Incidental Mutation 'IGL01070:Vps54'
ID52223
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 #IGL01070
Quality Score
Status
Chromosome11
Chromosomal Location21239281-21321136 bp(+) (GRCm38)
Type of Mutationmissense
DNA Base Change (assembly) T to A at 21312268 bp
ZygosityHeterozygous
Amino Acid Change Valine to Aspartic acid at position 626 (V626D)
Ref Sequence ENSEMBL: ENSMUSP00000116739 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000006221] [ENSMUST00000109578] [ENSMUST00000132017]
Predicted Effect probably damaging
Transcript: ENSMUST00000006221
AA Change: V788D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: V788D

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 probably damaging
Transcript: ENSMUST00000109578
AA Change: V776D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: V776D

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 probably damaging
Transcript: ENSMUST00000132017
AA Change: V626D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: V626D

DomainStartEndE-ValueType
Pfam:DUF2450 72 238 1.4e-12 PFAM
Pfam:Vps54 573 707 7.8e-64 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153159
Predicted Effect noncoding transcript
Transcript: ENSMUST00000153411
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
1110038F14Rik G A 15: 76,950,275 V124I probably damaging Het
Adamts5 T C 16: 85,863,133 H757R probably damaging Het
Aen G A 7: 78,907,302 M299I probably damaging Het
Akap3 A T 6: 126,865,879 E487V possibly damaging Het
Bicd2 T C 13: 49,378,316 S271P probably damaging Het
Cfap206 C T 4: 34,721,562 S162N probably damaging Het
Cma1 A G 14: 55,942,697 S71P probably benign Het
Cspp1 T C 1: 10,088,145 Y494H probably damaging Het
Cyp39a1 A G 17: 43,683,022 K191R probably benign Het
Efr3a G A 15: 65,853,078 V507I probably benign Het
Fam178b C T 1: 36,564,403 R489Q possibly damaging Het
Kcnj4 A G 15: 79,484,579 L400P probably benign Het
Kif27 A G 13: 58,344,093 Y411H probably damaging Het
Mstn A T 1: 53,061,997 I78L possibly damaging Het
Nrap T C 19: 56,329,084 D1377G probably damaging Het
Pramel5 T G 4: 144,271,272 Y467S probably damaging Het
Prkg1 G A 19: 30,569,343 probably benign Het
Rbfox1 A C 16: 7,306,443 S219R possibly damaging Het
Rfng T C 11: 120,783,952 N71D probably damaging Het
Rp1 T C 1: 4,345,238 I1884V probably damaging Het
Rptn T A 3: 93,398,176 Y939N possibly damaging Het
Sart1 A G 19: 5,383,951 V322A probably benign Het
Shank3 T C 15: 89,549,416 S1455P probably damaging Het
Smc5 T A 19: 23,231,601 R703W possibly damaging Het
Sptan1 G A 2: 30,014,173 probably null Het
Tecta T C 9: 42,395,003 D43G probably damaging Het
Tmem67 A T 4: 12,054,750 M685K probably benign Het
Trac A G 14: 54,220,766 T82A probably benign Het
Trank1 A G 9: 111,366,793 N1295S probably damaging Het
Ttc36 T C 9: 44,801,590 probably null Het
Utp18 A T 11: 93,869,848 S384T possibly damaging Het
Vmn1r64 C A 7: 5,883,942 A201S probably benign Het
Vmn2r26 A T 6: 124,061,607 I714F probably benign Het
Wapl T C 14: 34,745,622 probably benign Het
Yars2 C T 16: 16,306,542 R338* probably null Het
Other mutations in Vps54
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00272:Vps54 APN 11 21277909 missense possibly damaging 0.74
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 On2013-06-21