Mutagenetix > Incidental Mutation

Incidental Mutation 'R6888:Vps52'

537076

Institutional Source

Beutler Lab

Gene Symbol

Vps52

Ensembl Gene

ENSMUSG00000024319

Gene Name

VPS52 GARP complex subunit

Synonyms

tclw5, ARE1, D430041K17Rik, tcl-w5, Sacm2l

MMRRC Submission

044982-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6888 (G1)

Quality Score

220.009

Status

Not validated

Chromosome

Chromosomal Location

34174786-34186009 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 34182180 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 518 (V518A)

Ref Sequence

ENSEMBL: ENSMUSP00000133926 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000025178] [ENSMUST00000173196]

AlphaFold

Q8C754

Predicted Effect

probably benign
Transcript: ENSMUST00000025178
AA Change: V586A

PolyPhen 2 Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000025178
Gene: ENSMUSG00000024319
AA Change: V586A

Domain	Start	End	E-Value	Type
low complexity region	1	11	N/A	INTRINSIC
low complexity region	24	45	N/A	INTRINSIC
Pfam:Sec3_C	79	244	4.6e-13	PFAM
Pfam:Vps52	94	601	5.1e-233	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000173196
AA Change: V518A

PolyPhen 2 Score 0.060 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000133926
Gene: ENSMUSG00000024319
AA Change: V518A

Domain	Start	End	E-Value	Type
low complexity region	18	39	N/A	INTRINSIC
Pfam:Vps52	88	120	2.7e-6	PFAM
Pfam:Vps52	116	527	3e-181	PFAM

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.4%
20x: 98.1%

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 that is similar to the yeast suppressor of actin mutations 2 gene. The yeast protein forms a subunit of the tetrameric Golgi-associated retrograde protein complex that is involved in vesicle trafficking from from both early and late endosomes, back to the trans-Golgi network. This gene is located on chromosome 6 in a head-to-head orientation with the gene encoding ribosomal protein S18. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
PHENOTYPE: Mice homozygous for a null mutation display early embryonic lethality. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Actg1	T	C	11: 120,238,141 (GRCm39)	Y190C	probably damaging	Het
Adgrv1	A	G	13: 81,656,788 (GRCm39)	I2902T	probably damaging	Het
AI429214	G	A	8: 37,460,987 (GRCm39)	G45D	possibly damaging	Het
Ambra1	A	G	2: 91,599,372 (GRCm39)	D164G	probably damaging	Het
Ap3b1	A	T	13: 94,545,299 (GRCm39)	Q184L	probably benign	Het
Arhgef17	T	C	7: 100,580,027 (GRCm39)	D307G	possibly damaging	Het
AY761185	A	T	8: 21,434,571 (GRCm39)	Y52*	probably null	Het
Bfsp1	A	G	2: 143,668,639 (GRCm39)	S647P	probably benign	Het
C130073F10Rik	A	G	4: 101,747,453 (GRCm39)	V192A	probably benign	Het
Cacna1g	T	A	11: 94,350,033 (GRCm39)	D604V	probably benign	Het
Ccdc170	T	C	10: 4,496,854 (GRCm39)	V458A	possibly damaging	Het
Ccdc187	G	A	2: 26,179,746 (GRCm39)	R238W	probably damaging	Het
Cdh1	A	G	8: 107,384,946 (GRCm39)	S380G	probably benign	Het
Cdk5rap3	T	C	11: 96,807,018 (GRCm39)	H4R	probably benign	Het
Cftr	G	A	6: 18,313,729 (GRCm39)		probably null	Het
Cstpp1	A	G	2: 91,252,239 (GRCm39)	Y41H	probably damaging	Het
Dnajc16	A	G	4: 141,504,303 (GRCm39)	V219A	probably benign	Het
Drd3	A	T	16: 43,637,502 (GRCm39)	I266F	probably benign	Het
Dut	A	G	2: 125,099,044 (GRCm39)	D177G	probably benign	Het
Esr1	A	G	10: 4,807,076 (GRCm39)	I331V	probably benign	Het
Gm11110	A	G	17: 57,409,143 (GRCm39)		probably benign	Het
Grm7	G	T	6: 111,335,314 (GRCm39)	G575V	possibly damaging	Het
Heatr3	A	G	8: 88,897,512 (GRCm39)	Y531C	probably damaging	Het
Igfn1	A	G	1: 135,910,218 (GRCm39)	V122A	probably benign	Het
Igsf21	T	C	4: 139,762,054 (GRCm39)	D208G	probably benign	Het
Kntc1	T	C	5: 123,949,373 (GRCm39)	Y1915H	probably damaging	Het
Lamc1	A	T	1: 153,138,238 (GRCm39)	D205E	probably damaging	Het
Limch1	C	T	5: 67,179,269 (GRCm39)	T713I	probably benign	Het
Lrp1b	A	G	2: 41,361,138 (GRCm39)	I555T	probably benign	Het
Lrp2	A	T	2: 69,354,485 (GRCm39)	F448I	probably damaging	Het
Marchf6	T	C	15: 31,459,379 (GRCm39)	K896E	probably benign	Het
Mroh4	T	C	15: 74,485,098 (GRCm39)	Y469C	possibly damaging	Het
Niban3	G	T	8: 72,056,383 (GRCm39)	R361L	probably benign	Het
Nos3	T	C	5: 24,588,333 (GRCm39)	V1060A	possibly damaging	Het
Nr1h4	A	G	10: 89,292,404 (GRCm39)	I406T	probably damaging	Het
Odf2l	T	C	3: 144,854,379 (GRCm39)		probably null	Het
Or2y15	A	T	11: 49,351,087 (GRCm39)	T194S	probably damaging	Het
Or5d14	A	G	2: 87,880,608 (GRCm39)	M120T	probably damaging	Het
Pals2	T	G	6: 50,157,257 (GRCm39)		probably null	Het
Pbx2	A	G	17: 34,813,081 (GRCm39)	Y119C	possibly damaging	Het
Pdcd6ip	C	A	9: 113,500,905 (GRCm39)	A526S	probably benign	Het
Prx	G	A	7: 27,219,059 (GRCm39)	D1187N	possibly damaging	Het
Ptpro	G	A	6: 137,357,198 (GRCm39)	V230I	probably benign	Het
Rtn3	C	T	19: 7,434,614 (GRCm39)	M440I	probably benign	Het
Sar1b	T	C	11: 51,679,019 (GRCm39)	I96T	probably damaging	Het
Sds	T	C	5: 120,618,965 (GRCm39)		probably null	Het
Secisbp2	A	G	13: 51,833,977 (GRCm39)	T706A	probably benign	Het
Sorcs3	A	T	19: 48,682,263 (GRCm39)	M433L	possibly damaging	Het
Sppl2a	A	G	2: 126,746,912 (GRCm39)	V472A	probably damaging	Het
Tbc1d9	A	G	8: 83,998,217 (GRCm39)	E1258G	possibly damaging	Het
Tbxas1	C	A	6: 38,929,008 (GRCm39)		probably benign	Het
Tg	T	C	15: 66,568,095 (GRCm39)	I1333T	probably damaging	Het
Tmem108	C	T	9: 103,376,915 (GRCm39)	G178D	probably damaging	Het
Tmem174	A	G	13: 98,773,569 (GRCm39)	L87P	probably damaging	Het
Tmppe	T	A	9: 114,233,769 (GRCm39)	S23T	probably damaging	Het
Ttn	G	A	2: 76,591,447 (GRCm39)	T21074I	probably benign	Het
Tub	A	G	7: 108,628,505 (GRCm39)	M338V	probably null	Het
Vmn1r160	A	T	7: 22,571,531 (GRCm39)	R295*	probably null	Het
Wdr59	A	G	8: 112,177,675 (GRCm39)	V909A	probably benign	Het
Wnk1	T	C	6: 119,925,742 (GRCm39)	T1241A	probably benign	Het
Zfp882	G	A	8: 72,668,130 (GRCm39)	C319Y	probably benign	Het
Znfx1	A	T	2: 166,880,860 (GRCm39)	I308N	possibly damaging	Het

