Incidental Mutation 'R0118:Vps35'
ID 20929
Institutional Source Beutler Lab
Gene Symbol Vps35
Ensembl Gene ENSMUSG00000031696
Gene Name VPS35 retromer complex component
Synonyms Mem3
MMRRC Submission 038404-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0118 (G1)
Quality Score 222
Status Validated (trace)
Chromosome 8
Chromosomal Location 85987014-86026146 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 86021582 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Isoleucine at position 3 (T3I)
Ref Sequence ENSEMBL: ENSMUSP00000034131 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034131] [ENSMUST00000034132] [ENSMUST00000170141] [ENSMUST00000210146] [ENSMUST00000211396] [ENSMUST00000211597]
AlphaFold Q9EQH3
Predicted Effect probably benign
Transcript: ENSMUST00000034131
AA Change: T3I

PolyPhen 2 Score 0.039 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000034131
Gene: ENSMUSG00000031696
AA Change: T3I

DomainStartEndE-ValueType
Pfam:Vps35 15 753 6.8e-303 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000034132
SMART Domains Protein: ENSMUSP00000034132
Gene: ENSMUSG00000031697

DomainStartEndE-ValueType
Pfam:ORC6 6 108 1.5e-16 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000170141
SMART Domains Protein: ENSMUSP00000126925
Gene: ENSMUSG00000031697

