Incidental Mutation 'R4707:Vps9d1'
ID 355334
Institutional Source Beutler Lab
Gene Symbol Vps9d1
Ensembl Gene ENSMUSG00000001062
Gene Name VPS9 domain containing 1
Synonyms 2410004N05Rik, 1300018I17Rik
MMRRC Submission 041955-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R4707 (G1)
Quality Score 225
Status Not validated
Chromosome 8
Chromosomal Location 123969095-123980961 bp(-) (GRCm39)
Type of Mutation critical splice donor site
DNA Base Change (assembly) G to A at 123975351 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000122184 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000117643] [ENSMUST00000118279] [ENSMUST00000122363] [ENSMUST00000127664] [ENSMUST00000155869]
AlphaFold Q8C190
Predicted Effect probably benign
Transcript: ENSMUST00000117643
SMART Domains Protein: ENSMUSP00000113748
Gene: ENSMUSG00000001062

DomainStartEndE-ValueType
low complexity region 96 108 N/A INTRINSIC
coiled coil region 187 220 N/A INTRINSIC
low complexity region 266 279 N/A INTRINSIC
low complexity region 442 453 N/A INTRINSIC
Pfam:VPS9 528 645 8.5e-27 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000118279
SMART Domains Protein: ENSMUSP00000113634
Gene: ENSMUSG00000001062

DomainStartEndE-ValueType
low complexity region 96 108 N/A INTRINSIC
coiled coil region 187 220 N/A INTRINSIC
low complexity region 266 279 N/A INTRINSIC
low complexity region 442 453 N/A INTRINSIC
Pfam:VPS9 528 645 1.2e-25 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000122363
SMART Domains Protein: ENSMUSP00000113575
Gene: ENSMUSG00000001062

DomainStartEndE-ValueType
low complexity region 96 108 N/A INTRINSIC
coiled coil region 187 220 N/A INTRINSIC
low complexity region 266 279 N/A INTRINSIC
low complexity region 442 453 N/A INTRINSIC
Pfam:VPS9 528 644 5.6e-27 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124508
Predicted Effect probably benign
Transcript: ENSMUST00000127664
SMART Domains Protein: ENSMUSP00000118564
Gene: ENSMUSG00000092329

DomainStartEndE-ValueType
Pfam:Glycos_transf_2 104 287 7.4e-31 PFAM
Pfam:Glyco_transf_7C 261 331 4.9e-8 PFAM
RICIN 406 531 9.28e-27 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000127978
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130965
Predicted Effect probably benign
Transcript: ENSMUST00000155869
SMART Domains Protein: ENSMUSP00000122184
Gene: ENSMUSG00000001062

DomainStartEndE-ValueType
low complexity region 96 108 N/A INTRINSIC
coiled coil region 187 223 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130275
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146136
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129591
Predicted Effect noncoding transcript
Transcript: ENSMUST00000149490
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137569
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155853
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.7%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 115 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700010I14Rik A G 17: 9,224,544 (GRCm39) K450R probably damaging Het