Other mutations in Vps52

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00946:Vps52	APN	17	34,175,932 (GRCm39)	missense	possibly damaging	0.96
IGL01098:Vps52	APN	17	34,181,704 (GRCm39)	missense	possibly damaging	0.90
IGL01705:Vps52	APN	17	34,185,042 (GRCm39)	missense	probably damaging	1.00
IGL01722:Vps52	APN	17	34,180,589 (GRCm39)	nonsense	probably null
IGL02992:Vps52	APN	17	34,177,324 (GRCm39)	missense	probably damaging	0.97
IGL03279:Vps52	APN	17	34,176,848 (GRCm39)	missense	probably damaging	0.96
R0363:Vps52	UTSW	17	34,181,091 (GRCm39)	missense	probably benign	0.26
R0762:Vps52	UTSW	17	34,178,985 (GRCm39)	missense	probably damaging	1.00
R1065:Vps52	UTSW	17	34,180,213 (GRCm39)	missense	probably benign	0.02
R1506:Vps52	UTSW	17	34,176,868 (GRCm39)	missense	probably damaging	1.00
R3760:Vps52	UTSW	17	34,179,162 (GRCm39)	missense	possibly damaging	0.64
R4714:Vps52	UTSW	17	34,180,153 (GRCm39)	missense	probably benign	0.25
R5381:Vps52	UTSW	17	34,177,275 (GRCm39)	missense	possibly damaging	0.77
R5590:Vps52	UTSW	17	34,180,195 (GRCm39)	missense	probably benign	0.01
R5928:Vps52	UTSW	17	34,180,100 (GRCm39)	missense	possibly damaging	0.85
R6003:Vps52	UTSW	17	34,175,068 (GRCm39)	start codon destroyed	probably null	0.01
R6302:Vps52	UTSW	17	34,182,189 (GRCm39)	missense	probably damaging	1.00
R6574:Vps52	UTSW	17	34,181,452 (GRCm39)	missense	probably null	0.34
R6695:Vps52	UTSW	17	34,182,173 (GRCm39)	nonsense	probably null
R7022:Vps52	UTSW	17	34,178,293 (GRCm39)	missense	probably benign	0.04
R7136:Vps52	UTSW	17	34,184,262 (GRCm39)	missense	probably benign	0.00
R7380:Vps52	UTSW	17	34,177,283 (GRCm39)	missense	possibly damaging	0.82
R7727:Vps52	UTSW	17	34,181,108 (GRCm39)	missense	probably benign	0.21
R7888:Vps52	UTSW	17	34,184,725 (GRCm39)	missense	probably damaging	0.98
R8385:Vps52	UTSW	17	34,181,791 (GRCm39)	missense	probably damaging	1.00
R8956:Vps52	UTSW	17	34,177,049 (GRCm39)	missense	probably benign	0.01
R9457:Vps52	UTSW	17	34,181,156 (GRCm39)	missense	probably damaging	0.97

Predicted Primers

PCR Primer
(F):5'- ATGGTAATGCTGCTCCTCCC -3'
(R):5'- CAGGGCTATAGTACATGCACAC -3'

Sequencing Primer
(F):5'- CACGGGGGTCCCTACAG -3'
(R):5'- TGTAGCTATAGTACACACACATGC -3'

Posted On

2018-10-18