Mutagenetix > Incidental Mutation

Incidental Mutation 'R7269:Vps54'

574628

Institutional Source

Beutler Lab

Gene Symbol

Vps54

Ensembl Gene

ENSMUSG00000020128

Gene Name

VPS54 GARP complex subunit

Synonyms

5330404P15Rik, Vps54l, mSLP8, wr

MMRRC Submission

045320-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.933) question?

Stock #

R7269 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

21189281-21271136 bp(+) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

T to A at 21227670 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000116739 (fasta)

Gene Model

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

AlphaFold

Q5SPW0

Predicted Effect

probably null
Transcript: ENSMUST00000006221

SMART Domains

Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128

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 null
Transcript: ENSMUST00000006221

SMART Domains

Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128

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 null
Transcript: ENSMUST00000109578

SMART Domains

Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128

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 null
Transcript: ENSMUST00000109578

SMART Domains

Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128

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 null
Transcript: ENSMUST00000132017

SMART Domains

Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128

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

Predicted Effect

probably null
Transcript: ENSMUST00000132017

SMART Domains

Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128

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

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.2%

Validation Efficiency

98% (85/87)

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: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2700062C07Rik	A	T	18: 24,606,013 (GRCm39)	N36I	probably damaging	Het
A430033K04Rik	T	A	5: 138,645,014 (GRCm39)	Y300N	possibly damaging	Het
Adipor2	T	C	6: 119,347,205 (GRCm39)	Q26R	probably benign	Het
Ahnak	T	A	19: 8,983,981 (GRCm39)	M1755K	probably damaging	Het
Ahnak2	A	T	12: 112,780,802 (GRCm38)	V70E		Het
AI837181	C	A	19: 5,476,462 (GRCm39)	S208R	probably damaging	Het
Arhgap35	T	G	7: 16,295,652 (GRCm39)	M1138L	probably benign	Het
Card14	T	G	11: 119,228,573 (GRCm39)	L633R	probably damaging	Het
Carmil3	A	G	14: 55,731,352 (GRCm39)	T144A	probably benign	Het
Cbfa2t2	T	A	2: 154,357,895 (GRCm39)	N223K	probably benign	Het
Ccdc39	T	C	3: 33,884,254 (GRCm39)	I363V	probably benign	Het
Ccng2	C	G	5: 93,421,202 (GRCm39)	S237R	probably benign	Het
Ccpg1	G	T	9: 72,920,609 (GRCm39)	R741S	probably benign	Het
Cenpc1	A	G	5: 86,161,366 (GRCm39)	F855L	probably damaging	Het
Cenpc1	A	T	5: 86,180,277 (GRCm39)	M665K	probably benign	Het
Cp	A	G	3: 20,037,641 (GRCm39)	H832R	probably damaging	Het
Defa24	A	G	8: 22,224,565 (GRCm39)	I5V	probably benign	Het
Dlc1	A	C	8: 37,046,407 (GRCm39)	L730R	probably damaging	Het
Dmbt1	A	T	7: 130,668,351 (GRCm39)	I536F	unknown	Het
Dscam	G	A	16: 96,479,601 (GRCm39)	T1182I	probably benign	Het
Eea1	A	T	10: 95,854,000 (GRCm39)	I553F	probably damaging	Het
Far1	T	C	7: 113,160,654 (GRCm39)	V400A	probably benign	Het
Fbrsl1	A	T	5: 110,580,880 (GRCm39)	S126T	probably benign	Het
Frmpd2	A	T	14: 33,244,838 (GRCm39)	E552V	possibly damaging	Het
Gm5431	T	A	11: 48,779,237 (GRCm39)	T562S	probably benign	Het
Gm5475	T	C	15: 100,324,890 (GRCm39)	F106S	unknown	Het
Gpr12	T	C	5: 146,520,188 (GRCm39)	T245A	probably damaging	Het
Gsta2	A	G	9: 78,239,419 (GRCm39)	Y166H	probably benign	Het
H6pd	A	G	4: 150,067,369 (GRCm39)	V347A	probably benign	Het
Ifih1	T	C	2: 62,475,977 (GRCm39)	T100A	probably benign	Het
Ift70b	A	G	2: 75,767,838 (GRCm39)	F305S	probably damaging	Het
