Mutagenetix > Incidental Mutations

Incidental Mutation 'R6657:Vps53'

526674

Institutional Source

Beutler Lab

Gene Symbol

Vps53

Ensembl Gene

ENSMUSG00000017288

Gene Name

VPS53 GARP complex subunit

Synonyms

2310040I21Rik, 3100002B05Rik, 2010002A08Rik

MMRRC Submission

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

R6657 (G1)

Quality Score

187.009

Status

Validated

Chromosome

Chromosomal Location

76046226-76179647 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 76134427 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 197 (I197N)

Ref Sequence

ENSEMBL: ENSMUSP00000130499 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000056601] [ENSMUST00000094015] [ENSMUST00000108419] [ENSMUST00000163878] [ENSMUST00000166752] [ENSMUST00000167114] [ENSMUST00000169734] [ENSMUST00000170730]

AlphaFold

Q8CCB4

Predicted Effect

probably damaging
Transcript: ENSMUST00000056601
AA Change: I197N

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

SMART Domains

Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288
AA Change: I197N

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: I168N

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

SMART Domains

Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288
AA Change: I168N

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 damaging
Transcript: ENSMUST00000108419
AA Change: I197N

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

SMART Domains

Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288
AA Change: I197N

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

noncoding transcript
Transcript: ENSMUST00000143459

Predicted Effect

probably benign
Transcript: ENSMUST00000163878

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000166084

Predicted Effect

unknown
Transcript: ENSMUST00000166436
AA Change: I125N

SMART Domains

Protein: ENSMUSP00000131387
Gene: ENSMUSG00000017288
AA Change: I125N

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 damaging
Transcript: ENSMUST00000166752
AA Change: I197N

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

SMART Domains

Protein: ENSMUSP00000129159
Gene: ENSMUSG00000017288
AA Change: I197N

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: 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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000169532

Predicted Effect

probably damaging
Transcript: ENSMUST00000169734
AA Change: I197N

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

SMART Domains

Protein: ENSMUSP00000130499
Gene: ENSMUSG00000017288
AA Change: I197N

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: ENSMUST00000170143

Predicted Effect

probably benign
Transcript: ENSMUST00000170730

SMART Domains

Protein: ENSMUSP00000127364
Gene: ENSMUSG00000017288

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:Vps53_N	54	123	3e-34	PFAM

Meta Mutation Damage Score

0.9159

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.9%
20x: 94.0%

Validation Efficiency

98% (48/49)

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: 48 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933405L10Rik	T	G	8: 105,708,818	L36R	probably damaging	Het
Akr1b3	C	T	6: 34,310,004	V206M	possibly damaging	Het
Akr1b7	A	C	6: 34,416,200	D106A	probably damaging	Het
Bhlhe40	TG	TGG	6: 108,664,857	254	probably null	Het
Chst5	C	T	8: 111,890,274	R238Q	probably benign	Het
Cpxm2	T	C	7: 132,049,077	Y618C	probably damaging	Het
Csnk1d	T	C	11: 120,964,994	E405G	possibly damaging	Het
Ctsh	A	T	9: 90,060,502	M37L	probably benign	Het
Eml5	T	G	12: 98,791,405	I1843L	probably damaging	Het
Ep400	C	A	5: 110,693,545		probably benign	Het
Fbln2	A	G	6: 91,259,750	N749S	possibly damaging	Het
Gpc5	A	G	14: 115,370,198	H404R	probably benign	Het
Hyal6	A	G	6: 24,734,758	D230G	possibly damaging	Het
Itga5	T	C	15: 103,350,795	D735G	probably damaging	Het
Kansl2	T	A	15: 98,524,670	Q339L	possibly damaging	Het
Lrp4	T	A	2: 91,492,053	M1078K	probably benign	Het
Mmp24	A	T	2: 155,798,179	Y143F	probably damaging	Het
Mroh7	A	T	4: 106,702,500	C743*	probably null	Het
Myh14	T	C	7: 44,637,846	N618D	probably damaging	Het
Myo19	A	T	11: 84,897,196	M324L	probably benign	Het
Nectin2	T	C	7: 19,738,140	N108S	probably benign	Het
Nrg2	A	G	18: 36,196,589	I191T	probably damaging	Het
Odf4	T	C	11: 68,926,812	N18D	probably benign	Het
Olfr1109	T	A	2: 87,093,059	I113F	probably benign	Het
Pcsk2	T	G	2: 143,690,366	L145V	probably damaging	Het
Pdzrn3	C	A	6: 101,151,022	Q894H	probably benign	Het
Pfpl	G	A	19: 12,429,926	V514I	probably benign	Het
Plbd1	A	T	6: 136,617,252	M333K	probably damaging	Het
Plec	A	T	15: 76,178,156	M2554K	possibly damaging	Het
Psmb5	A	G	14: 54,614,383	Y115H	possibly damaging	Het
Rictor	A	G	15: 6,759,496	N198D	possibly damaging	Het
Rsrc2	A	G	5: 123,739,567		probably benign	Het
Sec16a	C	T	2: 26,425,864	W262*	probably null	Het
Sfmbt1	A	G	14: 30,766,096	D8G	possibly damaging	Het
Sptbn5	T	G	2: 120,076,400		probably benign	Het
Sqor	A	G	2: 122,807,594	D139G	possibly damaging	Het
Sugt1	A	T	14: 79,607,261	T139S	probably benign	Het
Tcp11	G	A	17: 28,071,672	P159S	probably damaging	Het
Tmem262	A	G	19: 6,080,512	T89A	possibly damaging	Het
Tnfaip6	C	A	2: 52,043,783	T50N	probably damaging	Het
Ttll9	T	C	2: 152,984,262	Y131H	probably damaging	Het
Vmn1r173	T	A	7: 23,702,895	M185K	probably damaging	Het
Vmn2r111	T	C	17: 22,559,051	N549S	possibly damaging	Het
Vmn2r52	G	A	7: 10,159,163	T683I	probably damaging	Het
Washc4	T	A	10: 83,558,618	F269L	possibly damaging	Het
Wdfy4	C	T	14: 33,047,251	V2086M	possibly damaging	Het
Zfp592	A	T	7: 81,025,486	T733S	possibly damaging	Het
Zfp599	A	G	9: 22,250,242	F209S	probably damaging	Het

