Transcript: ENSMUST00000113101
AA Change: D167G
SMART Domains Protein: ENSMUSP00000108725
Gene: ENSMUSG00000026867
AA Change: D167G

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 unknown
Transcript: ENSMUST00000113111
AA Change: D515G
SMART Domains Protein: ENSMUSP00000108735
Gene: ENSMUSG00000026867
AA Change: D515G

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 noncoding transcript
Transcript: ENSMUST00000167251
Predicted Effect noncoding transcript
Transcript: ENSMUST00000201772
Coding Region Coverage
  • 1x: 98.3%
  • 3x: 97.3%
  • 10x: 95.2%
  • 20x: 90.8%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aatf C T 11: 84,401,099 (GRCm39) G174D probably damaging Het
Abcc1 G T 16: 14,228,781 (GRCm39) G343C probably damaging Het
Asic2 T C 11: 80,780,646 (GRCm39) N370S probably benign Het
Btnl9 T C 11: 49,060,395 (GRCm39) E451G probably damaging Het
Cblb A G 16: 51,994,733 (GRCm39) H658R possibly damaging Het
Cdca2 T C 14: 67,917,733 (GRCm39) E555G possibly damaging Het
Chfr A G 5: 110,300,995 (GRCm39) S299G possibly damaging Het
Eea1 A G 10: 95,861,916 (GRCm39) E741G probably benign Het
Glyat C T 19: 12,627,645 (GRCm39) T80M probably benign Het
Gpr87 T C 3: 59,086,747 (GRCm39) S253G probably damaging Het
Hapstr1 T A 16: 8,673,721 (GRCm39) V216E probably damaging Het
Hmgxb3 A G 18: 61,296,049 (GRCm39) S320P probably damaging Het
Kcnq5 C T 1: 21,549,692 (GRCm39) G345D probably damaging Het
Kif5c T C 2: 49,648,870 (GRCm39) V938A probably benign Het
Klk14 G A 7: 43,341,501 (GRCm39) C51Y probably damaging Het
Madd G T 2: 91,000,980 (GRCm39) T467K possibly damaging Het
Mamdc4 T C 2: 25,455,890 (GRCm39) D706G probably damaging Het
Map2 A G 1: 66,452,292 (GRCm39) H476R probably damaging Het
Mgat4f A G 1: 134,317,666 (GRCm39) D146G probably damaging Het
Mpeg1 T C 19: 12,439,057 (GRCm39) S172P probably damaging Het
Nkx2-3 A T 19: 43,601,093 (GRCm39) T52S probably benign Het
Nup210 C T 6: 91,062,970 (GRCm39) V230I probably damaging Het
Or1j19 T A 2: 36,677,193 (GRCm39) Y219N probably damaging Het
Or51f2 T C 7: 102,527,100 (GRCm39) S258P probably damaging Het
Or5g9 G T 2: 85,552,666 (GRCm39) A306S probably benign Het
Pepd A G 7: 34,642,115 (GRCm39) probably null Het
Ppp1r36 T A 12: 76,484,760 (GRCm39) W238R probably damaging Het
Ppp1r36 G T 12: 76,484,761 (GRCm39) W238L possibly damaging Het
Prpf6 T G 2: 181,249,958 (GRCm39) D39E probably benign Het
Rassf5 T A 1: 131,108,932 (GRCm39) Q163L possibly damaging Het
Rbm43 T A 2: 51,815,607 (GRCm39) T205S probably benign Het
Relch T A 1: 105,647,226 (GRCm39) V672D probably damaging Het
Robo4 CGG CG 9: 37,322,786 (GRCm39) probably null Het
Sds C A 5: 120,621,715 (GRCm39) Q286K possibly damaging Het
Slc35a3 A T 3: 116,474,839 (GRCm39) C184* probably null Het
Smg1 G A 7: 117,738,659 (GRCm39) T3530I possibly damaging Het
Sspo T C 6: 48,470,214 (GRCm39) V591A probably benign Het
Stam2 T C 2: 52,610,929 (GRCm39) D31G probably damaging Het
Star A G 8: 26,299,945 (GRCm39) K96E probably damaging Het
Syne3 A G 12: 104,921,931 (GRCm39) L495P probably damaging Het
Tceanc2 A T 4: 107,022,846 (GRCm39) M47K probably benign Het
Tecpr2 T C 12: 110,881,118 (GRCm39) L85P probably damaging Het
Tmem241 C T 18: 12,176,320 (GRCm39) R116K probably benign Het
Yipf2 G A 9: 21,503,487 (GRCm39) A20V probably benign Het
Zc3h4 T A 7: 16,162,930 (GRCm39) D443E unknown Het
Zfp184 T A 13: 22,142,747 (GRCm39) V151D probably benign Het
Zhx1 T C 15: 57,916,695 (GRCm39) Y517C 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
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'- CAAAGCCAACTGTGAAAGGTTG -3'
(R):5'- GCCCTGGCCATTGATAATCTC -3'

Sequencing Primer
(F):5'- TCTACAGAGTGAGTTCTAGGACAGCC -3'
(R):5'- GGCCATTGATAATCTCGTTATATGTC -3'
Posted On 2016-10-05