Incidental Mutation 'R0570:Gapvd1'
ID 46345
Institutional Source Beutler Lab
Gene Symbol Gapvd1
Ensembl Gene ENSMUSG00000026867
Gene Name GTPase activating protein and VPS9 domains 1
Synonyms 2010005B09Rik, 4432404J10Rik
MMRRC Submission 038761-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0570 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 34566190-34645297 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 34618552 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Histidine at position 274 (Y274H)
Ref Sequence ENSEMBL: ENSMUSP00000108723 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028224] [ENSMUST00000102800] [ENSMUST00000113099] [ENSMUST00000142436]
AlphaFold Q6PAR5
Predicted Effect probably damaging
Transcript: ENSMUST00000028224
AA Change: Y274H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000028224
Gene: ENSMUSG00000026867
AA Change: Y274H

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: Y274H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000099864
Gene: ENSMUSG00000026867
AA Change: Y274H

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: Y274H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000108723
Gene: ENSMUSG00000026867
AA Change: Y274H

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: ENSMUST00000113103
AA Change: Y104H
SMART Domains Protein: ENSMUSP00000108727
Gene: ENSMUSG00000026867
AA Change: Y104H

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 unknown
Transcript: ENSMUST00000137528
AA Change: Y136H
SMART Domains Protein: ENSMUSP00000120138
Gene: ENSMUSG00000026867
AA Change: Y136H

