Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL01611:Vps54'

92085

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Vps54

Ensembl Gene

ENSMUSG00000020128

Gene Name

VPS54 GARP complex subunit

Synonyms

5330404P15Rik, wr, mSLP8, Vps54l

Accession Numbers

Essential gene?

Probably essential (E-score: 0.904) question?

Stock #

IGL01611

Quality Score

Status

Chromosome

Chromosomal Location

21239281-21321136 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 21311082 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Aspartic acid at position 583 (V583D)

Ref Sequence

ENSEMBL: ENSMUSP00000116739 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000006221] [ENSMUST00000109578] [ENSMUST00000132017]

AlphaFold

Q5SPW0

Predicted Effect

probably damaging
Transcript: ENSMUST00000006221
AA Change: V745D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: V745D

Domain	Start	End	E-Value	Type
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 benign
Transcript: ENSMUST00000109578
AA Change: V733D

PolyPhen 2 Score 0.109 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: V733D

Domain	Start	End	E-Value	Type
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: V583D

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: V583D

Domain	Start	End	E-Value	Type
Pfam:DUF2450	72	238	1.4e-12	PFAM
Pfam:Vps54	573	707	7.8e-64	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000143932

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: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930447C04Rik	A	G	12: 72,907,870	L209S	possibly damaging	Het
Abcc2	G	T	19: 43,826,629	V1152F	probably damaging	Het
Adam9	C	T	8: 24,967,196	V639I	probably benign	Het
Cdc6	A	G	11: 98,915,163	I388V	probably benign	Het
Chrm5	C	T	2: 112,480,306	W155*	probably null	Het
Chrna9	A	G	5: 65,970,944	D161G	probably damaging	Het
Det1	A	G	7: 78,827,954	V541A	possibly damaging	Het
Efhc1	G	T	1: 20,990,687	*649L	probably null	Het
Ehbp1	C	T	11: 22,172,883	V146M	probably damaging	Het
Enam	A	C	5: 88,503,749	D1039A	probably damaging	Het
Fam20b	A	T	1: 156,702,465	V133E	probably benign	Het
Frem2	T	A	3: 53,655,709	Q459L	probably benign	Het
Gapdhs	C	T	7: 30,730,441		probably benign	Het
Gm3404	T	A	5: 146,528,347	V299D	possibly damaging	Het
Gorasp2	C	A	2: 70,689,260	H310N	possibly damaging	Het
Gpr157	T	C	4: 150,101,637	S219P	possibly damaging	Het
Gpt2	T	A	8: 85,519,538	C375*	probably null	Het
Gtf2h3	T	C	5: 124,595,685	S274P	probably damaging	Het
Hmg20b	C	T	10: 81,347,475	V83M	probably benign	Het
Igf2r	G	T	17: 12,725,415	Y400*	probably null	Het
Ipo9	A	T	1: 135,386,693	W942R	possibly damaging	Het
Iqch	T	C	9: 63,496,237		probably null	Het
Kcnh3	T	C	15: 99,229,502	L393P	probably benign	Het
Kcnk12	T	A	17: 87,797,067	I130L	probably benign	Het
Lcorl	T	C	5: 45,747,092	T205A	probably damaging	Het
Lpar6	G	T	14: 73,239,438	A280S	probably damaging	Het
Mgarp	A	T	3: 51,389,149	V152E	probably damaging	Het
Pard3b	A	G	1: 62,637,862	D1184G	probably damaging	Het
Pcnt	A	G	10: 76,436,424		probably null	Het
Pde6b	A	G	5: 108,403,396	N182S	possibly damaging	Het
Pom121	T	C	5: 135,383,672	K516E	unknown	Het
Psmg2	G	A	18: 67,653,223	V218I	probably benign	Het
Ptpn18	T	C	1: 34,459,817		probably benign	Het
Rapgef5	C	T	12: 117,753,419		probably benign	Het
Ryr2	A	G	13: 11,591,316	L4460S	possibly damaging	Het
Sema6b	T	C	17: 56,129,969		probably null	Het
Serpinb6d	T	A	13: 33,666,392	C67*	probably null	Het
Sorbs2	T	G	8: 45,795,344	V510G	probably null	Het
Spic	T	A	10: 88,676,002	I131F	possibly damaging	Het
Spire2	T	C	8: 123,359,398	S290P	probably damaging	Het
Tas2r117	C	T	6: 132,803,484	S195F	probably benign	Het
Tas2r117	T	C	6: 132,803,487	V196A	probably damaging	Het
Tff1	C	T	17: 31,162,729	G58D	probably damaging	Het
Tmprss11g	T	C	5: 86,490,781	T283A	probably benign	Het
Toporsl	T	A	4: 52,610,794	L229H	probably damaging	Het
Vmn2r80	G	A	10: 79,171,654	G488D	probably damaging	Het
Vwa1	T	C	4: 155,770,798	E286G	possibly damaging	Het
Vwde	A	T	6: 13,219,978	I58N	probably damaging	Het
Zbtb11	T	C	16: 55,980,610	V109A	probably damaging	Het
Zfp319	C	T	8: 95,328,912	R221Q	probably benign	Het

Other mutations in Vps54

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00272:Vps54	APN	11	21277909	missense	possibly damaging	0.74
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
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
muddle	UTSW	11	21277670	splice site	probably null
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
R8011:Vps54	UTSW	11	21275095	missense	probably damaging	0.99
R8193:Vps54	UTSW	11	21292045	missense	probably benign	0.00
R8282:Vps54	UTSW	11	21300464	intron	probably benign
R8534:Vps54	UTSW	11	21277706	missense	probably benign	0.05
R8559:Vps54	UTSW	11	21264815	missense	probably damaging	1.00
R9034:Vps54	UTSW	11	21263273	missense	probably benign	0.29
R9096:Vps54	UTSW	11	21277913	missense	possibly damaging	0.90
R9253:Vps54	UTSW	11	21308771	missense	probably benign
R9359:Vps54	UTSW	11	21292108	missense	probably benign
R9367:Vps54	UTSW	11	21300234	missense	probably benign	0.00
Z1177:Vps54	UTSW	11	21263206	start gained	probably benign

Posted On

2013-12-09