Mutagenetix > Incidental Mutation

Incidental Mutation 'R1720:Vps54'

191394

Institutional Source

Beutler Lab

Gene Symbol

Vps54

Ensembl Gene

ENSMUSG00000020128

Gene Name

VPS54 GARP complex subunit

Synonyms

5330404P15Rik, Vps54l, mSLP8, wr

MMRRC Submission

039752-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.933) question?

Stock #

R1720 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

21189281-21271136 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 21256519 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 663 (F663L)

Ref Sequence

ENSEMBL: ENSMUSP00000105206 (fasta)

Gene Model

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

AlphaFold

Q5SPW0

Predicted Effect

probably damaging
Transcript: ENSMUST00000006221
AA Change: F675L

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: F675L

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 damaging
Transcript: ENSMUST00000109578
AA Change: F663L

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

SMART Domains

Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: F663L

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: F513L

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: F513L

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

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.7%
20x: 93.8%

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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acot5	A	G	12: 84,122,655 (GRCm39)	D413G	probably benign	Het
Actr5	G	T	2: 158,478,057 (GRCm39)	V476F	possibly damaging	Het
Adhfe1	G	A	1: 9,637,125 (GRCm39)	D426N	probably benign	Het
Adra1a	T	C	14: 66,875,727 (GRCm39)	L234P	probably damaging	Het
Akap9	G	T	5: 4,022,791 (GRCm39)	V1207L	possibly damaging	Het
Anapc2	A	G	2: 25,164,724 (GRCm39)	D36G	probably benign	Het
Apol8	A	G	15: 77,633,566 (GRCm39)	S337P	possibly damaging	Het
Asxl3	A	T	18: 22,585,492 (GRCm39)	D139V	probably damaging	Het
Atp13a4	A	T	16: 29,227,746 (GRCm39)	V1037E	probably damaging	Het
Baat	A	T	4: 49,490,231 (GRCm39)	F284L	probably benign	Het
Bltp3b	T	C	10: 89,618,448 (GRCm39)	V141A	probably damaging	Het
C1qtnf6	A	T	15: 78,411,640 (GRCm39)	F40Y	probably damaging	Het
Caskin2	G	A	11: 115,693,608 (GRCm39)	H508Y	probably damaging	Het
Cass4	A	T	2: 172,269,654 (GRCm39)	I579F	probably damaging	Het
Cdk15	A	G	1: 59,328,917 (GRCm39)	Y277C	probably damaging	Het
Cit	G	A	5: 116,105,956 (GRCm39)	D947N	probably damaging	Het
Clint1	T	A	11: 45,778,237 (GRCm39)	I126K	probably damaging	Het
Col6a4	C	T	9: 105,903,671 (GRCm39)	G1640E	probably damaging	Het
Ddx10	T	C	9: 53,149,371 (GRCm39)	K119E	probably damaging	Het
Dennd1a	G	A	2: 37,690,209 (GRCm39)	Q964*	probably null	Het
Dnhd1	T	C	7: 105,343,035 (GRCm39)	F1460L	probably benign	Het
Edc3	T	C	9: 57,655,462 (GRCm39)		probably null	Het
Edn1	A	G	13: 42,458,826 (GRCm39)	E163G	probably benign	Het
Efl1	A	T	7: 82,332,929 (GRCm39)	D317V	possibly damaging	Het
Elapor2	T	G	5: 9,478,407 (GRCm39)	C424G	probably damaging	Het
F2	A	T	2: 91,459,175 (GRCm39)	Y430*	probably null	Het
Faap100	C	T	11: 120,265,407 (GRCm39)	V490M	probably damaging	Het
Fuz	G	T	7: 44,546,415 (GRCm39)	G104W	probably damaging	Het
Greb1l	C	A	18: 10,553,848 (GRCm39)	H1616Q	probably benign	Het
