Incidental Mutation 'R7690:Gapvd1'
ID 593316
Institutional Source Beutler Lab
Gene Symbol Gapvd1
Ensembl Gene ENSMUSG00000026867
Gene Name GTPase activating protein and VPS9 domains 1
Synonyms 2010005B09Rik, 4432404J10Rik
MMRRC Submission 045754-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R7690 (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 G at 34619134 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Proline at position 80 (T80P)
Ref Sequence ENSEMBL: ENSMUSP00000099864 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028224] [ENSMUST00000102800] [ENSMUST00000113099] [ENSMUST00000142436]
AlphaFold Q6PAR5
Predicted Effect possibly damaging
Transcript: ENSMUST00000028224
AA Change: T80P

PolyPhen 2 Score 0.680 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000028224
Gene: ENSMUSG00000026867
AA Change: T80P

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 possibly damaging
Transcript: ENSMUST00000102800
AA Change: T80P

PolyPhen 2 Score 0.680 (Sensitivity: 0.86; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000099864
Gene: ENSMUSG00000026867
AA Change: T80P

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 possibly damaging
Transcript: ENSMUST00000113099
AA Change: T80P

PolyPhen 2 Score 0.552 (Sensitivity: 0.88; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000108723
Gene: ENSMUSG00000026867
AA Change: T80P

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: ENSMUST00000113103
SMART Domains Protein: ENSMUSP00000108727
Gene: ENSMUSG00000026867

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 benign
Transcript: ENSMUST00000137528
SMART Domains Protein: ENSMUSP00000120138
Gene: ENSMUSG00000026867

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 possibly damaging
Transcript: ENSMUST00000142436
AA Change: T80P

PolyPhen 2 Score 0.552 (Sensitivity: 0.88; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000126225
Gene: ENSMUSG00000026867
AA Change: T80P

DomainStartEndE-ValueType
SCOP:d1wer__ 95 135 6e-4 SMART
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.8%
  • 20x: 99.3%
Validation Efficiency 97% (57/59)
Allele List at MGI
Other mutations in this stock
Total: 59 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca12 T A 1: 71,353,313 (GRCm39) T710S probably benign Het
Adgrl2 A G 3: 148,522,934 (GRCm39) L430P Het
Agap1 T C 1: 89,770,793 (GRCm39) S648P probably benign Het
Alox5 T C 6: 116,392,417 (GRCm39) H368R probably damaging Het
Ano2 T C 6: 125,990,161 (GRCm39) F761L probably damaging Het
Aox4 T C 1: 58,303,076 (GRCm39) V1169A probably damaging Het
Apbb1ip T A 2: 22,706,996 (GRCm39) M11K unknown Het
Arl5a G T 2: 52,302,077 (GRCm39) H112Q possibly damaging Het
Ccdc18 C T 5: 108,376,528 (GRCm39) T1323I probably benign Het
Cmtm5 G A 14: 55,173,938 (GRCm39) probably benign Het
Cul2 T C 18: 3,419,420 (GRCm39) Y194H probably benign Het
Daglb T C 5: 143,479,938 (GRCm39) I415T possibly damaging Het
Ddx28 A G 8: 106,736,963 (GRCm39) V365A probably damaging Het
Dnah6 T C 6: 73,146,063 (GRCm39) probably null Het
Eppk1 T A 15: 75,995,946 (GRCm39) T312S probably benign Het
Erich4 C A 7: 25,314,710 (GRCm39) V68L possibly damaging Het
Fam171a2 G A 11: 102,328,660 (GRCm39) P700S probably benign Het
Fat3 T C 9: 15,909,477 (GRCm39) N2175S probably damaging Het
Fcrl6 T G 1: 172,426,223 (GRCm39) R191S probably damaging Het
Fpgt A G 3: 154,793,467 (GRCm39) S187P probably damaging Het
Gclm A G 3: 122,039,705 (GRCm39) N24S probably damaging Het
Gdf15 A G 8: 71,083,997 (GRCm39) I89T possibly damaging Het
Gpn2 A G 4: 133,318,693 (GRCm39) E306G probably damaging Het
Iars2 A T 1: 185,053,194 (GRCm39) L359Q probably damaging Het
Kbtbd4 T G 2: 90,736,240 (GRCm39) C84G possibly damaging Het
Manea A G 4: 26,327,910 (GRCm39) V377A probably benign Het
Map4 C T 9: 109,828,861 (GRCm39) T82I probably damaging Het
Mocos C T 18: 24,797,082 (GRCm39) H81Y probably damaging Het
Mtx1 T A 3: 89,120,088 (GRCm39) T87S Het
Muc6 G C 7: 141,217,659 (GRCm39) P2338R probably damaging Het
Myom2 A T 8: 15,161,717 (GRCm39) probably null Het
Mzt1 C T 14: 99,278,024 (GRCm39) C48Y probably damaging Het
Nlrp9b C A 7: 19,758,295 (GRCm39) P511T probably benign Het
Noc2l A G 4: 156,322,088 (GRCm39) E135G probably benign Het
Nova1 G A 12: 46,767,549 (GRCm39) P124L unknown Het
Pax8 T A 2: 24,331,682 (GRCm39) T134S probably benign Het
Pde4a T A 9: 21,077,300 (GRCm39) L26Q probably damaging Het
Pde6b G A 5: 108,567,384 (GRCm39) E254K probably damaging Het
Pdlim7 A G 13: 55,656,744 (GRCm39) I70T probably damaging Het
Pinx1 T A 14: 64,101,660 (GRCm39) probably null Het
Pomt2 C A 12: 87,177,141 (GRCm39) R352L probably damaging Het
Rapgef5 G A 12: 117,685,105 (GRCm39) V519I possibly damaging Het
Rnps1 A G 17: 24,637,168 (GRCm39) E16G unknown Het
Slc4a5 T C 6: 83,262,854 (GRCm39) F782S probably damaging Het
Snap91 A G 9: 86,707,031 (GRCm39) V253A possibly damaging Het
Syce3 T C 15: 89,281,544 (GRCm39) M32V possibly damaging Het
Tcaf3 C A 6: 42,574,069 (GRCm39) V48L probably damaging Het
Tenm4 T C 7: 96,512,740 (GRCm39) V1366A probably benign Het
Tnxb G A 17: 34,908,494 (GRCm39) M1382I probably benign Het
Tnxb G A 17: 34,908,501 (GRCm39) G1385R probably damaging Het
Top3a G T 11: 60,647,206 (GRCm39) L238I probably damaging Het
Trim9 A T 12: 70,295,117 (GRCm39) N742K probably benign Het
Trp63 T A 16: 25,695,483 (GRCm39) Y482N unknown Het
Ttc23 T G 7: 67,319,918 (GRCm39) F192V possibly damaging Het
Uck1 A G 2: 32,148,184 (GRCm39) V180A probably benign Het
Vwa5b1 G A 4: 138,318,244 (GRCm39) T541I probably damaging Het
Zfp456 G T 13: 67,514,913 (GRCm39) H264Q probably damaging Het
Zfpm2 T G 15: 40,818,162 (GRCm39) V165G possibly damaging Het
Zup1 C T 10: 33,806,151 (GRCm39) probably null 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
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'- TGCATAATACAGTTGCCATACAAGG -3'
(R):5'- AGGTATGGCGGTCTTTACTCAC -3'

Sequencing Primer
(F):5'- TTGCCATACAAGGAGGTAAAAAC -3'
(R):5'- CTCAGAGTTTAGCAATTCAAGGAG -3'
Posted On 2019-11-12