Mutagenetix > Incidental Mutation

Incidental Mutation 'R1280:Vps54'

151007

Institutional Source

Beutler Lab

Gene Symbol

Vps54

Ensembl Gene

ENSMUSG00000020128

Gene Name

VPS54 GARP complex subunit

Synonyms

5330404P15Rik, Vps54l, mSLP8, wr

MMRRC Submission

039346-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.931) question?

Stock #

R1280 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

21189281-21271136 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 21227868 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 273 (I273N)

Ref Sequence

ENSEMBL: ENSMUSP00000006221 (fasta)

Gene Model

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

AlphaFold

Q5SPW0

PDB Structure

C-terminal domain of Vps54 subunit of the GARP complex [X-RAY DIFFRACTION]
Vps54 C-terminal domain [X-RAY DIFFRACTION]

Predicted Effect

possibly damaging
Transcript: ENSMUST00000006221
AA Change: I273N

PolyPhen 2 Score 0.878 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: I273N

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: I261N

PolyPhen 2 Score 0.719 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: I261N

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

noncoding transcript
Transcript: ENSMUST00000118219

Predicted Effect

possibly damaging
Transcript: ENSMUST00000132017
AA Change: I147N

PolyPhen 2 Score 0.470 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: I147N

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: ENSMUST00000132146

Coding Region Coverage

1x: 99.0%
3x: 98.2%
10x: 96.1%
20x: 92.1%

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: 20 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Alkbh2	C	T	5: 114,262,287 (GRCm39)	E148K	probably damaging	Het
Atp5mc3	G	T	2: 73,739,714 (GRCm39)	T42K	possibly damaging	Het
Brd2	T	C	17: 34,333,124 (GRCm39)	M60V	possibly damaging	Het
Cabp1	T	C	5: 115,313,530 (GRCm39)	N226S	probably benign	Het
Cers6	G	A	2: 68,899,033 (GRCm39)	V224I	probably benign	Het
Entpd2	C	T	2: 25,289,496 (GRCm39)	S326F	probably damaging	Het
Fez1	GACAAACA	GACA	9: 36,781,845 (GRCm39)		probably null	Het
Gjb3	G	A	4: 127,220,224 (GRCm39)	R103W	probably damaging	Het
Klhdc7a	G	A	4: 139,692,764 (GRCm39)	R728C	probably benign	Het
Myo18b	A	G	5: 112,871,671 (GRCm39)		probably null	Het
Mzf1	A	T	7: 12,787,010 (GRCm39)	L20Q	probably damaging	Het
Neil1	T	C	9: 57,054,185 (GRCm39)	Y45C	probably damaging	Het
Or2ad1	C	T	13: 21,326,337 (GRCm39)	V297I	probably benign	Het
Rbm12	T	C	2: 155,938,749 (GRCm39)	K508E	probably damaging	Het
Socs4	A	T	14: 47,528,370 (GRCm39)	Q435L	probably benign	Het
Tdrd9	T	C	12: 112,005,842 (GRCm39)	V905A	probably damaging	Het
Tekt4	T	A	17: 25,690,861 (GRCm39)	W56R	probably damaging	Het
Ttn	A	T	2: 76,608,508 (GRCm39)	I16059N	possibly damaging	Het
Ubqln3	A	G	7: 103,791,283 (GRCm39)	V269A	possibly damaging	Het
Zfp831	A	G	2: 174,545,852 (GRCm39)	K1319R	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
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
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'- GAGGCTGTTACCTTTGGGGAAGAAG -3'
(R):5'- AGACATACCGGAAGCTGTGAATGC -3'

Sequencing Primer
(F):5'- GTAAGTGAACATGTCTCCTTTGCAC -3'
(R):5'- TGTGAATGCCCTGAAGCTC -3'

Posted On

2014-01-29