Grm1	G	T	10: 10,622,538 (GRCm39)		probably null	Het
Gucy2d	G	T	7: 98,126,437 (GRCm39)	A1098S	probably benign	Het
H1f0	T	A	15: 78,913,195 (GRCm39)	S92T	possibly damaging	Het
Hbb-bt	T	A	7: 103,463,083 (GRCm39)		probably benign	Het
Heg1	G	A	16: 33,527,549 (GRCm39)	A170T	probably benign	Het
Hspa4l	A	T	3: 40,736,049 (GRCm39)	K578*	probably null	Het
Ikbke	A	G	1: 131,186,947 (GRCm39)	S582P	possibly damaging	Het
Itga6	T	A	2: 71,650,510 (GRCm39)	F185L	probably damaging	Het
Itgal	T	A	7: 126,906,099 (GRCm39)	D396E	probably benign	Het
Kif5b	T	C	18: 6,213,427 (GRCm39)	H687R	probably benign	Het
Kmt2c	T	C	5: 25,504,182 (GRCm39)	N3709D	probably benign	Het
Lipf	A	T	19: 33,943,066 (GRCm39)	K125*	probably null	Het
Lrif1	A	T	3: 106,640,452 (GRCm39)	E512D	probably damaging	Het
Matn2	T	A	15: 34,345,420 (GRCm39)	Y142*	probably null	Het
Med13l	A	G	5: 118,880,060 (GRCm39)	T1051A	probably damaging	Het
Mpp3	T	A	11: 101,916,582 (GRCm39)	M1L	possibly damaging	Het
Mro	C	T	18: 74,009,806 (GRCm39)	S159L	probably benign	Het
Myh15	T	A	16: 48,913,145 (GRCm39)	D367E	probably damaging	Het
Myo1g	T	C	11: 6,462,490 (GRCm39)	Q547R	probably benign	Het
Neb	T	C	2: 52,097,733 (GRCm39)	I902M	probably benign	Het
Nsd1	G	A	13: 55,394,711 (GRCm39)	D771N	probably damaging	Het
Or10x4	A	G	1: 174,219,486 (GRCm39)	I284V	probably benign	Het
Or14a256	T	C	7: 86,265,664 (GRCm39)	N63S	probably damaging	Het
Or2a20	T	C	6: 43,194,494 (GRCm39)	S216P	probably damaging	Het
Or4e5	A	C	14: 52,728,051 (GRCm39)	Y40*	probably null	Het
Or8b48	C	T	9: 38,492,585 (GRCm39)	T4I	probably benign	Het
Penk	A	G	4: 4,134,240 (GRCm39)	Y136H	probably damaging	Het
Prdm6	C	T	18: 53,673,272 (GRCm39)	S144L	probably benign	Het
Ptprq	T	A	10: 107,522,155 (GRCm39)	I599F	probably damaging	Het
Racgap1	A	T	15: 99,526,650 (GRCm39)	C304*	probably null	Het
Rbp3	T	C	14: 33,678,866 (GRCm39)	V938A	probably benign	Het
Rpp30	A	G	19: 36,071,827 (GRCm39)	K132E	probably damaging	Het
Rxfp2	A	T	5: 149,966,564 (GRCm39)	R101*	probably null	Het
Ryr1	A	T	7: 28,801,295 (GRCm39)	V823E	probably damaging	Het
S100pbp	A	T	4: 129,075,886 (GRCm39)	D146E	probably damaging	Het
Sdr9c7	T	A	10: 127,738,127 (GRCm39)	V135E	probably damaging	Het
Serpinb12	A	G	1: 106,874,344 (GRCm39)	D23G	probably damaging	Het
Serpinf1	T	A	11: 75,304,807 (GRCm39)	T185S	probably null	Het
Slc23a1	A	C	18: 35,758,904 (GRCm39)	C96G	possibly damaging	Het
Slc5a4a	C	T	10: 76,025,103 (GRCm39)		probably null	Het
Spmap1	A	G	11: 97,662,435 (GRCm39)	F146L	probably damaging	Het
Suco	A	T	1: 161,661,623 (GRCm39)	L936Q	probably damaging	Het
Tmem144	T	C	3: 79,732,606 (GRCm39)	Y224C	probably damaging	Het
Tpm4	T	A	8: 72,898,598 (GRCm39)		probably null	Het
Ttn	T	C	2: 76,560,414 (GRCm39)	E29329G	probably damaging	Het
Txn1	T	C	4: 57,943,922 (GRCm39)	I101V	probably benign	Het
Ube2o	A	T	11: 116,435,433 (GRCm39)	C452S	probably benign	Het
Uxs1	A	T	1: 43,804,081 (GRCm39)	I278N	probably damaging	Het
Wdfy3	CG	C	5: 102,074,391 (GRCm39)		probably null	Het
Zc3h11a	A	G	1: 133,549,439 (GRCm39)	S741P	probably damaging	Het
Zdbf2	G	A	1: 63,342,436 (GRCm39)	V272I	possibly damaging	Het
Zdhhc24	A	G	19: 4,928,979 (GRCm39)	N68S	probably damaging	Het
Znfx1	A	T	2: 166,885,986 (GRCm39)	L858*	probably null	Het

