Mutagenetix > Incidental Mutation

Incidental Mutation 'R5381:Vps52'

424758

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

042956-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R5381 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

34174786-34186009 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 34177275 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Glycine at position 106 (S106G)

Ref Sequence

ENSEMBL: ENSMUSP00000133926 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000008812] [ENSMUST00000025178] [ENSMUST00000173196] [ENSMUST00000174609]

AlphaFold

Q8C754

Predicted Effect

probably benign
Transcript: ENSMUST00000008812

SMART Domains

Protein: ENSMUSP00000008812
Gene: ENSMUSG00000008668

Domain	Start	End	E-Value	Type
Pfam:Ribosomal_S13	14	142	2.2e-59	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000025178
AA Change: S106G

PolyPhen 2 Score 0.606 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000025178
Gene: ENSMUSG00000024319
AA Change: S106G

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

noncoding transcript
Transcript: ENSMUST00000122652

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000172550

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000172558

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000172799

Predicted Effect

possibly damaging
Transcript: ENSMUST00000173196
AA Change: S106G

PolyPhen 2 Score 0.769 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000133926
Gene: ENSMUSG00000024319
AA Change: S106G

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173445

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174662

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174745

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173318

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174175

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174620

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174588

Predicted Effect

probably benign
Transcript: ENSMUST00000174609

SMART Domains

Protein: ENSMUSP00000138296
Gene: ENSMUSG00000008668

Domain	Start	End	E-Value	Type
Pfam:Ribosomal_S13	14	107	2.1e-21	PFAM

Meta Mutation Damage Score

0.2884

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.1%

Validation Efficiency

100% (74/74)

