Mutagenetix > Incidental Mutation

Incidental Mutation 'R5338:Vps53'

423649

Institutional Source

Beutler Lab

Gene Symbol

Vps53

Ensembl Gene

ENSMUSG00000017288

Gene Name

VPS53 GARP complex subunit

Synonyms

2310040I21Rik, 3100002B05Rik, 2010002A08Rik

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5338 (G1)

Quality Score

111

Status

Not validated

Chromosome

Chromosomal Location

75937052-76070464 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 75972034 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 271 (E271G)

Ref Sequence

ENSEMBL: ENSMUSP00000131663 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000056601] [ENSMUST00000094015] [ENSMUST00000108419] [ENSMUST00000166752] [ENSMUST00000167114] [ENSMUST00000169734]

AlphaFold

Q8CCB4

Predicted Effect

probably damaging
Transcript: ENSMUST00000056601
AA Change: E548G

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288
AA Change: E548G

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:DUF2450	25	225	5.9e-11	PFAM
Pfam:Vps53_N	39	453	1.9e-176	PFAM
low complexity region	520	533	N/A	INTRINSIC
low complexity region	820	832	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000094015
AA Change: E519G

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

SMART Domains

Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288
AA Change: E519G

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:Vps53_N	39	96	6.2e-21	PFAM
Pfam:Vps53_N	93	424	1.4e-133	PFAM
low complexity region	491	504	N/A	INTRINSIC
low complexity region	791	803	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000108419
AA Change: E371G

PolyPhen 2 Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288
AA Change: E371G

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:DUF2450	25	224	4e-11	PFAM
Pfam:Vps53_N	39	233	5.2e-87	PFAM
Pfam:Vps53_N	226	276	1.6e-14	PFAM
low complexity region	343	356	N/A	INTRINSIC
low complexity region	643	655	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000143163

Predicted Effect

probably damaging
Transcript: ENSMUST00000166752
AA Change: E500G

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000129159
Gene: ENSMUSG00000017288
AA Change: E500G

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:DUF2450	25	225	8.2e-12	PFAM
Pfam:Vps53_N	39	230	6e-87	PFAM
Pfam:Vps53_N	226	405	1.4e-60	PFAM
low complexity region	472	485	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000167114
AA Change: E271G

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

SMART Domains

Protein: ENSMUSP00000131663
Gene: ENSMUSG00000017288
AA Change: E271G

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:Vps53_N	39	101	1.2e-21	PFAM
Pfam:Vps53_N	104	176	3.1e-15	PFAM
low complexity region	243	256	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000169734

SMART Domains

Protein: ENSMUSP00000130499
Gene: ENSMUSG00000017288

Domain	Start	End	E-Value	Type
Pfam:DUF2450	5	225	5.1e-12	PFAM
Pfam:Vps53_N	39	329	1e-137	PFAM