Itga2	C	T	13: 115,023,225 (GRCm39)	W59*	probably null	Het
Knstrn	T	A	2: 118,661,869 (GRCm39)		probably null	Het
Kprp	A	G	3: 92,731,178 (GRCm39)	V624A	probably damaging	Het
Lmbrd2	A	G	15: 9,194,771 (GRCm39)	Y591C	probably damaging	Het
Map7d1	A	G	4: 126,126,666 (GRCm39)	V842A	unknown	Het
Mboat2	A	T	12: 24,881,708 (GRCm39)	T4S	probably benign	Het
Mcph1	T	A	8: 18,657,288 (GRCm39)		probably null	Het
Mrtfb	A	T	16: 13,218,898 (GRCm39)	M515L	possibly damaging	Het
Muc5b	A	G	7: 141,411,272 (GRCm39)	D1406G	unknown	Het
Mylk	G	A	16: 34,605,381 (GRCm39)	G3D	probably damaging	Het
Ndst4	A	G	3: 125,232,007 (GRCm39)	D192G	probably damaging	Het
Nemp1	G	T	10: 127,531,345 (GRCm39)	R361L	probably damaging	Het
Nol4	A	C	18: 23,172,846 (GRCm39)	V85G	probably benign	Het
Nrbf2	G	A	10: 67,103,605 (GRCm39)	T166M	probably damaging	Het
Obscn	T	C	11: 58,933,838 (GRCm39)	E5342G	probably damaging	Het
Or10al7	C	A	17: 38,366,442 (GRCm39)	C5F	probably damaging	Het
Or4f47	T	A	2: 111,972,905 (GRCm39)	F205Y	probably damaging	Het
Or4p19	C	T	2: 88,242,839 (GRCm39)	M54I	possibly damaging	Het
Or51d1	T	G	7: 102,348,252 (GRCm39)	L269R	probably damaging	Het
Or7d10	A	G	9: 19,831,631 (GRCm39)	N42S	possibly damaging	Het
Pakap	G	T	4: 57,855,217 (GRCm39)	R182L	probably damaging	Het
Pde4dip	A	G	3: 97,674,275 (GRCm39)	S214P	probably damaging	Het
Per3	A	T	4: 151,116,393 (GRCm39)	C278*	probably null	Het
Pi4k2a	T	C	19: 42,079,125 (GRCm39)	L62P	probably damaging	Het
Plekha7	C	A	7: 115,780,447 (GRCm39)	G126W	probably damaging	Het
Ppp1r13b	T	C	12: 111,801,353 (GRCm39)	K567E	probably damaging	Het
Pradc1	T	A	6: 85,424,548 (GRCm39)	Q134L	probably benign	Het
Pwp2	A	G	10: 78,012,170 (GRCm39)	F628L	probably benign	Het
Rab5c	C	T	11: 100,606,928 (GRCm39)	G217D	probably benign	Het
Rad51ap2	G	T	12: 11,506,807 (GRCm39)	S243I	possibly damaging	Het
Rasgrp4	C	A	7: 28,847,855 (GRCm39)	R432S	probably damaging	Het
Rhot2	C	T	17: 26,061,402 (GRCm39)		probably null	Het
Scn2a	T	A	2: 65,594,113 (GRCm39)	L1654Q	probably damaging	Het
Skint6	A	T	4: 112,711,686 (GRCm39)		probably null	Het
Slc22a28	T	A	19: 8,094,491 (GRCm39)	T177S	probably benign	Het
Slc25a24	G	T	3: 109,065,960 (GRCm39)	Q272H	probably null	Het
Slc3a1	A	T	17: 85,339,873 (GRCm39)	I144F	probably damaging	Het
Smg9	C	T	7: 24,105,495 (GRCm39)	R176C	possibly damaging	Het
Sorl1	A	T	9: 41,948,499 (GRCm39)	L762Q	probably damaging	Het
Srebf2	C	A	15: 82,088,270 (GRCm39)	P1079T	probably benign	Het
Sub1	A	T	15: 11,993,937 (GRCm39)	S4T	probably benign	Het
Tacr1	A	T	6: 82,469,692 (GRCm39)	Y192F	probably benign	Het
Tm4sf19	A	T	16: 32,224,814 (GRCm39)	H54L	probably damaging	Het
Tnxb	T	C	17: 34,914,428 (GRCm39)	L1838P	probably damaging	Het
Trmt1l	T	C	1: 151,333,539 (GRCm39)	S681P	possibly damaging	Het
Ttn	A	G	2: 76,738,176 (GRCm39)	V4167A	unknown	Het
Unc13d	T	A	11: 115,959,056 (GRCm39)	M702L	probably benign	Het
Vgll3	A	G	16: 65,636,404 (GRCm39)	H240R	probably benign	Het
Vmn1r189	C	G	13: 22,286,737 (GRCm39)	W33C	probably benign	Het
Vmn2r17	G	A	5: 109,576,337 (GRCm39)	A403T	possibly damaging	Het
Vmn2r2	G	A	3: 64,033,998 (GRCm39)	T508I	probably benign	Het
Wfs1	G	A	5: 37,125,134 (GRCm39)	Q586*	probably null	Het
Zbp1	A	T	2: 173,055,665 (GRCm39)	H166Q	unknown	Het
Zcchc3	G	A	2: 152,256,294 (GRCm39)	A135V	probably benign	Het
Zfp51	T	C	17: 21,683,960 (GRCm39)	Y192H	probably benign	Het
Zkscan2	T	C	7: 123,088,994 (GRCm39)	T426A	probably benign	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
R1720:Vps54	UTSW	11	21,256,519 (GRCm39)	missense	probably damaging	1.00
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
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'- GTGAACATGTCTCCTTTGCAC -3'
(R):5'- AACACCTGCACTGTAGGCTG -3'

Sequencing Primer
(F):5'- ACATTTATCTATCTTTGGGCGACAC -3'
(R):5'- GTGTACAGTGGCCATTAACTTCAG -3'

Posted On

2019-09-23