Other mutations in Vps53

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00475:Vps53	APN	11	76077035	splice site	probably null
IGL01596:Vps53	APN	11	76063037	missense	probably damaging	1.00
IGL01655:Vps53	APN	11	76063034	missense	probably damaging	0.97
IGL02275:Vps53	APN	11	76047123	missense	probably benign	0.03
IGL02321:Vps53	APN	11	76048538	missense	possibly damaging	0.60
IGL02581:Vps53	APN	11	76102057	missense	probably damaging	0.99
IGL02821:Vps53	APN	11	76136317	splice site	probably benign
IGL02958:Vps53	APN	11	76117711	missense	probably damaging	1.00
IGL03001:Vps53	APN	11	76138324	missense	probably damaging	1.00
PIT4519001:Vps53	UTSW	11	76117173	missense	probably damaging	1.00
R0257:Vps53	UTSW	11	76177385	intron	probably benign
R0391:Vps53	UTSW	11	76121579	missense	probably benign	0.31
R0421:Vps53	UTSW	11	76082670	missense	probably damaging	1.00
R0882:Vps53	UTSW	11	76082659	missense	probably damaging	1.00
R2509:Vps53	UTSW	11	76066835	missense	possibly damaging	0.49
R3622:Vps53	UTSW	11	76117783	missense	probably benign	0.00
R5137:Vps53	UTSW	11	76166248	missense	probably damaging	1.00
R5338:Vps53	UTSW	11	76081208	missense	probably damaging	1.00
R5756:Vps53	UTSW	11	76092330	splice site	probably benign
R5786:Vps53	UTSW	11	76063007	missense	probably benign	0.08
R5961:Vps53	UTSW	11	76048490	missense	probably damaging	1.00
R6059:Vps53	UTSW	11	76066867	missense	possibly damaging	0.57
R6273:Vps53	UTSW	11	76102018	missense	probably benign	0.16
R6490:Vps53	UTSW	11	76077055	missense	probably benign	0.03
R6671:Vps53	UTSW	11	76134506	missense	probably damaging	1.00
R6772:Vps53	UTSW	11	76179498	start codon destroyed	probably null
R7378:Vps53	UTSW	11	76077074	missense	possibly damaging	0.88
R7735:Vps53	UTSW	11	76047136	missense	probably damaging	1.00
R8066:Vps53	UTSW	11	76136307	missense	probably damaging	1.00
Z1177:Vps53	UTSW	11	76136198	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- TGCAGACAATGGAGAGTTGTGC -3'
(R):5'- GATATCTGGGTCTCGCAAGTC -3'

Sequencing Primer
(F):5'- CACATGAGTGTACTAGTTGACTTG -3'
(R):5'- GTCTCGCAAGTCGTCCCAC -3'

Posted On

2018-07-23