Mutagenetix > Incidental Mutation

Incidental Mutation 'R0391:Vps53'

31714

Institutional Source

Beutler Lab

Gene Symbol

Vps53

Ensembl Gene

ENSMUSG00000017288

Gene Name

VPS53 GARP complex subunit

Synonyms

2310040I21Rik, 3100002B05Rik, 2010002A08Rik

MMRRC Submission

038597-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R0391 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

75937052-76070464 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 76012405 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 209 (T209I)

Ref Sequence

ENSEMBL: ENSMUSP00000129159 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000056601] [ENSMUST00000094015] [ENSMUST00000108419] [ENSMUST00000163878] [ENSMUST00000166752] [ENSMUST00000169734] [ENSMUST00000167114]

AlphaFold

Q8CCB4

Predicted Effect

probably benign
Transcript: ENSMUST00000056601
AA Change: T209I

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288
AA Change: T209I

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 benign
Transcript: ENSMUST00000094015
AA Change: T180I

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288
AA Change: T180I

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: T209I

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288
AA Change: T209I

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: ENSMUST00000141773

Predicted Effect

probably benign
Transcript: ENSMUST00000163878

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000166084

Predicted Effect

unknown
Transcript: ENSMUST00000166436
AA Change: T137I

SMART Domains

Protein: ENSMUSP00000131387
Gene: ENSMUSG00000017288
AA Change: T137I

Domain	Start	End	E-Value	Type
Pfam:DUF2450	1	155	1.6e-8	PFAM
Pfam:Vps53_N	1	204	6.1e-91	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000166752
AA Change: T209I

PolyPhen 2 Score 0.314 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000129159
Gene: ENSMUSG00000017288
AA Change: T209I

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 benign
Transcript: ENSMUST00000169734
AA Change: T209I

PolyPhen 2 Score 0.005 (Sensitivity: 0.97; Specificity: 0.74)

SMART Domains

Protein: ENSMUSP00000130499
Gene: ENSMUSG00000017288
AA Change: T209I

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000169532

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000170143

Predicted Effect

probably benign
Transcript: ENSMUST00000167114

SMART Domains

Protein: ENSMUSP00000131663
Gene: ENSMUSG00000017288

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

Meta Mutation Damage Score

0.0923

Coding Region Coverage

1x: 99.1%
3x: 98.2%
10x: 95.9%
20x: 91.8%

Validation Efficiency

97% (97/100)