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.5%
20x: 95.8%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein with sequence similarity to the yeast Vps53p protein. Vps53p is involved in retrograde vesicle trafficking in late Golgi. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality prior to E12.5 with trophoblast cell hyperplasia. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A4gnt	T	A	9: 99,502,597 (GRCm39)	N252K	probably damaging	Het
Abhd16a	A	G	17: 35,313,278 (GRCm39)	E132G	probably damaging	Het
Adgrv1	G	A	13: 81,677,165 (GRCm39)	R1889W	possibly damaging	Het
Aftph	A	T	11: 20,677,203 (GRCm39)	D135E	probably benign	Het
Arf1	A	C	11: 59,104,041 (GRCm39)	F63V	probably damaging	Het
Atg14	G	A	14: 47,805,656 (GRCm39)	R70C	probably damaging	Het
B3gnt7	T	A	1: 86,233,366 (GRCm39)	F87Y	probably damaging	Het
Bcat1	A	G	6: 144,953,353 (GRCm39)	Y345H	possibly damaging	Het
Birc2	G	T	9: 7,857,360 (GRCm39)	T371K	probably benign	Het
Ccdc175	A	T	12: 72,231,745 (GRCm39)	S5T	probably damaging	Het
Ccdc186	A	T	19: 56,801,689 (GRCm39)	S143T	possibly damaging	Het
Cct6b	A	T	11: 82,653,015 (GRCm39)	M28K	possibly damaging	Het
Cers4	C	A	8: 4,565,680 (GRCm39)	A42D	probably damaging	Het
Crmp1	G	T	5: 37,437,018 (GRCm39)	V236L	probably benign	Het
Ctdspl2	T	A	2: 121,811,793 (GRCm39)	N212K	probably benign	Het
Dclk3	T	C	9: 111,298,127 (GRCm39)	V557A	possibly damaging	Het
Dnmt1	A	T	9: 20,864,015 (GRCm39)	H23Q	probably benign	Het
Dpp8	G	T	9: 64,971,206 (GRCm39)	E609*	probably null	Het
Dtx3	C	A	10: 127,028,919 (GRCm39)	M106I	probably benign	Het
Ero1b	A	C	13: 12,589,732 (GRCm39)	D45A	probably damaging	Het
Fcho2	T	A	13: 98,867,399 (GRCm39)	D688V	probably damaging	Het
Fhod3	A	T	18: 25,161,138 (GRCm39)	S557C	probably damaging	Het
Flnc	T	C	6: 29,444,063 (GRCm39)	S626P	possibly damaging	Het
Foxi3	G	T	6: 70,937,602 (GRCm39)	G278V	probably damaging	Het
Gbp10	A	G	5: 105,372,166 (GRCm39)	L198P	probably damaging	Het
Gcn1	A	G	5: 115,721,462 (GRCm39)	T458A	probably benign	Het
Gigyf1	C	T	5: 137,521,422 (GRCm39)		probably benign	Het
Gtpbp2	A	C	17: 46,478,760 (GRCm39)	T526P	probably damaging	Het
Gys2	A	G	6: 142,400,239 (GRCm39)	L324S	probably damaging	Het
Hpn	C	A	7: 30,802,781 (GRCm39)	V119L	probably benign	Het
Ino80d	C	A	1: 63,098,098 (GRCm39)	V599L	probably benign	Het
Kcnh3	G	T	15: 99,140,275 (GRCm39)	G1054*	probably null	Het
Maml1	A	T	11: 50,157,778 (GRCm39)	D132E	probably benign	Het
Mastl	A	T	2: 23,023,503 (GRCm39)	S407T	probably benign	Het
Mettl1	T	C	10: 126,878,954 (GRCm39)	W3R	probably damaging	Het
Mprip	A	G	11: 59,651,399 (GRCm39)	Y1701C	probably damaging	Het
Mylk3	T	C	8: 86,069,350 (GRCm39)	N484D	probably damaging	Het
Nod2	G	A	8: 89,399,413 (GRCm39)		probably null	Het
Nrde2	A	T	12: 100,097,037 (GRCm39)	F921Y	probably damaging	Het
Nup88	G	T	11: 70,835,734 (GRCm39)	T575N	probably damaging	Het
Nxpe3	T	C	16: 55,686,706 (GRCm39)	T101A	possibly damaging	Het
Or1o3	T	A	17: 37,574,532 (GRCm39)	T8S	probably benign	Het
Or2r11	A	G	6: 42,437,908 (GRCm39)	M15T	probably benign	Het
Or4c109	C	T	2: 88,817,809 (GRCm39)	V246I	possibly damaging	Het
Or52e15	A	G	7: 104,645,514 (GRCm39)	L199S	possibly damaging	Het
Or8g32	A	T	9: 39,305,371 (GRCm39)	I92F	probably damaging	Het
Pcnx3	A	T	19: 5,722,624 (GRCm39)	L1356Q	probably damaging	Het
Pkd1	A	T	17: 24,813,510 (GRCm39)	M4017L	probably benign	Het
Polg2	A	G	11: 106,670,064 (GRCm39)	C69R	possibly damaging	Het
Prr5l	T	G	2: 101,547,452 (GRCm39)	S358R	probably benign	Het
Ptprg	A	G	14: 12,154,111 (GRCm38)	T611A	probably benign	Het
Ryk	G	T	9: 102,774,516 (GRCm39)	E417*	probably null	Het
Sbp	T	C	17: 24,161,396 (GRCm39)		probably benign	Het
Sema4a	T	C	3: 88,358,804 (GRCm39)	T155A	probably benign	Het
Shank3	A	G	15: 89,415,914 (GRCm39)		probably null	Het
Slc35d2	A	T	13: 64,245,496 (GRCm39)	M294K	possibly damaging	Het
Slc41a3	A	T	6: 90,589,153 (GRCm39)	N88I	possibly damaging	Het
Slit3	A	G	11: 35,512,975 (GRCm39)	T534A	probably benign	Het
Ssx2ip	A	G	3: 146,142,296 (GRCm39)		probably null	Het
Stard13	T	C	5: 150,983,063 (GRCm39)	K648R	probably damaging	Het
Tanc1	A	T	2: 59,626,178 (GRCm39)	T512S	probably damaging	Het
Tbcc	T	C	17: 47,202,082 (GRCm39)	V156A	probably benign	Het
Terf1	T	G	1: 15,901,787 (GRCm39)	I273R	possibly damaging	Het
Tesc	A	G	5: 118,197,523 (GRCm39)	Y179C	probably damaging	Het
Ttc3	T	G	16: 94,184,900 (GRCm39)	V40G	probably damaging	Het
Tysnd1	T	A	10: 61,532,028 (GRCm39)	F227I	probably damaging	Het
Wdfy4	C	T	14: 32,812,823 (GRCm39)	R1650H	probably damaging	Het