DomainStartEndE-ValueType
PDB:3M03|C 18 111 2e-51 PDB
Predicted Effect noncoding transcript
Transcript: ENSMUST00000209228
Predicted Effect noncoding transcript
Transcript: ENSMUST00000209733
Predicted Effect probably benign
Transcript: ENSMUST00000210146
Predicted Effect noncoding transcript
Transcript: ENSMUST00000211154
Predicted Effect noncoding transcript
Transcript: ENSMUST00000211479
Predicted Effect probably benign
Transcript: ENSMUST00000211396
Predicted Effect probably benign
Transcript: ENSMUST00000211597
Meta Mutation Damage Score 0.0825 question?
Coding Region Coverage
  • 1x: 98.8%
  • 3x: 97.2%
  • 10x: 89.3%
  • 20x: 67.4%
Validation Efficiency 98% (50/51)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to a group of vacuolar protein sorting (VPS) genes. The encoded protein is a component of a large multimeric complex, termed the retromer complex, involved in retrograde transport of proteins from endosomes to the trans-Golgi network. The close structural similarity between the yeast and human proteins that make up this complex suggests a similarity in function. Expression studies in yeast and mammalian cells indicate that this protein interacts directly with VPS35, which serves as the core of the retromer complex. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a gene trap allele die prior to E10. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 49 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adamts15 T C 9: 30,823,040 (GRCm39) R343G probably damaging Het
Asxl2 T G 12: 3,546,923 (GRCm39) V569G probably damaging Het
Azin2 A C 4: 128,843,430 (GRCm39) H85Q probably damaging Het
Cacna1a C T 8: 85,262,712 (GRCm39) R324C probably damaging Het
Ccr3 C A 9: 123,829,647 (GRCm39) Y327* probably null Het
Cers2 T C 3: 95,227,537 (GRCm39) F55S probably benign Het
Cic C T 7: 24,985,459 (GRCm39) S301L probably damaging Het
Cntnap2 T C 6: 45,037,326 (GRCm39) probably null Het
Cpn2 T C 16: 30,079,186 (GRCm39) R172G probably benign Het
Ctdnep1 T C 11: 69,879,557 (GRCm39) probably null Het
Dennd3 T A 15: 73,436,925 (GRCm39) Y1051N probably damaging Het
Dmap1 T G 4: 117,533,680 (GRCm39) Y196S probably damaging Het
Entpd7 G A 19: 43,692,751 (GRCm39) W102* probably null Het
Frem2 A T 3: 53,442,664 (GRCm39) C2624* probably null Het
Gdpd3 A G 7: 126,370,165 (GRCm39) Y238C probably damaging Het
Gjb3 A G 4: 127,220,451 (GRCm39) V27A probably damaging Het
Kat6b T C 14: 21,720,042 (GRCm39) F1465L probably damaging Het
Klra17 A T 6: 129,808,552 (GRCm39) M227K probably benign Het
Map6 A G 7: 98,966,824 (GRCm39) D348G possibly damaging Het
Mapkbp1 T C 2: 119,855,696 (GRCm39) S1472P probably benign Het
Megf6 C A 4: 154,339,098 (GRCm39) P545Q probably damaging Het
Mertk C T 2: 128,601,086 (GRCm39) R357W probably damaging Het
Mesd T A 7: 83,544,835 (GRCm39) I104N probably damaging Het
Mrm3 T A 11: 76,140,781 (GRCm39) V263E possibly damaging Het
Ndst4 T A 3: 125,405,210 (GRCm39) Y488* probably null Het
Nfat5 C T 8: 108,065,707 (GRCm39) R156W probably damaging Het
Nfs1 T C 2: 155,976,444 (GRCm39) H150R probably damaging Het
Odad3 A T 9: 21,906,353 (GRCm39) N224K probably benign Het
Or1n1b A G 2: 36,780,035 (GRCm39) M275T probably benign Het
Or8b56 T C 9: 38,739,154 (GRCm39) S50P possibly damaging Het
Or8g19 T A 9: 39,055,399 (GRCm39) M1K probably null Het
Or9q1 A G 19: 13,804,929 (GRCm39) F277S possibly damaging Het
Pcdh8 T C 14: 80,004,848 (GRCm39) Y1059C probably damaging Het
Pik3r5 T A 11: 68,381,306 (GRCm39) L164Q probably damaging Het
Polr3g T C 13: 81,824,240 (GRCm39) probably benign Het
Ppm1e T A 11: 87,122,564 (GRCm39) K464N probably benign Het
Rims1 T C 1: 22,416,631 (GRCm39) T1037A probably damaging Het
Rpgrip1l A T 8: 91,996,750 (GRCm39) I108N probably damaging Het
Sfi1 CCTCTC CCTCTCTC 11: 3,127,419 (GRCm39) probably benign Het
Spem1 T C 11: 69,712,371 (GRCm39) K98E possibly damaging Het
St7l T C 3: 104,796,619 (GRCm39) V237A probably damaging Het
Tbc1d16 T C 11: 119,048,642 (GRCm39) H337R probably damaging Het
Tbc1d32 T A 10: 55,893,701 (GRCm39) I1291F probably benign Het
Tnfaip6 G T 2: 51,933,827 (GRCm39) E61* probably null Het
Trib2 A T 12: 15,843,929 (GRCm39) W102R probably damaging Het
Uimc1 G T 13: 55,233,457 (GRCm39) N66K probably damaging Het
Vmn1r63 T A 7: 5,805,838 (GRCm39) T265S probably benign Het
Yeats2 T A 16: 19,975,692 (GRCm39) L63* probably null Het
Zfp282 A G 6: 47,869,866 (GRCm39) R304G probably benign Het
Other mutations in Vps35
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01745:Vps35 APN 8 86,000,092 (GRCm39) splice site probably benign
IGL02604:Vps35 APN 8 86,013,018 (GRCm39) missense probably damaging 1.00
IGL03278:Vps35 APN 8 86,021,590 (GRCm39) unclassified probably benign
IGL03326:Vps35 APN 8 86,001,526 (GRCm39) nonsense probably null
PIT4151001:Vps35 UTSW 8 86,010,677 (GRCm39) missense possibly damaging 0.95
R0226:Vps35 UTSW 8 86,000,204 (GRCm39) missense probably damaging 0.97
R1079:Vps35 UTSW 8 86,005,683 (GRCm39) missense probably damaging 1.00
R1477:Vps35 UTSW 8 86,014,429 (GRCm39) missense probably damaging 1.00
R1969:Vps35 UTSW 8 86,005,623 (GRCm39) missense possibly damaging 0.90
R2082:Vps35 UTSW 8 85,990,094 (GRCm39) missense possibly damaging 0.95
R2156:Vps35 UTSW 8 86,013,129 (GRCm39) missense probably benign 0.06
R2341:Vps35 UTSW 8 86,001,443 (GRCm39) splice site probably benign
R3752:Vps35 UTSW 8 86,001,460 (GRCm39) missense probably benign 0.34
R4589:Vps35 UTSW 8 86,014,331 (GRCm39) missense probably damaging 1.00
R4745:Vps35 UTSW 8 85,987,891 (GRCm39) missense probably benign
R4790:Vps35 UTSW 8 86,005,486 (GRCm39) splice site probably null
R4827:Vps35 UTSW 8 86,000,186 (GRCm39) missense possibly damaging 0.94
R4953:Vps35 UTSW 8 86,008,475 (GRCm39) missense probably damaging 1.00
R6277:Vps35 UTSW 8 85,987,857 (GRCm39) missense possibly damaging 0.80
R6291:Vps35 UTSW 8 86,026,086 (GRCm39) start codon destroyed probably benign 0.07
R6434:Vps35 UTSW 8 86,000,124 (GRCm39) missense possibly damaging 0.53
R7175:Vps35 UTSW 8 85,990,189 (GRCm39) splice site probably null
R7206:Vps35 UTSW 8 86,014,350 (GRCm39) missense probably damaging 1.00
R7309:Vps35 UTSW 8 86,001,596 (GRCm39) missense probably benign 0.05
R7479:Vps35 UTSW 8 85,997,434 (GRCm39) missense probably benign 0.17
R7547:Vps35 UTSW 8 85,989,999 (GRCm39) missense probably damaging 1.00
R7761:Vps35 UTSW 8 86,010,707 (GRCm39) missense possibly damaging 0.91
R7812:Vps35 UTSW 8 86,010,818 (GRCm39) missense probably benign 0.01
R8312:Vps35 UTSW 8 86,001,498 (GRCm39) missense possibly damaging 0.65
R8356:Vps35 UTSW 8 85,987,934 (GRCm39) missense possibly damaging 0.63
R8403:Vps35 UTSW 8 86,001,487 (GRCm39) missense probably benign
R8456:Vps35 UTSW 8 85,987,934 (GRCm39) missense possibly damaging 0.63
R9189:Vps35 UTSW 8 86,007,898 (GRCm39) missense possibly damaging 0.67
R9615:Vps35 UTSW 8 86,010,633 (GRCm39) missense probably benign 0.00
X0020:Vps35 UTSW 8 85,990,050 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GAGTCTCTACAGTGCTAAGCACAGATG -3'
(R):5'- CCTACCACAGGTTTCTTTGATGCCAG -3'

Sequencing Primer
(F):5'- GAGCAGAGATGACATAATCTTACAAC -3'
(R):5'- gcctgcttccatctccc -3'
Posted On 2013-04-11