Mutagenetix > Incidental Mutations

Incidental Mutation 'R1883:Vps54'

209285

Institutional Source

Beutler Lab

Gene Symbol

Vps54

Ensembl Gene

ENSMUSG00000020128

Gene Name

VPS54 GARP complex subunit

Synonyms

5330404P15Rik, wr, mSLP8, Vps54l

MMRRC Submission

039904-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.898) question?

Stock #

R1883 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

21239281-21321136 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 21312967 bp

Zygosity

Heterozygous

Amino Acid Change

Threonine to Serine at position 685 (T685S)

Ref Sequence

ENSEMBL: ENSMUSP00000116739 (fasta)

Gene Model

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

Predicted Effect

probably benign
Transcript: ENSMUST00000006221
AA Change: T847S

PolyPhen 2 Score 0.388 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: T847S

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

possibly damaging
Transcript: ENSMUST00000109578
AA Change: T835S

PolyPhen 2 Score 0.822 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: T835S

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

possibly damaging
Transcript: ENSMUST00000132017
AA Change: T685S

PolyPhen 2 Score 0.913 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: T685S

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: ENSMUST00000153159

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000153411

Coding Region Coverage

1x: 97.3%
3x: 96.8%
10x: 95.4%
20x: 93.0%

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: 89 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921507P07Rik	T	C	6: 50,574,453	T339A	probably benign	Het
Ano9	T	C	7: 141,102,331	E677G	probably benign	Het
Auh	G	A	13: 52,835,496	P308L	probably benign	Het
Brs3	T	C	X: 57,047,089	I311T	probably benign	Het
Capn9	A	G	8: 124,611,558	K552R	probably benign	Het
Catsperg1	C	T	7: 29,182,236		probably null	Het
Cdc16	A	G	8: 13,775,738	N449D	probably damaging	Het
Cdyl2	A	T	8: 116,595,163	N208K	probably damaging	Het
Cnot4	C	T	6: 35,078,157	V66I	probably damaging	Het
Cntn4	A	G	6: 106,679,392	T885A	probably benign	Het
Col20a1	C	T	2: 180,992,910	T131I	possibly damaging	Het
Crybg2	C	A	4: 134,074,283	S918*	probably null	Het
Dact2	A	T	17: 14,197,823	S207T	possibly damaging	Het
Dbnl	G	A	11: 5,799,247	G356E	probably benign	Het
Ddx18	C	A	1: 121,567,916		probably benign	Het
Dis3	A	T	14: 99,091,469	H282Q	probably benign	Het
Dnah3	T	C	7: 120,077,919	D453G	probably benign	Het
Dst	T	C	1: 34,189,308	V1994A	possibly damaging	Het
Dusp8	C	T	7: 142,084,348		probably null	Het
Eipr1	A	T	12: 28,766,851	H69L	possibly damaging	Het
Eml1	A	G	12: 108,463,652	R65G	probably damaging	Het
Epha7	C	T	4: 28,950,362	H722Y	possibly damaging	Het
Epyc	A	T	10: 97,675,833	K229N	possibly damaging	Het
Extl1	A	G	4: 134,364,606	I312T	probably benign	Het
F13a1	G	C	13: 36,989,007	A133G	probably benign	Het
Fam185a	G	T	5: 21,425,244	C26F	possibly damaging	Het
Fam186b	T	C	15: 99,278,798	N737S	probably damaging	Het
Fam78b	A	G	1: 167,001,602	I13V	probably benign	Het
Fat1	A	T	8: 45,051,147	Q4559L	probably benign	Het
Fnip1	T	C	11: 54,515,547	S1157P	probably damaging	Het
Foxj3	A	C	4: 119,610,029	M190L	probably benign	Het
Gm5096	T	C	18: 87,756,545	L64P	probably damaging	Het
Heatr3	T	C	8: 88,144,593	Y192H	possibly damaging	Het