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: 97 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9530002B09Rik	T	A	4: 122,594,970 (GRCm39)		probably benign	Het
Abcc2	G	A	19: 43,810,044 (GRCm39)		probably benign	Het
Abcc8	C	G	7: 45,771,597 (GRCm39)	G838A	probably damaging	Het
Akr1c21	G	A	13: 4,631,199 (GRCm39)	A245T	probably damaging	Het
Anapc15-ps	T	C	10: 95,509,139 (GRCm39)	E47G	probably damaging	Het
Apoa1	A	G	9: 46,141,140 (GRCm39)	T79A	probably benign	Het
Atp6v1b1	A	G	6: 83,733,903 (GRCm39)	H378R	possibly damaging	Het
C4b	A	G	17: 34,954,588 (GRCm39)		probably benign	Het
Catsperd	A	T	17: 56,969,821 (GRCm39)	E638D	probably benign	Het
Cckar	C	T	5: 53,863,595 (GRCm39)		probably null	Het
Cfap100	C	T	6: 90,382,321 (GRCm39)		probably benign	Het
Chd1	G	T	17: 15,970,156 (GRCm39)	G970C	probably damaging	Het
Col14a1	A	G	15: 55,309,655 (GRCm39)		probably benign	Het
Col17a1	C	T	19: 47,652,263 (GRCm39)	V698M	probably damaging	Het
Cpeb1	T	C	7: 81,011,473 (GRCm39)	D156G	possibly damaging	Het
Cryl1	A	G	14: 57,541,232 (GRCm39)	Y151H	possibly damaging	Het
Csmd3	C	A	15: 47,520,969 (GRCm39)	V1881L	probably damaging	Het
Ctnnal1	C	T	4: 56,847,921 (GRCm39)	A73T	probably damaging	Het
Cyp2c37	T	C	19: 39,982,950 (GRCm39)	S180P	probably damaging	Het
Cyp2c54	T	C	19: 40,060,613 (GRCm39)	T123A	possibly damaging	Het
Dennd6b	T	C	15: 89,071,417 (GRCm39)	D304G	probably damaging	Het
Dnmt3l	T	C	10: 77,887,750 (GRCm39)		probably benign	Het
Eci1	G	A	17: 24,652,234 (GRCm39)		probably null	Het
Efhc1	A	G	1: 21,030,412 (GRCm39)	Y115C	probably damaging	Het
Ern1	T	A	11: 106,298,004 (GRCm39)	K706*	probably null	Het
Ghrl	T	C	6: 113,696,299 (GRCm39)	E31G	probably damaging	Het
Gpr108	A	C	17: 57,550,101 (GRCm39)	V179G	probably benign	Het
Henmt1	A	G	3: 108,865,851 (GRCm39)		probably benign	Het
Ift172	A	G	5: 31,444,011 (GRCm39)	V69A	probably damaging	Het
Il17ra	T	C	6: 120,453,940 (GRCm39)		probably benign	Het
Il17rb	T	C	14: 29,726,304 (GRCm39)	N95D	probably benign	Het
Il17rb	G	T	14: 29,728,112 (GRCm39)		probably null	Het
Iqub	G	A	6: 24,446,154 (GRCm39)	L757F	probably benign	Het
Itpr1	T	C	6: 108,355,128 (GRCm39)	V473A	probably benign	Het
Itpr2	T	G	6: 146,131,271 (GRCm39)	N1978H	probably damaging	Het
Klk1b26	T	A	7: 43,662,151 (GRCm39)	F3Y	probably damaging	Het
Lars1	A	G	18: 42,384,428 (GRCm39)	V50A	probably benign	Het
Lax1	G	T	1: 133,607,804 (GRCm39)	H312Q	probably benign	Het
Lctl	T	C	9: 64,029,596 (GRCm39)		probably benign	Het
Lrp2	T	A	2: 69,287,202 (GRCm39)	D3745V	probably damaging	Het
Lrp2	G	A	2: 69,290,681 (GRCm39)		probably benign	Het
Lvrn	A	T	18: 46,983,533 (GRCm39)	H92L	probably benign	Het
Marchf1	A	G	8: 66,871,625 (GRCm39)	T385A	probably damaging	Het
Marf1	C	T	16: 13,960,398 (GRCm39)	A549T	probably damaging	Het
Mbd5	T	C	2: 49,162,428 (GRCm39)	V970A	possibly damaging	Het
Mccc1	A	G	3: 36,017,719 (GRCm39)		probably benign	Het
Mpp4	A	T	1: 59,182,988 (GRCm39)		probably benign	Het
Mrnip	G	A	11: 50,090,747 (GRCm39)	A304T	probably damaging	Het
Muc5b	T	C	7: 141,418,819 (GRCm39)	S3922P	possibly damaging	Het
Myh3	T	A	11: 66,987,333 (GRCm39)		probably benign	Het
Nbea	A	T	3: 55,944,698 (GRCm39)	H555Q	probably damaging	Het