Other mutations in Vps54

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00272:Vps54	APN	11	21,227,909 (GRCm39)	missense	possibly damaging	0.74
IGL01070:Vps54	APN	11	21,262,268 (GRCm39)	missense	probably damaging	1.00
IGL01398:Vps54	APN	11	21,245,403 (GRCm39)	splice site	probably benign
IGL01450:Vps54	APN	11	21,241,135 (GRCm39)	missense	probably benign	0.00
IGL01611:Vps54	APN	11	21,261,082 (GRCm39)	missense	probably damaging	1.00
IGL01801:Vps54	APN	11	21,225,131 (GRCm39)	critical splice donor site	probably null
IGL01872:Vps54	APN	11	21,256,940 (GRCm39)	missense	probably damaging	0.99
IGL02071:Vps54	APN	11	21,225,071 (GRCm39)	missense	probably null	0.00
IGL02186:Vps54	APN	11	21,256,947 (GRCm39)	missense	probably damaging	1.00
IGL03358:Vps54	APN	11	21,218,799 (GRCm39)	missense	probably damaging	1.00
muddle	UTSW	11	21,227,670 (GRCm39)	splice site	probably null
R0031:Vps54	UTSW	11	21,262,899 (GRCm39)	missense	probably damaging	1.00
R0147:Vps54	UTSW	11	21,250,259 (GRCm39)	missense	probably benign	0.02
R0158:Vps54	UTSW	11	21,256,962 (GRCm39)	missense	probably damaging	1.00
R0385:Vps54	UTSW	11	21,256,381 (GRCm39)	missense	possibly damaging	0.94
R0420:Vps54	UTSW	11	21,261,071 (GRCm39)	splice site	probably benign
R0582:Vps54	UTSW	11	21,250,137 (GRCm39)	missense	probably damaging	1.00
R0602:Vps54	UTSW	11	21,256,434 (GRCm39)	missense	possibly damaging	0.92
R1051:Vps54	UTSW	11	21,228,001 (GRCm39)	frame shift	probably null
R1280:Vps54	UTSW	11	21,227,868 (GRCm39)	missense	possibly damaging	0.88
R1875:Vps54	UTSW	11	21,250,251 (GRCm39)	missense	probably benign	0.00
R1883:Vps54	UTSW	11	21,262,967 (GRCm39)	missense	possibly damaging	0.91
R1971:Vps54	UTSW	11	21,242,051 (GRCm39)	missense	probably damaging	1.00
R2063:Vps54	UTSW	11	21,227,955 (GRCm39)	missense	probably damaging	1.00
R2171:Vps54	UTSW	11	21,248,810 (GRCm39)	missense	probably benign	0.16
R2518:Vps54	UTSW	11	21,256,394 (GRCm39)	missense	probably benign	0.01
R3801:Vps54	UTSW	11	21,218,832 (GRCm39)	missense	probably benign	0.00
R4049:Vps54	UTSW	11	21,250,183 (GRCm39)	missense	probably benign	0.00
R4108:Vps54	UTSW	11	21,262,877 (GRCm39)	missense	probably benign	0.02
R4560:Vps54	UTSW	11	21,262,260 (GRCm39)	missense	possibly damaging	0.91
R4668:Vps54	UTSW	11	21,249,989 (GRCm39)	missense	probably benign	0.04
R4772:Vps54	UTSW	11	21,262,952 (GRCm39)	missense	probably damaging	1.00
R5061:Vps54	UTSW	11	21,269,881 (GRCm39)	utr 3 prime	probably benign
R5611:Vps54	UTSW	11	21,261,130 (GRCm39)	missense	possibly damaging	0.65
R5638:Vps54	UTSW	11	21,258,799 (GRCm39)	missense	probably damaging	1.00
R5670:Vps54	UTSW	11	21,214,864 (GRCm39)	missense	probably damaging	1.00
R7095:Vps54	UTSW	11	21,221,720 (GRCm39)	missense	probably benign	0.12
R7175:Vps54	UTSW	11	21,265,028 (GRCm39)	critical splice donor site	probably null
R7179:Vps54	UTSW	11	21,248,791 (GRCm39)	missense	probably damaging	1.00
R7269:Vps54	UTSW	11	21,227,670 (GRCm39)	splice site	probably null
R7286:Vps54	UTSW	11	21,225,005 (GRCm39)	missense	probably benign	0.30
R7344:Vps54	UTSW	11	21,224,999 (GRCm39)	missense	probably damaging	1.00
R7552:Vps54	UTSW	11	21,248,831 (GRCm39)	missense	probably benign	0.08
R7897:Vps54	UTSW	11	21,213,307 (GRCm39)	missense	probably benign	0.02
R8011:Vps54	UTSW	11	21,225,095 (GRCm39)	missense	probably damaging	0.99
R8193:Vps54	UTSW	11	21,242,045 (GRCm39)	missense	probably benign	0.00
R8282:Vps54	UTSW	11	21,250,464 (GRCm39)	intron	probably benign
R8534:Vps54	UTSW	11	21,227,706 (GRCm39)	missense	probably benign	0.05
R8559:Vps54	UTSW	11	21,214,815 (GRCm39)	missense	probably damaging	1.00
R9034:Vps54	UTSW	11	21,213,273 (GRCm39)	missense	probably benign	0.29
R9096:Vps54	UTSW	11	21,227,913 (GRCm39)	missense	possibly damaging	0.90
R9253:Vps54	UTSW	11	21,258,771 (GRCm39)	missense	probably benign
R9359:Vps54	UTSW	11	21,242,108 (GRCm39)	missense	probably benign
R9367:Vps54	UTSW	11	21,250,234 (GRCm39)	missense	probably benign	0.00
Z1177:Vps54	UTSW	11	21,213,206 (GRCm39)	start gained	probably benign

Predicted Primers

PCR Primer
(F):5'- GACCGGCTTTAGACATCTTCAGCTC -3'
(R):5'- GGCACATCTCAGGATCAGTCGTTAG -3'

Sequencing Primer
(F):5'- GTAGCAGTTACTAAGCTCCGTCAG -3'
(R):5'- TGTCTCTTAGCCTAGCCAAAATCAG -3'

Posted On

2014-05-14