Hexdc	T	A	11: 121,207,698	S3T	probably benign	Het
Klf3	C	T	5: 64,822,881	P5S	probably damaging	Het
Klf9	C	T	19: 23,164,737	S187L	probably damaging	Het
Krt9	T	C	11: 100,188,697	H623R	unknown	Het
Krtap2-4	G	C	11: 99,614,679		probably benign	Het
Lmtk3	T	C	7: 45,786,849	Y84H	probably damaging	Het
Mroh3	G	T	1: 136,206,993	A166D	probably damaging	Het
Musk	C	A	4: 58,373,189	P697T	probably benign	Het
Nek9	A	G	12: 85,332,556	L192P	probably damaging	Het
Nipbl	A	C	15: 8,327,132	F1590C	probably damaging	Het
Nrk	G	T	X: 139,007,173	V1455F	probably damaging	Het
Nsun3	T	C	16: 62,735,293	D290G	probably damaging	Het
Obscn	T	C	11: 59,078,203	T222A	probably damaging	Het
Olfr446	T	C	6: 42,927,830	S200P	probably damaging	Het
Olfr583	T	C	7: 103,051,982	I228T	probably benign	Het
Olfr6	T	C	7: 106,956,774	H54R	probably benign	Het
Osbpl11	T	G	16: 33,214,353	H237Q	probably benign	Het
Pde10a	A	T	17: 8,978,944	T671S	possibly damaging	Het
Pkd2	A	T	5: 104,483,228	N506I	probably damaging	Het
Ppp3cb	A	G	14: 20,523,845	V274A	possibly damaging	Het
Prex1	T	C	2: 166,583,272	D938G	probably benign	Het
Ptch1	G	A	13: 63,512,027	Q1134*	probably null	Het
Rasgrf2	A	G	13: 91,969,030	V820A	probably benign	Het
Rimbp2	C	T	5: 128,803,934	V137M	possibly damaging	Het
Rpa1	A	G	11: 75,318,483	V137A	probably benign	Het
Rps6ka1	A	C	4: 133,864,043	I299S	probably damaging	Het
Scn3b	A	C	9: 40,279,373		probably null	Het
Sdha	A	T	13: 74,333,136	I317N	probably damaging	Het
Serpina1d	T	A	12: 103,765,778	D274V	possibly damaging	Het
Sik3	C	G	9: 46,221,089	H1276Q	probably benign	Het
Snx14	T	A	9: 88,402,261	E451D	probably benign	Het
Swt1	T	A	1: 151,423,533	K8*	probably null	Het
Tas1r3	G	T	4: 155,862,153	P332T	probably damaging	Het
Tas2r126	A	T	6: 42,435,027	T165S	probably benign	Het
Tecpr1	A	G	5: 144,206,529	V676A	probably benign	Het
Tg	A	G	15: 66,671,309	E24G	probably damaging	Het
Tlr7	C	T	X: 167,306,472	G673S	probably benign	Het
Tnxb	T	A	17: 34,689,565	D1520E	probably benign	Het
Trabd	A	G	15: 89,081,981	E47G	probably damaging	Het
Trim29	T	A	9: 43,311,405	I177N	probably damaging	Het
Ubxn2a	A	T	12: 4,894,563	L53*	probably null	Het
Ulk2	A	G	11: 61,830,612	L208P	probably damaging	Het
Unc80	G	A	1: 66,525,770	C872Y	possibly damaging	Het
Vac14	A	G	8: 110,711,687	H644R	probably damaging	Het
Vmn1r20	C	A	6: 57,432,321	H211N	probably benign	Het
Vmn1r31	C	T	6: 58,472,044	V279I	probably damaging	Het
Vmn2r18	G	T	5: 151,575,725	Q425K	probably benign	Het
Vmn2r60	T	C	7: 42,136,670	V299A	probably damaging	Het
Vwa5b1	A	G	4: 138,575,389	W932R	probably damaging	Het
Wdr53	A	T	16: 32,256,498	I174F	possibly damaging	Het
Zfp157	A	G	5: 138,444,840	D31G	probably damaging	Het
Zfp60	T	C	7: 27,750,010	L701P	probably benign	Het
Zfp609	A	T	9: 65,794,758	M204K	probably benign	Het
Zfp831	A	G	2: 174,704,077	H1325R	possibly damaging	Het
Zfp995	A	T	17: 21,880,641	I204N	probably benign	Het
Zp2	C	T	7: 120,133,401	D641N	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
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
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

Predicted Primers

PCR Primer
(F):5'- GTCCAGTGAGAAAGCAGTGTGC -3'
(R):5'- ATCCATTATCGCTACAAGCTTAGC -3'

Sequencing Primer
(F):5'- TGAAATATATTTTCTGCCATGGTGC -3'
(R):5'- CGCTACAAGCTTAGCTGAAATTTC -3'

Posted On

2014-06-30