Abcd2 T C 15: 91,043,385 (GRCm39) D601G probably benign Het
Abcf3 A G 16: 20,367,808 (GRCm39) K56E possibly damaging Het
Acaca T C 11: 84,203,680 (GRCm39) V1477A probably damaging Het
Adamts20 G A 15: 94,231,528 (GRCm39) P887L possibly damaging Het
Ahnak T G 19: 8,994,099 (GRCm39) S5128A probably benign Het
Ahsa2 C A 11: 23,443,162 (GRCm39) V197F probably benign Het
Ak9 C A 10: 41,221,456 (GRCm39) H402N probably benign Het
Alpk1 G T 3: 127,481,241 (GRCm39) N175K possibly damaging Het
Als2 A G 1: 59,254,472 (GRCm39) V295A probably benign Het
Ankrd16 A G 2: 11,783,608 (GRCm39) D70G probably damaging Het
Apob A T 12: 8,056,205 (GRCm39) K1562N probably damaging Het
Arfgap2 C A 2: 91,100,316 (GRCm39) S250R probably damaging Het
Arhgef10l C T 4: 140,264,194 (GRCm39) M671I possibly damaging Het
Atrnl1 A G 19: 57,617,590 (GRCm39) I122V probably damaging Het
B4galnt2 C T 11: 95,766,923 (GRCm39) probably null Het
C8a A G 4: 104,713,618 (GRCm39) Y171H probably damaging Het
Cacnb4 A G 2: 52,364,927 (GRCm39) V112A probably benign Het
Capn9 G T 8: 125,340,195 (GRCm39) C566F possibly damaging Het
Ccdc88a T A 11: 29,397,956 (GRCm39) S230T probably benign Het
Cd300c2 A T 11: 114,887,811 (GRCm39) F197Y probably benign Het
Chd5 A G 4: 152,445,039 (GRCm39) Y340C probably damaging Het
Chrd A T 16: 20,557,558 (GRCm39) I726F possibly damaging Het
Chrna10 G A 7: 101,762,426 (GRCm39) P255S possibly damaging Het
Clasp1 T A 1: 118,470,927 (GRCm39) Y197* probably null Het
Cyp2c69 C G 19: 39,837,852 (GRCm39) G410A probably benign Het
Cyp2e1 G A 7: 140,343,821 (GRCm39) V20I possibly damaging Het
Dapp1 T C 3: 137,638,928 (GRCm39) D225G probably benign Het
Dnah5 A T 15: 28,372,521 (GRCm39) D2924V probably damaging Het
Efcab12 A T 6: 115,791,510 (GRCm39) L554Q possibly damaging Het
Emsy T C 7: 98,246,311 (GRCm39) T228A possibly damaging Het
Evc2 G A 5: 37,579,204 (GRCm39) V1106I probably benign Het
Exoc8 G T 8: 125,624,209 (GRCm39) Q53K possibly damaging Het
Fbn2 A T 18: 58,189,344 (GRCm39) V1594D probably damaging Het
Fer1l4 T C 2: 155,887,543 (GRCm39) Y551C possibly damaging Het
Fhip1a G T 3: 85,595,877 (GRCm39) T115K probably damaging Het
Fmnl3 A G 15: 99,221,362 (GRCm39) M481T probably benign Het
Fras1 A G 5: 96,883,097 (GRCm39) N2543S probably damaging Het
Fsd2 T C 7: 81,209,428 (GRCm39) D138G probably damaging Het
Gda C T 19: 21,405,992 (GRCm39) V5I probably benign Het
Glt8d2 A T 10: 82,496,583 (GRCm39) D158E probably damaging Het
Gpx6 C T 13: 21,496,434 (GRCm39) Q3* probably null Het
Greb1l A G 18: 10,532,922 (GRCm39) M830V probably benign Het
Hnrnpul1 A C 7: 25,426,258 (GRCm39) V531G probably damaging Het
Ifi206 A T 1: 173,308,432 (GRCm39) H521Q probably benign Het
Igsf3 G C 3: 101,365,410 (GRCm39) R1127P probably benign Het
Il1rl1 A G 1: 40,489,348 (GRCm39) R367G probably damaging Het
Islr T C 9: 58,064,970 (GRCm39) D179G possibly damaging Het
Jcad G T 18: 4,649,338 (GRCm39) E70* probably null Het
Kcnd2 T C 6: 21,723,211 (GRCm39) I467T probably benign Het
Lrrc27 A G 7: 138,822,614 (GRCm39) T502A probably benign Het
Lrrtm3 T A 10: 63,923,781 (GRCm39) H462L probably benign Het
