Incidental Mutation 'IGL00272:Vps54'
ID14816
Institutional Source Australian Phenomics Network (link to record)
Gene Symbol Vps54
Ensembl Gene ENSMUSG00000020128
Gene NameVPS54 GARP complex subunit
Synonyms5330404P15Rik, wr, mSLP8, Vps54l
Accession Numbers
Is this an essential gene? Probably essential (E-score: 0.940) question?
Stock #IGL00272
Quality Score
Status
Chromosome11
Chromosomal Location21239281-21321136 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to A at 21277909 bp
ZygosityHeterozygous
Amino Acid Change Tyrosine to Asparagine at position 275 (Y275N)
Ref Sequence ENSEMBL: ENSMUSP00000105206 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006221] [ENSMUST00000109578] [ENSMUST00000132017]
Predicted Effect probably benign
Transcript: ENSMUST00000006221
AA Change: Y287N

PolyPhen 2 Score 0.184 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: Y287N

DomainStartEndE-ValueType
low complexity region 3 16 N/A INTRINSIC
Pfam:DUF2450 198 364 2.1e-12 PFAM
Pfam:Vps54 736 868 3.3e-56 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000109578
AA Change: Y275N

PolyPhen 2 Score 0.740 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: Y275N

DomainStartEndE-ValueType
low complexity region 3 16 N/A INTRINSIC
Pfam:DUF2450 186 352 2.3e-12 PFAM
Pfam:Vps54 723 857 1.6e-63 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000118219
Predicted Effect possibly damaging
Transcript: ENSMUST00000132017
AA Change: Y161N

PolyPhen 2 Score 0.495 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: Y161N