Other mutations in Vps53

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00475:Vps53	APN	11	75,967,861 (GRCm39)	splice site	probably null
IGL01596:Vps53	APN	11	75,953,863 (GRCm39)	missense	probably damaging	1.00
IGL01655:Vps53	APN	11	75,953,860 (GRCm39)	missense	probably damaging	0.97
IGL02275:Vps53	APN	11	75,937,949 (GRCm39)	missense	probably benign	0.03
IGL02321:Vps53	APN	11	75,939,364 (GRCm39)	missense	possibly damaging	0.60
IGL02581:Vps53	APN	11	75,992,883 (GRCm39)	missense	probably damaging	0.99
IGL02821:Vps53	APN	11	76,027,143 (GRCm39)	splice site	probably benign
IGL02958:Vps53	APN	11	76,008,537 (GRCm39)	missense	probably damaging	1.00
IGL03001:Vps53	APN	11	76,029,150 (GRCm39)	missense	probably damaging	1.00
PIT4519001:Vps53	UTSW	11	76,007,999 (GRCm39)	missense	probably damaging	1.00
R0257:Vps53	UTSW	11	76,068,211 (GRCm39)	intron	probably benign
R0391:Vps53	UTSW	11	76,012,405 (GRCm39)	missense	probably benign	0.31
R0421:Vps53	UTSW	11	75,973,496 (GRCm39)	missense	probably damaging	1.00
R0882:Vps53	UTSW	11	75,973,485 (GRCm39)	missense	probably damaging	1.00
R2509:Vps53	UTSW	11	75,957,661 (GRCm39)	missense	possibly damaging	0.49
R3622:Vps53	UTSW	11	76,008,609 (GRCm39)	missense	probably benign	0.00
R5137:Vps53	UTSW	11	76,057,074 (GRCm39)	missense	probably damaging	1.00
R5756:Vps53	UTSW	11	75,983,156 (GRCm39)	splice site	probably benign
R5786:Vps53	UTSW	11	75,953,833 (GRCm39)	missense	probably benign	0.08
R5961:Vps53	UTSW	11	75,939,316 (GRCm39)	missense	probably damaging	1.00
R6059:Vps53	UTSW	11	75,957,693 (GRCm39)	missense	possibly damaging	0.57
R6273:Vps53	UTSW	11	75,992,844 (GRCm39)	missense	probably benign	0.16
R6490:Vps53	UTSW	11	75,967,881 (GRCm39)	missense	probably benign	0.03
R6657:Vps53	UTSW	11	76,025,253 (GRCm39)	missense	probably damaging	1.00
R6671:Vps53	UTSW	11	76,025,332 (GRCm39)	missense	probably damaging	1.00
R6772:Vps53	UTSW	11	76,070,324 (GRCm39)	start codon destroyed	probably null
R7378:Vps53	UTSW	11	75,967,900 (GRCm39)	missense	possibly damaging	0.88
R7735:Vps53	UTSW	11	75,937,962 (GRCm39)	missense	probably damaging	1.00
R8066:Vps53	UTSW	11	76,027,133 (GRCm39)	missense	probably damaging	1.00
Z1177:Vps53	UTSW	11	76,027,024 (GRCm39)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- GGGCAGTCTCTGACTATAAGGTG -3'
(R):5'- GTACTGTAGCCAGCCTTTCC -3'

Sequencing Primer
(F):5'- TTGCTCCTGAGAGGCTAAGC -3'
(R):5'- GTAGCCAGCCTTTCCTCTGC -3'

Posted On

2016-08-04