Incidental Mutation 'R4305:Vps9d1'
ID 324000
Institutional Source Beutler Lab
Gene Symbol Vps9d1
Ensembl Gene ENSMUSG00000001062
Gene Name VPS9 domain containing 1
Synonyms 2410004N05Rik, 1300018I17Rik
MMRRC Submission 041091-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R4305 (G1)
Quality Score 225
Status Validated
Chromosome 8
Chromosomal Location 123969095-123980961 bp(-) (GRCm39)
Type of Mutation intron
DNA Base Change (assembly) G to T at 123974976 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: ENSMUST00000149490
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137569
Predicted Effect noncoding transcript
Transcript: ENSMUST00000146136
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130275
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130965
Predicted Effect noncoding transcript
Transcript: ENSMUST00000129591
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155853
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
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 95.2%
Validation Efficiency 92% (36/39)
Allele List at MGI
Other mutations in this stock
Total: 26 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A830018L16Rik C A 1: 12,042,300 (GRCm39) S440* probably null Het
Abl2 T A 1: 156,469,133 (GRCm39) M695K probably damaging Het
Asap2 T C 12: 21,279,482 (GRCm39) I426T probably damaging Het
Atxn7l1 T C 12: 33,391,991 (GRCm39) M93T probably damaging Het
Ccr5 T C 9: 123,925,111 (GRCm39) L238P possibly damaging Het
Cd27 A G 6: 125,211,633 (GRCm39) V98A probably benign Het
Ceacam23 T A 7: 17,639,118 (GRCm39) Y372N probably benign Het
Cfap47 C G X: 78,541,635 (GRCm39) K469N probably damaging Het
Chrdl2 A G 7: 99,671,229 (GRCm39) T116A probably damaging Het
Epha6 T C 16: 60,346,883 (GRCm39) probably null Het
Garin1b A G 6: 29,326,611 (GRCm39) S243G probably damaging Het
Gart T C 16: 91,430,880 (GRCm39) E394G possibly damaging Het
Krt1 AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC AAGCTGCCACCCCCAAAGCCACCACCGCCGTAGCTGCCACCCCCAAAGCCACCAC 15: 101,758,813 (GRCm39) probably benign Het
Lpar6 G A 14: 73,476,381 (GRCm39) R114Q probably damaging Het
Med23 G T 10: 24,780,168 (GRCm39) E573* probably null Het
Mtch2 A G 2: 90,689,827 (GRCm39) I183V probably benign Het
Nlrp3 C T 11: 59,438,836 (GRCm39) R138* probably null Het
Notch1 T C 2: 26,367,936 (GRCm39) D657G probably damaging Het
Or4k37 A G 2: 111,159,643 (GRCm39) D293G probably null Het
Rbm20 A G 19: 53,831,691 (GRCm39) S642G probably damaging Het
Tex11 C A X: 99,977,021 (GRCm39) A487S possibly damaging Het
Ttn T C 2: 76,748,681 (GRCm39) S4123G probably benign Het
Ugt3a1 A C 15: 9,306,360 (GRCm39) S170R possibly damaging Het
Vmn2r71 G T 7: 85,273,360 (GRCm39) D725Y probably damaging Het
Yeats2 A G 16: 20,027,172 (GRCm39) T808A probably damaging Het
Zdhhc4 C T 5: 143,310,099 (GRCm39) 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
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
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'- GAGCAACTTGACTGCAGAACC -3'
(R):5'- AGCACTAATTAGGTGCTCTCTACC -3'

Sequencing Primer
(F):5'- TTGACTGCAGAACCTCCTGAG -3'
(R):5'- CTTCAAGTCTGCCTTCCTGAGTAAAG -3'
Posted On 2015-06-24