Incidental Mutation 'IGL02716:Vps29'
ID304750
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Vps29
Ensembl Gene ENSMUSG00000029462
Gene NameVPS29 retromer complex component
SynonymsPEP11, 2010015D08Rik
Accession Numbers
Is this an essential gene? Probably essential (E-score: 0.959) question?
Stock #IGL02716
Quality Score
Status
Chromosome5
Chromosomal Location122354369-122364984 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) A to G at 122362066 bp
ZygosityHeterozygous
Amino Acid Change Threonine to Alanine at position 85 (T85A)
Ref Sequence ENSEMBL: ENSMUSP00000123593 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031419] [ENSMUST00000111729] [ENSMUST00000117868] [ENSMUST00000118765] [ENSMUST00000118830] [ENSMUST00000145821] [ENSMUST00000154686] [ENSMUST00000155671]
Predicted Effect probably benign
Transcript: ENSMUST00000031419
SMART Domains Protein: ENSMUSP00000031419
Gene: ENSMUSG00000029463

DomainStartEndE-ValueType
Pfam:FAM216B 50 160 6e-49 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000111729
SMART Domains Protein: ENSMUSP00000107358
Gene: ENSMUSG00000029462

DomainStartEndE-ValueType
low complexity region 26 42 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000117868
AA Change: T76A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
SMART Domains Protein: ENSMUSP00000113345
Gene: ENSMUSG00000029462
AA Change: T76A

DomainStartEndE-ValueType
Pfam:Metallophos_2 1 143 1.1e-23 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000118765
SMART Domains Protein: ENSMUSP00000112579
Gene: ENSMUSG00000029462

DomainStartEndE-ValueType
PDB:1W24|A 1 65 7e-42 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000118830
AA Change: T80A

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000113525
Gene: ENSMUSG00000029462
AA Change: T80A

DomainStartEndE-ValueType
Pfam:Metallophos_2 6 162 1.6e-23 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132785
Predicted Effect probably benign
Transcript: ENSMUST00000145821
AA Change: T85A

PolyPhen 2 Score 0.203 (Sensitivity: 0.92; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000123593
Gene: ENSMUSG00000029462
AA Change: T85A

DomainStartEndE-ValueType
Pfam:Metallophos_2 11 124 1e-13 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000154686
Predicted Effect probably benign
Transcript: ENSMUST00000155671
AA Change: T76A

PolyPhen 2 Score 0.027 (Sensitivity: 0.95; Specificity: 0.81)
SMART Domains Protein: ENSMUSP00000121020
Gene: ENSMUSG00000029462
AA Change: T76A