Niban3	T	A	8: 72,055,143 (GRCm39)		probably benign	Het
Nlrp9c	A	T	7: 26,070,901 (GRCm39)		probably benign	Het
Nmur1	A	T	1: 86,315,400 (GRCm39)	V178E	probably damaging	Het
Nod2	T	G	8: 89,390,406 (GRCm39)	S238A	probably benign	Het
Ogfod1	A	T	8: 94,789,651 (GRCm39)	T451S	probably damaging	Het
Or1e17	T	C	11: 73,831,935 (GRCm39)	F288L	probably damaging	Het
Or2d36	T	A	7: 106,747,394 (GRCm39)	Y290*	probably null	Het
Or2z8	C	T	8: 72,812,244 (GRCm39)	T240M	probably damaging	Het
Or8b8	G	A	9: 37,809,138 (GRCm39)	G146D	probably benign	Het
Pcdh20	T	C	14: 88,706,104 (GRCm39)	I399V	probably benign	Het
Pdlim1	G	T	19: 40,232,017 (GRCm39)	H120Q	probably damaging	Het
Plg	T	C	17: 12,637,968 (GRCm39)	V798A	probably damaging	Het
Polr2c	A	G	8: 95,584,403 (GRCm39)	I39V	possibly damaging	Het
Ppfia2	C	A	10: 106,666,575 (GRCm39)		probably benign	Het
Ppp1r3a	A	T	6: 14,719,696 (GRCm39)	I406N	probably benign	Het
Psg28	A	T	7: 18,160,098 (GRCm39)	M366K	probably benign	Het
Rad54b	T	C	4: 11,601,702 (GRCm39)	I419T	probably damaging	Het
Rnf43	A	G	11: 87,622,108 (GRCm39)	Q403R	possibly damaging	Het
Sema6a	G	A	18: 47,423,112 (GRCm39)		probably null	Het
Slc28a3	A	G	13: 58,717,229 (GRCm39)		probably benign	Het
Smad2	A	T	18: 76,422,108 (GRCm39)		probably null	Het
Smad4	G	A	18: 73,791,720 (GRCm39)	P274S	probably benign	Het
Smchd1	A	T	17: 71,710,149 (GRCm39)	V906D	probably damaging	Het
Soat2	C	A	15: 102,067,188 (GRCm39)	R320S	possibly damaging	Het
Spata33	C	T	8: 123,948,626 (GRCm39)	A57V	probably damaging	Het
Stab1	A	G	14: 30,865,375 (GRCm39)	L1814P	probably benign	Het
Stab2	T	C	10: 86,783,008 (GRCm39)	K680R	probably benign	Het
Stil	A	G	4: 114,898,369 (GRCm39)		probably null	Het
Sympk	T	A	7: 18,780,774 (GRCm39)	L759H	probably benign	Het
Tet1	A	T	10: 62,650,325 (GRCm39)		probably null	Het
Tfpi2	A	T	6: 3,965,460 (GRCm39)	N117K	probably benign	Het
Tle3	A	G	9: 61,323,943 (GRCm39)	Y766C	probably damaging	Het
Trpt1	C	A	19: 6,975,298 (GRCm39)		probably null	Het
Tshz1	A	G	18: 84,034,174 (GRCm39)	F78S	possibly damaging	Het
Ttc1	T	C	11: 43,629,635 (GRCm39)	D177G	probably damaging	Het
Ttc13	T	A	8: 125,401,140 (GRCm39)	Y741F	probably damaging	Het
Ulk3	C	T	9: 57,502,115 (GRCm39)	S462L	probably benign	Het
Utrn	C	T	10: 12,401,077 (GRCm39)		probably benign	Het
V1rd19	A	C	7: 23,703,010 (GRCm39)	T159P	probably damaging	Het
Vars1	T	C	17: 35,230,462 (GRCm39)	V515A	possibly damaging	Het
Vmn1r85	A	G	7: 12,818,515 (GRCm39)	Y210H	probably benign	Het
Vmn2r89	A	G	14: 51,693,435 (GRCm39)	T262A	probably damaging	Het
Wdfy2	T	C	14: 63,162,582 (GRCm39)	F95L	possibly damaging	Het
Wwp1	G	T	4: 19,627,911 (GRCm39)	S694Y	probably damaging	Het
Zbtb8b	T	A	4: 129,326,463 (GRCm39)	D201V	probably damaging	Het
Zmym5	A	C	14: 57,041,908 (GRCm39)	N123K	possibly 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
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
R5338:Vps53	UTSW	11	75,972,034 (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'- AAACAGGCTCATCTGAGTCGGCAG -3'
(R):5'- ACCTCACAGTAGGGAAGAGTGACC -3'

Sequencing Primer
(F):5'- TGAGTCGGCAGACCCTTG -3'
(R):5'- gacagagcacttgcctcc -3'

Posted On

2013-04-24