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000169207
Meta Mutation Damage Score 0.2290 question?
Coding Region Coverage
  • 1x: 99.6%
  • 3x: 98.9%
  • 10x: 97.0%
  • 20x: 94.3%
Validation Efficiency 100% (85/85)
Allele List at MGI
Other mutations in this stock
Total: 85 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700067K01Rik C A 8: 84,729,733 (GRCm39) probably benign Het
Aadacl3 C T 4: 144,190,130 (GRCm39) W57* probably null Het
Abca2 G T 2: 25,337,417 (GRCm39) probably null Het
Abca3 A G 17: 24,593,373 (GRCm39) I257V probably benign Het
Adamts2 A G 11: 50,666,963 (GRCm39) D420G probably damaging Het
Adamts5 A G 16: 85,696,135 (GRCm39) F341L probably damaging Het
Ahnak T A 19: 8,991,062 (GRCm39) D4115E probably damaging Het
Arhgap20 T C 9: 51,751,751 (GRCm39) S365P possibly damaging Het
Atrn G A 2: 130,822,054 (GRCm39) V916I probably benign Het
Blmh T C 11: 76,856,651 (GRCm39) V82A probably damaging Het
C1ra A T 6: 124,490,664 (GRCm39) Y19F probably benign Het
Cactin A G 10: 81,159,067 (GRCm39) E306G probably damaging Het
Celsr1 C T 15: 85,787,566 (GRCm39) R2724Q probably benign Het
Clca4b T C 3: 144,631,110 (GRCm39) E250G probably benign Het
Col17a1 A T 19: 47,654,317 (GRCm39) S647T possibly damaging Het
Cope T A 8: 70,759,181 (GRCm39) D74E probably damaging Het
Dsg1c T C 18: 20,403,435 (GRCm39) I198T probably damaging Het
Elfn2 T C 15: 78,557,434 (GRCm39) N371S probably damaging Het
Elmo2 G T 2: 165,146,839 (GRCm39) A246D probably benign Het
Ewsr1 A T 11: 5,035,935 (GRCm39) M187K possibly damaging Het
Faap100 A T 11: 120,265,114 (GRCm39) S587R possibly damaging Het
Fam234b C T 6: 135,186,247 (GRCm39) S85L probably benign Het
Fanca A T 8: 124,033,169 (GRCm39) S292R probably benign Het
Fanci G A 7: 79,093,711 (GRCm39) C1021Y probably damaging Het
Fhod3 T C 18: 25,245,640 (GRCm39) I1230T probably benign Het
Fmo5 T C 3: 97,536,456 (GRCm39) L27S probably damaging Het
Fmo9 A G 1: 166,502,031 (GRCm39) V147A probably null Het
Fnbp4 A G 2: 90,583,301 (GRCm39) Y309C probably damaging Het
Foxb1 T C 9: 69,666,844 (GRCm39) T229A probably benign Het
Gbp8 T C 5: 105,165,541 (GRCm39) probably null Het
Gcn1 T A 5: 115,730,480 (GRCm39) L888Q probably damaging Het
Gm17490 T C 2: 11,630,460 (GRCm39) probably benign Het
Gtf2ird2 T A 5: 134,237,785 (GRCm39) probably null Het
H2-Q1 A G 17: 35,540,373 (GRCm39) T153A possibly damaging Het
Ina A C 19: 47,011,938 (GRCm39) E452A probably benign Het
Kars1 A G 8: 112,721,494 (GRCm39) probably null Het
Kif1c A G 11: 70,595,291 (GRCm39) E124G probably damaging Het
Lpin3 T C 2: 160,745,944 (GRCm39) probably benign Het
Lrp1 A T 10: 127,390,878 (GRCm39) C3006* probably null Het
Lyst T C 13: 13,883,971 (GRCm39) L2953P probably benign Het
Mb21d2 G A 16: 28,748,324 (GRCm39) A31V probably benign Het
Melk T C 4: 44,308,906 (GRCm39) Y88H probably damaging Het
Myrf A G 19: 10,189,161 (GRCm39) S857P probably damaging Het
Nos2 A G 11: 78,826,187 (GRCm39) I153M possibly damaging Het
Or4n4 T G 14: 50,519,370 (GRCm39) L113F probably benign Het
Otof A G 5: 30,529,225 (GRCm39) probably benign Het
Patl2 A G 2: 121,955,789 (GRCm39) V249A probably damaging Het
Pcgf5 A G 19: 36,389,580 (GRCm39) Y19C probably benign Het
Pcnt A T 10: 76,247,941 (GRCm39) V951E probably damaging Het
Pcolce2 T C 9: 95,520,710 (GRCm39) V29A probably benign Het
Pdgfrb A T 18: 61,210,775 (GRCm39) M761L probably benign Het
Pi16 A T 17: 29,538,189 (GRCm39) M1L possibly damaging Het
Pkd2 T A 5: 104,603,471 (GRCm39) probably benign Het
Plcb2 A G 2: 118,547,806 (GRCm39) W474R probably benign Het
Psapl1 A G 5: 36,361,624 (GRCm39) D72G possibly damaging Het
Ptpn5 T A 7: 46,728,681 (GRCm39) probably benign Het
Ptprg A G 14: 12,215,896 (GRCm38) E1115G probably damaging Het
Rassf1 C T 9: 107,435,165 (GRCm39) T224I probably damaging Het
Rbpms2 T A 9: 65,566,476 (GRCm39) C168* probably null Het
Rhag A G 17: 41,139,804 (GRCm39) probably benign Het
Rhebl1 C T 15: 98,779,034 (GRCm39) V17I probably benign Het
Rnf130 A T 11: 49,986,703 (GRCm39) D349V possibly damaging Het
Rprd1a A G 18: 24,642,952 (GRCm39) L60P probably damaging Het
Rspry1 T C 8: 95,356,420 (GRCm39) I25T probably damaging Het
Ruvbl2 C T 7: 45,071,621 (GRCm39) V421M probably damaging Het
Sap30 T C 8: 57,936,000 (GRCm39) N209D possibly damaging Het
Sfswap T C 5: 129,581,042 (GRCm39) probably benign Het
Slc1a2 G A 2: 102,586,352 (GRCm39) V319M probably damaging Het
Smad2 T C 18: 76,422,250 (GRCm39) probably benign Het
Spdya T C 17: 71,869,585 (GRCm39) probably null Het
Stk39 G A 2: 68,240,392 (GRCm39) T113M probably damaging Het
Tanc1 A G 2: 59,626,382 (GRCm39) probably benign Het
Tas2r122 T C 6: 132,688,774 (GRCm39) K40E probably damaging Het
Tph2 G T 10: 115,010,039 (GRCm39) probably benign Het
Trip12 G A 1: 84,729,269 (GRCm39) S1083F probably damaging Het
Tsc2 A T 17: 24,845,701 (GRCm39) C206S probably damaging Het
Tsc22d4 A G 5: 137,760,681 (GRCm39) Q34R possibly damaging Het
Uroc1 G T 6: 90,315,546 (GRCm39) M142I possibly damaging Het
Uso1 T C 5: 92,347,682 (GRCm39) S766P probably benign Het
Usp21 G A 1: 171,111,319 (GRCm39) probably benign Het
Usp48 T A 4: 137,360,437 (GRCm39) I658K possibly damaging Het
Vmn1r206 T C 13: 22,804,583 (GRCm39) H208R probably damaging Het
Vmn2r109 C T 17: 20,760,937 (GRCm39) A807T probably damaging Het
Zfp329 A T 7: 12,544,379 (GRCm39) C382S probably damaging Het
Zfp341 A G 2: 154,487,988 (GRCm39) E817G probably benign 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
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
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'- ACCTGCATCAGGTTAAATCTTGCCAC -3'
(R):5'- AGCTCCTCGTAGAGGATGAAGACCAC -3'

Sequencing Primer
(F):5'- TTGCCACCTCATTAATAGGAGC -3'
(R):5'- TGAAGACCACCTGGAAACAG -3'
Posted On 2013-06-11