DomainStartEndE-ValueType
Pfam:DUF2450 72 238 1.4e-12 PFAM
Pfam:Vps54 573 707 7.8e-64 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000132146
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 encodes for a protein that in yeast forms part of a trimeric vacuolar-protein-sorting complex that is required for retrograde transport of proteins from prevacuoles to the late Golgi compartment. As in yeast, mammalian Vps54 proteins contain a coiled-coil region and dileucine motifs. Alternative splicing results in multiple transcript variants encoding different isoforms [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutants show progressive ataxia, tremors, and limb paralysis with degeneration of motor nerve cells of brainstem and spinal cord and atrophy of skeletal muscle beginning about 3-weeks of age. Mutants are sterile and most die by 3-months of age. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 35 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700030J22Rik A G 8: 116,973,540 V41A probably damaging Het
4932431P20Rik G T 7: 29,537,622 noncoding transcript Het
AI481877 A G 4: 59,086,961 F284L probably benign Het
Ankrd12 C T 17: 65,986,174 V755I probably benign Het
Arrdc3 T C 13: 80,890,572 S218P probably damaging Het
Bzw1 T C 1: 58,402,942 V292A possibly damaging Het
Cers2 T C 3: 95,321,900 Y228H probably damaging Het
Egf C T 3: 129,711,449 M625I probably benign Het
Fbxw8 A T 5: 118,068,097 H595Q probably benign Het
Fshr T A 17: 88,985,271 I660F probably benign Het
Gapdh C T 6: 125,162,507 V267M probably damaging Het
Ginm1 T C 10: 7,792,696 probably benign Het
Gja1 A G 10: 56,388,322 D259G probably benign Het
Gm21814 T A 6: 149,582,004 noncoding transcript Het
Gm26870 T C 9: 3,002,340 probably benign Het
Habp2 G A 19: 56,317,832 C482Y probably damaging Het
Knl1 A C 2: 119,064,083 N79T probably damaging Het
Lama3 G A 18: 12,491,548 C1450Y probably damaging Het
Lats2 T C 14: 57,691,569 T950A probably benign Het
Map2k2 T A 10: 81,121,073 M95K probably damaging Het
Med12l T A 3: 59,042,336 I160N probably damaging Het
Olfr1158 A T 2: 87,990,438 D109V probably damaging Het
Olfr1160 A G 2: 88,006,644 S45P probably damaging Het
Pes1 T C 11: 3,976,803 S362P probably damaging Het
Pih1h3b A G X: 140,105,962 I197V probably benign Het
Ppp6r2 G T 15: 89,285,813 A844S probably benign Het
Rnf130 A G 11: 50,093,796 I308V probably damaging Het
Scn11a T C 9: 119,816,603 N95S probably damaging Het
Skint2 A G 4: 112,624,212 T91A probably damaging Het
Smg1 A G 7: 118,198,271 probably benign Het
Snapc1 A G 12: 73,968,374 probably null Het
Stard10 A T 7: 101,321,966 Y47F probably damaging Het
Tenm3 C T 8: 48,417,060 V233I probably damaging Het
Tex14 G A 11: 87,535,643 S1165N probably damaging Het
Unc5a A G 13: 54,995,820 I106V probably benign Het
Other mutations in Vps54
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01070:Vps54 APN 11 21312268 missense probably damaging 1.00
IGL01398:Vps54 APN 11 21295403 splice site probably benign
IGL01450:Vps54 APN 11 21291135 missense probably benign 0.00
IGL01611:Vps54 APN 11 21311082 missense probably damaging 1.00
IGL01801:Vps54 APN 11 21275131 critical splice donor site probably null
IGL01872:Vps54 APN 11 21306940 missense probably damaging 0.99
IGL02071:Vps54 APN 11 21275071 missense probably null 0.00
IGL02186:Vps54 APN 11 21306947 missense probably damaging 1.00
IGL03358:Vps54 APN 11 21268799 missense probably damaging 1.00
R0031:Vps54 UTSW 11 21312899 missense probably damaging 1.00
R0147:Vps54 UTSW 11 21300259 missense probably benign 0.02
R0158:Vps54 UTSW 11 21306962 missense probably damaging 1.00
R0385:Vps54 UTSW 11 21306381 missense possibly damaging 0.94
R0420:Vps54 UTSW 11 21311071 splice site probably benign
R0582:Vps54 UTSW 11 21300137 missense probably damaging 1.00
R0602:Vps54 UTSW 11 21306434 missense possibly damaging 0.92
R1051:Vps54 UTSW 11 21278001 frame shift probably null
R1280:Vps54 UTSW 11 21277868 missense possibly damaging 0.88
R1720:Vps54 UTSW 11 21306519 missense probably damaging 1.00
R1875:Vps54 UTSW 11 21300251 missense probably benign 0.00
R1883:Vps54 UTSW 11 21312967 missense possibly damaging 0.91
R1971:Vps54 UTSW 11 21292051 missense probably damaging 1.00
R2063:Vps54 UTSW 11 21277955 missense probably damaging 1.00
R2171:Vps54 UTSW 11 21298810 missense probably benign 0.16
R2518:Vps54 UTSW 11 21306394 missense probably benign 0.01
R3801:Vps54 UTSW 11 21268832 missense probably benign 0.00
R4049:Vps54 UTSW 11 21300183 missense probably benign 0.00
R4108:Vps54 UTSW 11 21312877 missense probably benign 0.02
R4560:Vps54 UTSW 11 21312260 missense possibly damaging 0.91
R4668:Vps54 UTSW 11 21299989 missense probably benign 0.04
R4772:Vps54 UTSW 11 21312952 missense probably damaging 1.00
R5061:Vps54 UTSW 11 21319881 utr 3 prime probably benign
R5611:Vps54 UTSW 11 21311130 missense possibly damaging 0.65
R5638:Vps54 UTSW 11 21308799 missense probably damaging 1.00
R5670:Vps54 UTSW 11 21264864 missense probably damaging 1.00
R7095:Vps54 UTSW 11 21271720 missense probably benign 0.12
R7175:Vps54 UTSW 11 21315028 critical splice donor site probably null
R7179:Vps54 UTSW 11 21298791 missense probably damaging 1.00
R7269:Vps54 UTSW 11 21277670 splice site probably null
R7286:Vps54 UTSW 11 21275005 missense probably benign 0.30
R7344:Vps54 UTSW 11 21274999 missense probably damaging 1.00
R7552:Vps54 UTSW 11 21298831 missense probably benign 0.08
R7897:Vps54 UTSW 11 21263307 missense probably benign 0.02
R7980:Vps54 UTSW 11 21263307 missense probably benign 0.02
R8011:Vps54 UTSW 11 21275095 missense probably damaging 0.99
Z1177:Vps54 UTSW 11 21263206 start gained probably benign
Posted On2012-12-06