DomainStartEndE-ValueType
Pfam:Metallophos_2 1 158 3.4e-24 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000199086
Coding Region Coverage
Validation Efficiency
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 that, when functionally impaired, disrupt the efficient delivery of vacuolar hydrolases. The protein encoded by this gene is a component of a large multimeric complex, termed the retromer complex, which is involved in retrograde transport of proteins from endosomes to the trans-Golgi network. This VPS protein may be involved in the formation of the inner shell of the retromer coat for retrograde vesicles leaving the prevacuolar compartment. Alternative splice variants encoding different isoforms and representing non-protein coding transcripts have been found for this gene. [provided by RefSeq, Aug 2013]
Allele List at MGI
Other mutations in this stock
Total: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acsl6 T C 11: 54,327,276 S212P probably benign Het
Ago2 C T 15: 73,111,727 R711Q possibly damaging Het
Akp3 A C 1: 87,125,479 D91A probably damaging Het
Arhgap12 T A 18: 6,111,857 Q169L possibly damaging Het
Aspm A G 1: 139,479,687 Y2104C probably damaging Het
Baz2b G A 2: 59,962,524 S420L possibly damaging Het
Cenpo T C 12: 4,215,390 N210S possibly damaging Het
Chadl T C 15: 81,695,915 N40D probably damaging Het
Crebbp T C 16: 4,114,878 E586G probably benign Het
Cts7 T A 13: 61,356,608 Q47L probably benign Het
Cyp2c40 C A 19: 39,807,536 D133Y possibly damaging Het
Dnah3 A T 7: 119,937,023 M3679K probably damaging Het
Dym T C 18: 75,286,683 Y642H probably damaging Het
Efr3b T C 12: 3,984,627 D65G probably damaging Het
Elmo1 T A 13: 20,449,502 F445I probably damaging Het
Epdr1 C T 13: 19,594,570 V119M probably benign Het
Epha4 G T 1: 77,380,965 R799S probably damaging Het
Esyt3 A T 9: 99,317,224 V778E probably damaging Het
F10 A T 8: 13,048,177 K127* probably null Het
Fcgbp G A 7: 28,101,434 E1302K probably damaging Het
Fer1l4 A G 2: 156,029,715 F1382L probably damaging Het
Fhad1 T C 4: 141,918,331 I318V possibly damaging Het
Fscn2 A T 11: 120,366,724 T304S probably benign Het
Gab1 A T 8: 80,769,694 L659Q probably damaging Het
Gm4845 A C 1: 141,256,838 noncoding transcript Het
Gm572 A G 4: 148,654,870 M52V probably benign Het
Hmgcr T C 13: 96,660,012 probably null Het
Kcnk5 T C 14: 20,181,428 T9A probably damaging Het
Krt87 A C 15: 101,434,604 F243V possibly damaging Het
Mast1 G T 8: 84,935,723 P52Q probably damaging Het
Mcf2l A T 8: 12,997,277 Q211L probably benign Het
Mtus2 C A 5: 148,236,310 P968T probably benign Het
Mylk2 T C 2: 152,922,153 *614R probably null Het
Myo15b A T 11: 115,883,709 E2049V probably benign Het
Myo6 A T 9: 80,269,694 H581L probably damaging Het
Numb A T 12: 83,801,208 S241T possibly damaging Het
Olfr1265 G T 2: 90,037,794 V292L probably benign Het
Olfr1283 A T 2: 111,368,781 I50F probably benign Het
Olfr338 A G 2: 36,377,343 D189G possibly damaging Het
Phldb2 A G 16: 45,801,590 S676P probably damaging Het
Rttn G A 18: 89,048,417 E1196K possibly damaging Het
Skiv2l2 T G 13: 112,883,146 D810A probably benign Het
Slc13a3 G A 2: 165,406,715 P548S unknown Het
Slc2a7 A G 4: 150,160,010 probably benign Het
Slc37a1 T C 17: 31,328,161 S261P possibly damaging Het
Spryd3 T A 15: 102,133,461 Y42F possibly damaging Het
Srrm3 A G 5: 135,854,433 probably null Het
Stambp G A 6: 83,556,390 T297I probably damaging Het
Sypl T A 12: 32,967,669 Y129N probably damaging Het
Syt14 G A 1: 192,980,535 P368S possibly damaging Het
Tas2r122 T C 6: 132,711,264 D222G probably damaging Het
Tead2 C A 7: 45,232,296 Y79* probably null Het
Tmem251 A G 12: 102,744,829 T104A probably benign Het
Uso1 T C 5: 92,173,935 V229A probably damaging Het
Vmn1r238 A G 18: 3,123,124 S97P probably damaging Het
Vmn2r82 T A 10: 79,377,844 V88D probably benign Het
Wdr90 T A 17: 25,857,220 S500C probably damaging Het
Zfp958 G A 8: 4,625,967 probably null Het
Other mutations in Vps29
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01700:Vps29 APN 5 122362867 missense probably damaging 1.00
IGL02627:Vps29 APN 5 122362845 missense probably benign 0.00
R4807:Vps29 UTSW 5 122362888 missense probably damaging 1.00
R5619:Vps29 UTSW 5 122354448 utr 5 prime probably benign
R7431:Vps29 UTSW 5 122354478 missense probably benign
R7866:Vps29 UTSW 5 122362117 missense possibly damaging 0.91
R8167:Vps29 UTSW 5 122362814 missense possibly damaging 0.95
Posted On2015-04-16