Mbd5 T C 2: 49,140,168 (GRCm39) L44S probably damaging Het
Mccc1 C A 3: 36,030,022 (GRCm39) M429I probably damaging Het
Mgam A T 6: 40,691,566 (GRCm39) probably null Het
Mipep T A 14: 61,109,552 (GRCm39) I643N probably damaging Het
Mmrn1 A T 6: 60,965,457 (GRCm39) I1162L probably benign Het
Mrc2 G A 11: 105,239,257 (GRCm39) probably null Het
Mug1 G A 6: 121,861,600 (GRCm39) C1354Y probably damaging Het
Nbeal2 A T 9: 110,461,123 (GRCm39) S1647T probably benign Het
Ndufaf2 C G 13: 108,189,314 (GRCm39) A145P probably damaging Het
Nedd9 A T 13: 41,492,051 (GRCm39) probably null Het
Nr4a2 T A 2: 57,002,105 (GRCm39) H116L probably benign Het
Nwd2 A G 5: 63,951,665 (GRCm39) Y232C probably damaging Het
Odf4 A G 11: 68,817,514 (GRCm39) L58P probably damaging Het
Or2a20 T A 6: 43,193,883 (GRCm39) V12D probably benign Het
Or4a27 T A 2: 88,559,056 (GRCm39) M296L possibly damaging Het
Or4c116 A T 2: 88,942,576 (GRCm39) F93L probably damaging Het
Or4g17 T A 2: 111,209,990 (GRCm39) L215H probably damaging Het
Or7e165 C T 9: 19,694,596 (GRCm39) H18Y probably damaging Het
Or8g24 A G 9: 38,989,558 (GRCm39) V161A probably benign Het
Or8s5 G T 15: 98,238,659 (GRCm39) H70Q possibly damaging Het
Orc6 T A 8: 86,029,579 (GRCm39) I41K probably damaging Het
Pikfyve A G 1: 65,307,005 (GRCm39) T1798A probably benign Het
Prdx6b T C 2: 80,123,404 (GRCm39) L71P probably damaging Het
Prmt2 A G 10: 76,062,055 (GRCm39) I50T probably damaging Het
Ptdss1 T C 13: 67,143,482 (GRCm39) probably null Het
Pygl T C 12: 70,254,532 (GRCm39) T138A possibly damaging Het
Rab3c T C 13: 110,198,434 (GRCm39) E198G probably benign Het
Rbl2 A G 8: 91,812,196 (GRCm39) Y255C probably damaging Het
Rev3l T A 10: 39,699,393 (GRCm39) S1297T probably damaging Het
Rgma C A 7: 73,067,564 (GRCm39) T367K probably damaging Het
Rps6ka5 C T 12: 100,564,144 (GRCm39) probably null Het
Rslcan18 A T 13: 67,246,590 (GRCm39) C217S probably damaging Het
Rtp3 A G 9: 110,815,279 (GRCm39) probably benign Het
Ryr1 A T 7: 28,745,087 (GRCm39) N3848K probably damaging Het
Sema6a T A 18: 47,381,779 (GRCm39) T923S probably benign Het
Serpinb6d A T 13: 33,855,336 (GRCm39) T337S possibly damaging Het
Sf3b1 G A 1: 55,029,666 (GRCm39) T1112M probably damaging Het
Shroom3 G T 5: 93,090,945 (GRCm39) V1151F probably damaging Het
Sidt1 A T 16: 44,090,221 (GRCm39) Y369* probably null Het
Slc16a6 A G 11: 109,354,193 (GRCm39) S59P probably benign Het
Slc25a17 A C 15: 81,211,527 (GRCm39) L163W probably damaging Het
Slc44a3 T C 3: 121,320,723 (GRCm39) T93A possibly damaging Het
Sptbn1 T C 11: 30,087,197 (GRCm39) T1081A possibly damaging Het
Sptbn4 T C 7: 27,116,431 (GRCm39) D456G probably benign Het
Sycp1 C A 3: 102,760,805 (GRCm39) A703S possibly damaging Het
Tas2r118 T A 6: 23,969,225 (GRCm39) M279L probably benign Het
Tc2n T G 12: 101,660,832 (GRCm39) Q133H probably benign Het
Tctn1 A G 5: 122,399,468 (GRCm39) probably null Het
Tenm4 A C 7: 96,423,253 (GRCm39) K683Q probably damaging Het
Tex10 A T 4: 48,468,984 (GRCm39) S64T probably benign Het
Tex15 A G 8: 34,072,525 (GRCm39) T2691A probably benign Het
