Incidental Mutation 'R5647:Vps9d1'
ID 441223
Institutional Source Beutler Lab
Gene Symbol Vps9d1
Ensembl Gene ENSMUSG00000001062
Gene Name VPS9 domain containing 1
Synonyms 2410004N05Rik, 1300018I17Rik
MMRRC Submission 043295-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R5647 (G1)
Quality Score 225
Status Validated
Chromosome 8
Chromosomal Location 123969095-123980961 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 123975598 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Glutamine at position 149 (L149Q)
Ref Sequence ENSEMBL: ENSMUSP00000122184 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000117643] [ENSMUST00000118279] [ENSMUST00000122363] [ENSMUST00000127664] [ENSMUST00000155869]
AlphaFold Q8C190
Predicted Effect probably damaging
Transcript: ENSMUST00000117643
AA Change: L149Q

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000113748
Gene: ENSMUSG00000001062
AA Change: L149Q

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 damaging
Transcript: ENSMUST00000118279
AA Change: L149Q

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000113634
Gene: ENSMUSG00000001062
AA Change: L149Q

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 damaging
Transcript: ENSMUST00000122363
AA Change: L149Q

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000113575
Gene: ENSMUSG00000001062
AA Change: L149Q

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: ENSMUST00000137569
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130965
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146136
Predicted Effect probably damaging
Transcript: ENSMUST00000155869
AA Change: L149Q

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000122184
Gene: ENSMUSG00000001062
AA Change: L149Q

DomainStartEndE-ValueType
low complexity region 96 108 N/A INTRINSIC
coiled coil region 187 223 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155853
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130275
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129591
Predicted Effect noncoding transcript
Transcript: ENSMUST00000149490
Meta Mutation Damage Score 0.1997 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.0%
  • 20x: 94.7%
Validation Efficiency 95% (55/58)
Allele List at MGI
Other mutations in this stock
Total: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700010L04Rik T C 7: 82,505,606 (GRCm39) noncoding transcript Het
9330159F19Rik A T 10: 29,101,250 (GRCm39) D541V probably damaging Het
Abcc5 T C 16: 20,218,597 (GRCm39) I262V probably damaging Het
Acvr1c T A 2: 58,185,976 (GRCm39) D169V probably damaging Het
Aldh16a1 A G 7: 44,803,889 (GRCm39) V6A probably benign Het
Brd10 A G 19: 29,731,210 (GRCm39) S601P possibly damaging Het
Cd36 A C 5: 18,019,763 (GRCm39) S113A probably damaging Het
Cdt1 G T 8: 123,296,947 (GRCm39) R247L possibly damaging Het
Ces4a G A 8: 105,872,712 (GRCm39) V322M probably benign Het
Cngb3 A T 4: 19,364,266 (GRCm39) T157S possibly damaging Het
Cpped1 T C 16: 11,646,010 (GRCm39) probably benign Het
Ctr9 G T 7: 110,654,751 (GRCm39) R1094L unknown Het
Cyld A T 8: 89,461,554 (GRCm39) I664L probably benign Het
Dvl2 C T 11: 69,900,275 (GRCm39) P690S possibly damaging Het
Fbxo7 A C 10: 85,864,974 (GRCm39) E94D probably damaging Het
Fstl5 A C 3: 76,496,399 (GRCm39) K387N probably damaging Het
Gm9845 A C 3: 39,412,520 (GRCm39) noncoding transcript Het
Hk1 T C 10: 62,111,523 (GRCm39) D746G probably damaging Het
Lmbr1 A G 5: 29,468,391 (GRCm39) probably null Het
Lrp2 C T 2: 69,350,258 (GRCm39) A705T probably null Het
Lrrc37 T C 11: 103,508,300 (GRCm39) probably benign Het
Mybpc3 A G 2: 90,952,067 (GRCm39) probably null Het
Myo15b T A 11: 115,762,337 (GRCm39) L1219Q probably damaging Het
Naa35 G A 13: 59,770,680 (GRCm39) probably benign Het
Or4g16 G T 2: 111,137,392 (GRCm39) A281S possibly damaging Het
Or5b111 A T 19: 13,291,553 (GRCm39) I32N probably damaging Het
Or5b113 T C 19: 13,342,541 (GRCm39) V183A probably damaging Het
Pcdhb18 G A 18: 37,623,537 (GRCm39) R289Q probably benign Het
Pcnt T C 10: 76,221,675 (GRCm39) T1984A probably benign Het
Plcg1 T C 2: 160,593,588 (GRCm39) L251P probably benign Het
Plin1 T A 7: 79,371,320 (GRCm39) D468V probably benign Het
Pmp2 A G 3: 10,248,845 (GRCm39) V12A probably benign Het
Rnf19a T A 15: 36,266,109 (GRCm39) probably benign Het
Rnf214 G A 9: 45,779,344 (GRCm39) Q469* probably null Het
Rrp1b T G 17: 32,274,985 (GRCm39) probably benign Het
Rtl1 C T 12: 109,561,113 (GRCm39) R242Q unknown Het
Sema3e A T 5: 14,275,567 (GRCm39) E224V probably damaging Het
Sphkap A G 1: 83,385,720 (GRCm39) S5P probably damaging Het
Stab1 A C 14: 30,879,397 (GRCm39) Y694* probably null Het
Stambpl1 T C 19: 34,211,686 (GRCm39) L249P probably benign Het
Thap4 A T 1: 93,642,665 (GRCm39) H515Q probably damaging Het
Ticam1 TCACACA TCACA 17: 56,577,629 (GRCm39) probably null Het
Uaca A G 9: 60,779,380 (GRCm39) R1256G probably benign Het
Usp17lb T A 7: 104,489,881 (GRCm39) N348Y possibly damaging Het
Vmn1r42 A G 6: 89,822,314 (GRCm39) I85T probably benign Het
Zdhhc17 A T 10: 110,809,694 (GRCm39) I153N probably damaging Het
Zfp207 G A 11: 80,283,959 (GRCm39) S293N possibly damaging Het
Zfp346 A G 13: 55,270,170 (GRCm39) D198G probably damaging Het
Zfp953 A T 13: 67,491,536 (GRCm39) C139S possibly damaging 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
R4707:Vps9d1 UTSW 8 123,975,351 (GRCm39) critical splice donor site probably benign
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
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'- TCCATCATCTGCCGCTGTAG -3'
(R):5'- CTAGATCAGACTTCTGCATCCCG -3'

Sequencing Primer
(F):5'- TGTAGAGACAGGGTCTAAGGG -3'
(R):5'- CGTTCCTCCTCACCGACG -3'
Posted On 2016-11-08