Incidental Mutation 'IGL02627:Vps29'
ID 301136
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Vps29
Ensembl Gene ENSMUSG00000029462
Gene Name VPS29 retromer complex component
Synonyms PEP11, 2010015D08Rik
Accession Numbers
Essential gene? Probably essential (E-score: 0.964) question?
Stock # IGL02627
Quality Score
Status
Chromosome 5
Chromosomal Location 122492432-122503047 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 122500908 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Proline at position 158 (S158P)
Ref Sequence ENSEMBL: ENSMUSP00000121020 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000031419] [ENSMUST00000111729] [ENSMUST00000117868] [ENSMUST00000118765] [ENSMUST00000118830] [ENSMUST00000145821] [ENSMUST00000155671] [ENSMUST00000154686]
AlphaFold Q9QZ88
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
SMART Domains Protein: ENSMUSP00000113345
Gene: ENSMUSG00000029462

DomainStartEndE-ValueType
Pfam:Metallophos_2 1 143 1.1e-23 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000118765
AA Change: F79S

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000112579
Gene: ENSMUSG00000029462
AA Change: F79S

DomainStartEndE-ValueType
PDB:1W24|A 1 65 7e-42 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000118830
AA Change: S162P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000113525
Gene: ENSMUSG00000029462
AA Change: S162P

DomainStartEndE-ValueType
Pfam:Metallophos_2 6 162 1.6e-23 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132785
Predicted Effect probably benign
Transcript: ENSMUST00000145821
SMART Domains Protein: ENSMUSP00000123593
Gene: ENSMUSG00000029462

DomainStartEndE-ValueType
Pfam:Metallophos_2 11 124 1e-13 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000155671
AA Change: S158P

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000121020
Gene: ENSMUSG00000029462
AA Change: S158P

DomainStartEndE-ValueType
Pfam:Metallophos_2 1 158 3.4e-24 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000199086
Predicted Effect probably benign
Transcript: ENSMUST00000154686
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: 28 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700001O22Rik T A 2: 30,685,777 (GRCm39) K353M probably damaging Het
Arhgap32 T C 9: 32,157,302 (GRCm39) Y100H probably damaging Het
Cdc45 C T 16: 18,617,479 (GRCm39) M200I probably benign Het
Cfap418 G A 4: 10,898,039 (GRCm39) C207Y probably damaging Het
Ckap5 A T 2: 91,406,366 (GRCm39) N752I probably damaging Het
Dgkz T A 2: 91,769,055 (GRCm39) probably benign Het
Egfr T A 11: 16,819,346 (GRCm39) V292E probably damaging Het
Gnb3 T C 6: 124,811,678 (GRCm39) T329A probably damaging Het
Igkv3-2 A T 6: 70,675,810 (GRCm39) T40S probably damaging Het
Kcnq2 T C 2: 180,724,120 (GRCm39) probably benign Het
Mbip T C 12: 56,382,590 (GRCm39) Q292R probably benign Het
Mgat5b T C 11: 116,874,442 (GRCm39) Y625H probably damaging Het
Ms4a4d A T 19: 11,525,987 (GRCm39) E40D probably damaging Het
Naip1 T C 13: 100,562,156 (GRCm39) E1003G possibly damaging Het
Ncf2 G A 1: 152,686,759 (GRCm39) probably benign Het
Nfkbiz A G 16: 55,636,714 (GRCm39) V529A probably damaging Het
Osr2 A G 15: 35,300,600 (GRCm39) N52S possibly damaging Het
Prag1 A G 8: 36,606,593 (GRCm39) D778G possibly damaging Het
Rsl1d1 G T 16: 11,012,415 (GRCm39) A337E possibly damaging Het
Sall3 A T 18: 81,015,576 (GRCm39) L784Q possibly damaging Het
Spen A G 4: 141,200,326 (GRCm39) I2744T probably damaging Het
Tfip11 A C 5: 112,477,679 (GRCm39) S145R possibly damaging Het
Tonsl T C 15: 76,518,295 (GRCm39) D559G probably damaging Het
Trmt5 A T 12: 73,328,229 (GRCm39) S325T probably damaging Het
Ubr1 A T 2: 120,771,472 (GRCm39) V472D probably damaging Het
Vmn1r30 T A 6: 58,412,746 (GRCm39) T29S probably benign Het
Wdr82 T C 9: 106,053,886 (GRCm39) V79A possibly damaging Het
Wfdc16 T A 2: 164,480,383 (GRCm39) E37D possibly damaging Het
Other mutations in Vps29
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01700:Vps29 APN 5 122,500,930 (GRCm39) missense probably damaging 1.00
IGL02716:Vps29 APN 5 122,500,129 (GRCm39) missense probably benign 0.20
R4807:Vps29 UTSW 5 122,500,951 (GRCm39) missense probably damaging 1.00
R5619:Vps29 UTSW 5 122,492,511 (GRCm39) utr 5 prime probably benign
R7431:Vps29 UTSW 5 122,492,541 (GRCm39) missense probably benign
R7866:Vps29 UTSW 5 122,500,180 (GRCm39) missense possibly damaging 0.91
R8167:Vps29 UTSW 5 122,500,877 (GRCm39) missense possibly damaging 0.95
R8971:Vps29 UTSW 5 122,498,212 (GRCm39) missense probably benign 0.38
Posted On 2015-04-16