Tmem175 A T 5: 108,790,016 (GRCm39) T123S probably damaging Het
Tsc1 C A 2: 28,562,419 (GRCm39) S348R probably damaging Het
Ttll4 A T 1: 74,718,166 (GRCm39) T6S possibly damaging Het
Ttll8 A T 15: 88,801,293 (GRCm39) I465N probably damaging Het
Ubr3 A G 2: 69,768,714 (GRCm39) probably benign Het
Ugdh A T 5: 65,580,695 (GRCm39) probably null Het
Usp34 T C 11: 23,437,215 (GRCm39) L3326S probably damaging Het
Vmn2r125 A T 4: 156,702,276 (GRCm39) I21F probably damaging Het
Xab2 G A 8: 3,668,117 (GRCm39) R154C possibly damaging Het
Zbtb12 T C 17: 35,114,475 (GRCm39) S87P probably damaging Het
Zc3h12a A G 4: 125,014,686 (GRCm39) M266T probably damaging Het
Zfp108 G A 7: 23,959,837 (GRCm39) A143T probably benign Het
Other mutations in Vps9d1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00549:Vps9d1 APN 8 123,971,937 (GRCm39) missense probably damaging 1.00
IGL01112:Vps9d1 APN 8 123,972,769 (GRCm39) missense probably damaging 1.00
IGL01729:Vps9d1 APN 8 123,973,739 (GRCm39) missense probably damaging 1.00
R0568:Vps9d1 UTSW 8 123,973,487 (GRCm39) missense probably damaging 1.00
R1191:Vps9d1 UTSW 8 123,974,706 (GRCm39) missense possibly damaging 0.95
R1813:Vps9d1 UTSW 8 123,973,778 (GRCm39) missense probably damaging 0.99
R1896:Vps9d1 UTSW 8 123,973,778 (GRCm39) missense probably damaging 0.99
R2193:Vps9d1 UTSW 8 123,979,404 (GRCm39) missense probably damaging 1.00
R2256:Vps9d1 UTSW 8 123,971,860 (GRCm39) missense probably benign 0.18
R4305:Vps9d1 UTSW 8 123,974,976 (GRCm39) intron probably benign
R4458:Vps9d1 UTSW 8 123,974,487 (GRCm39) missense probably benign 0.30
R5366:Vps9d1 UTSW 8 123,971,853 (GRCm39) missense possibly damaging 0.89
R5392:Vps9d1 UTSW 8 123,980,752 (GRCm39) missense probably damaging 0.99
R5423:Vps9d1 UTSW 8 123,974,704 (GRCm39) critical splice donor site probably null
R5645:Vps9d1 UTSW 8 123,974,487 (GRCm39) missense probably benign 0.30
R5647:Vps9d1 UTSW 8 123,975,598 (GRCm39) missense probably damaging 1.00
R5695:Vps9d1 UTSW 8 123,973,655 (GRCm39) missense probably benign
R5908:Vps9d1 UTSW 8 123,973,563 (GRCm39) missense probably benign 0.28
R6061:Vps9d1 UTSW 8 123,972,410 (GRCm39) missense probably damaging 0.99
R6250:Vps9d1 UTSW 8 123,974,947 (GRCm39) critical splice acceptor site probably null
R6416:Vps9d1 UTSW 8 123,975,378 (GRCm39) missense probably damaging 1.00
R6747:Vps9d1 UTSW 8 123,980,746 (GRCm39) missense probably damaging 1.00
R7049:Vps9d1 UTSW 8 123,973,882 (GRCm39) nonsense probably null
R7584:Vps9d1 UTSW 8 123,977,456 (GRCm39) missense probably damaging 1.00
R8321:Vps9d1 UTSW 8 123,975,544 (GRCm39) missense possibly damaging 0.47
R9178:Vps9d1 UTSW 8 123,975,574 (GRCm39) missense probably damaging 0.97
R9218:Vps9d1 UTSW 8 123,977,674 (GRCm39) missense probably benign 0.12
R9366:Vps9d1 UTSW 8 123,974,486 (GRCm39) nonsense probably null
R9542:Vps9d1 UTSW 8 123,970,522 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GCTTTACTCAGGAAGGCAGACTTG -3'
(R):5'- AGGCCATGCAGAAGACATCG -3'

Sequencing Primer
(F):5'- CACCTAATTAGTGCTAGAGAGGAC -3'
(R):5'- CATGCAGAAGACATCGCTGGTG -3'
Posted On 2015-10-21