Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL01801:Vps54'

155531

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 #

IGL01801

Quality Score

Status

Chromosome

Chromosomal Location

21189281-21271136 bp(+) (GRCm39)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

T to C at 21225131 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000116739 (fasta)

Gene Model

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

noncoding transcript
Transcript: ENSMUST00000118219

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

noncoding transcript
Transcript: ENSMUST00000132146

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: 25 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4932415M13Rik	C	T	17: 54,031,870 (GRCm39)		noncoding transcript	Het
Acsm4	C	T	7: 119,306,486 (GRCm39)	T308I	possibly damaging	Het
Adamtsl1	A	G	4: 86,117,559 (GRCm39)	N174S	probably benign	Het
Atp1b1	C	T	1: 164,265,918 (GRCm39)	G281D	probably damaging	Het
Cacna1e	T	C	1: 154,347,086 (GRCm39)	N1027S	probably null	Het
Cacnb4	A	T	2: 52,324,723 (GRCm39)	N446K	probably benign	Het
Cfap210	A	T	2: 69,606,623 (GRCm39)		probably benign	Het
Col13a1	T	C	10: 61,679,393 (GRCm39)	D215G	probably damaging	Het
Cyp2d22	T	C	15: 82,257,046 (GRCm39)	T312A	probably benign	Het
Cyp4f40	A	T	17: 32,895,279 (GRCm39)	N467I	probably damaging	Het
Dnaaf10	T	C	11: 17,169,015 (GRCm39)	I62T	probably benign	Het
Ehd4	A	T	2: 119,932,822 (GRCm39)	D201E	probably damaging	Het
Farsb	T	C	1: 78,435,216 (GRCm39)	T444A	probably benign	Het
Gabra6	A	C	11: 42,205,935 (GRCm39)	I307R	probably damaging	Het
Impg2	G	A	16: 56,057,111 (GRCm39)	R287H	probably damaging	Het
Khdrbs1	A	G	4: 129,635,574 (GRCm39)	V127A	probably benign	Het
Lcp1	A	T	14: 75,436,815 (GRCm39)	T54S	probably benign	Het
Mrgpra6	T	C	7: 46,835,572 (GRCm39)	D283G	possibly damaging	Het
Mterf4	T	C	1: 93,232,642 (GRCm39)	R70G	probably benign	Het
Mtmr12	T	C	15: 12,270,045 (GRCm39)	L711P	probably damaging	Het
Or4n4	A	G	14: 50,519,665 (GRCm39)	I15T	probably benign	Het
Pax8	A	G	2: 24,334,576 (GRCm39)		probably null	Het
Prmt9	T	C	8: 78,289,069 (GRCm39)	V257A	probably damaging	Het
Sspo	T	C	6: 48,434,072 (GRCm39)	V959A	probably damaging	Het
Wdr70	C	T	15: 7,916,805 (GRCm39)		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
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
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

2014-02-04