Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL03358:Vps54'

420007

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Vps54

Ensembl Gene

ENSMUSG00000020128

Gene Name

VPS54 GARP complex subunit

Synonyms

5330404P15Rik, Vps54l, mSLP8, wr

Accession Numbers

Essential gene?

Probably essential (E-score: 0.931) question?

Stock #

IGL03358

Quality Score

Status

Chromosome

Chromosomal Location

21189281-21271136 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 21218799 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Histidine to Glutamine at position 119 (H119Q)

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: H131Q

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

SMART Domains

Protein: ENSMUSP00000006221
Gene: ENSMUSG00000020128
AA Change: H131Q

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: H119Q

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

SMART Domains

Protein: ENSMUSP00000105206
Gene: ENSMUSG00000020128
AA Change: H119Q

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: H5Q

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

SMART Domains

Protein: ENSMUSP00000116739
Gene: ENSMUSG00000020128
AA Change: H5Q

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

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: 24 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930453N24Rik	T	C	16: 64,586,909 (GRCm39)	I272V	possibly damaging	Het
4930590J08Rik	A	G	6: 91,905,716 (GRCm39)	N496D	probably damaging	Het
Adcy2	C	T	13: 68,877,396 (GRCm39)	G448E	probably damaging	Het
Alad	G	A	4: 62,428,844 (GRCm39)		probably benign	Het
Ank2	C	A	3: 126,749,519 (GRCm39)	E503D	probably damaging	Het
Appbp2	A	T	11: 85,100,860 (GRCm39)	M193K	probably benign	Het
Cd300a	G	A	11: 114,788,623 (GRCm39)	M204I	possibly damaging	Het
Cep350	T	A	1: 155,804,285 (GRCm39)	M933L	probably benign	Het
Cyp2s1	T	A	7: 25,507,573 (GRCm39)	N292I	probably damaging	Het
Gnl2	T	C	4: 124,946,387 (GRCm39)	I536T	probably damaging	Het
Ift140	C	T	17: 25,306,958 (GRCm39)	R898C	probably damaging	Het
Oosp2	A	T	19: 11,628,933 (GRCm39)	L56*	probably null	Het
Pars2	A	T	4: 106,510,239 (GRCm39)	H7L	probably benign	Het
Pbx4	T	C	8: 70,311,761 (GRCm39)	S59P	probably benign	Het
Psg20	G	T	7: 18,414,891 (GRCm39)	H332N	probably benign	Het
Rigi	T	C	4: 40,206,069 (GRCm39)	E841G	possibly damaging	Het
Slc6a13	G	A	6: 121,311,495 (GRCm39)	V384I	probably benign	Het
Spg21	G	A	9: 65,387,698 (GRCm39)	V164I	probably benign	Het
Tnc	A	T	4: 63,935,852 (GRCm39)	C361*	probably null	Het
Tsr1	T	C	11: 74,794,824 (GRCm39)	V493A	probably benign	Het
Ube2u	A	G	4: 100,404,472 (GRCm39)		probably benign	Het
Vav3	G	A	3: 109,554,989 (GRCm39)	G79E	probably damaging	Het
Vmn1r81	T	G	7: 11,994,232 (GRCm39)	R125S	possibly damaging	Het
Vmn2r45	A	C	7: 8,474,715 (GRCm39)	L771R	probably damaging	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
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
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

Posted On

2016-08-02