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700086D15Rik	G	T	11: 65,044,137 (GRCm39)	S19*	probably null	Het
4930432E11Rik	A	T	7: 29,262,393 (GRCm39)		noncoding transcript	Het
Acvr1c	T	C	2: 58,177,747 (GRCm39)	T241A	probably damaging	Het
Ankmy1	T	C	1: 92,804,284 (GRCm39)	T900A	probably benign	Het
Anp32a	A	C	9: 62,279,459 (GRCm39)	E107A	probably damaging	Het
Arhgef40	T	C	14: 52,229,306 (GRCm39)	I623T	probably damaging	Het
Camsap3	T	A	8: 3,653,812 (GRCm39)	I483N	probably damaging	Het
Card9	G	A	2: 26,248,895 (GRCm39)	L85F	probably damaging	Het
Cbfa2t2	T	G	2: 154,365,849 (GRCm39)	V353G	probably damaging	Het
Ccdc166	A	T	15: 75,852,701 (GRCm39)	L422*	probably null	Het
Ccdc198	T	C	14: 49,470,364 (GRCm39)	D185G	probably damaging	Het
Ccdc73	A	T	2: 104,820,270 (GRCm39)	N416Y	probably damaging	Het
Celsr2	A	T	3: 108,310,073 (GRCm39)	D1552E	probably damaging	Het
Ces1b	A	T	8: 93,791,647 (GRCm39)	N317K	probably benign	Het
Col6a3	T	C	1: 90,703,334 (GRCm39)	R2471G	unknown	Het
Crocc	C	T	4: 140,756,622 (GRCm39)	R1165H	possibly damaging	Het
Csmd3	T	A	15: 47,604,611 (GRCm39)	Y1955F	probably benign	Het
Ctbp1	A	T	5: 33,407,034 (GRCm39)	D232E	probably benign	Het
Cuedc1	T	A	11: 88,078,812 (GRCm39)		probably null	Het
Dctd	C	T	8: 48,590,449 (GRCm39)		probably benign	Het
Dusp6	G	A	10: 99,102,129 (GRCm39)	V226I	possibly damaging	Het
Gpr152	A	G	19: 4,192,516 (GRCm39)	E19G	probably damaging	Het
Ighv16-1	T	C	12: 114,032,593 (GRCm39)	T70A	probably benign	Het
Igkv4-80	A	C	6: 68,993,649 (GRCm39)	S81A	probably benign	Het
Il12b	C	A	11: 44,298,699 (GRCm39)	D51E	possibly damaging	Het
Il9r	T	G	11: 32,140,715 (GRCm39)	D435A	probably benign	Het
Jakmip2	T	C	18: 43,715,025 (GRCm39)	D167G	probably damaging	Het
Klrd1	A	G	6: 129,572,397 (GRCm39)	D63G	possibly damaging	Het
Lactb	A	G	9: 66,863,297 (GRCm39)	L439P	probably damaging	Het
Laptm5	T	C	4: 130,660,969 (GRCm39)		probably benign	Het
Lgals1	A	G	15: 78,814,223 (GRCm39)	D96G	probably benign	Het
Lrp8	A	T	4: 107,726,307 (GRCm39)	H871L	probably damaging	Het
Mfap4	A	T	11: 61,378,756 (GRCm39)	I235F	probably benign	Het
Muc6	G	A	7: 141,217,836 (GRCm39)	T2279I	possibly damaging	Het
Nlrp4b	T	A	7: 10,449,172 (GRCm39)	Y91*	probably null	Het
Osbp2	A	G	11: 3,655,593 (GRCm39)	Y383H	probably benign	Het
Otx1	C	A	11: 21,947,037 (GRCm39)	A91S	probably damaging	Het
Palb2	G	T	7: 121,727,636 (GRCm39)	T78K	probably benign	Het
Panx2	G	T	15: 88,944,433 (GRCm39)	V53L	probably damaging	Het
Pip4p1	T	C	14: 51,166,495 (GRCm39)	E161G	probably benign	Het
Pitx1	T	C	13: 55,973,892 (GRCm39)	Y313C	probably damaging	Het
Pjvk	A	G	2: 76,481,904 (GRCm39)		probably null	Het
Pnldc1	T	G	17: 13,109,283 (GRCm39)	K439T	probably benign	Het
Ppp4r4	A	C	12: 103,559,357 (GRCm39)	T513P	probably benign	Het
Pram1	A	T	17: 33,860,600 (GRCm39)	Q389L	probably damaging	Het
Prg4	T	C	1: 150,330,204 (GRCm39)		probably benign	Het
Prkch	C	A	12: 73,738,366 (GRCm39)	R158S	probably damaging	Het
Ptpn7	A	T	1: 135,070,906 (GRCm39)	M332L	probably damaging	Het
Rad51c	A	T	11: 87,288,459 (GRCm39)	D241E	probably benign	Het
Rara	T	G	11: 98,862,410 (GRCm39)	I270M	possibly damaging	Het
Ryr2	T	A	13: 11,571,544 (GRCm39)	D4898V	probably damaging	Het
Sec31b	C	T	19: 44,522,810 (GRCm39)	G218S	probably damaging	Het
Slc9a1	T	A	4: 133,149,382 (GRCm39)	L736Q	probably damaging	Het
Slco2a1	A	T	9: 102,945,213 (GRCm39)	D196V	probably damaging	Het
Sp3	C	A	2: 72,800,910 (GRCm39)	A368S	probably benign	Het
Stk24	A	T	14: 121,531,645 (GRCm39)	L337Q	possibly damaging	Het
Tbc1d13	A	G	2: 30,027,379 (GRCm39)	T96A	probably benign	Het
Tm2d3	G	A	7: 65,351,420 (GRCm39)	G225S	probably damaging	Het
Urb2	T	C	8: 124,756,651 (GRCm39)	V786A	probably benign	Het
Usp32	C	T	11: 84,949,953 (GRCm39)		probably benign	Het
Usp54	C	T	14: 20,636,144 (GRCm39)	G300D	probably damaging	Het
Vmn1r124	T	A	7: 20,994,323 (GRCm39)	N74Y	probably damaging	Het
Vmn1r77	T	A	7: 11,775,952 (GRCm39)	C175S	probably damaging	Het
Vmn2r62	G	T	7: 42,437,219 (GRCm39)	Q422K	probably benign	Het
Vmn2r76	A	G	7: 85,874,496 (GRCm39)	F827S	probably damaging	Het
Zdhhc1	CGGGGG	CGGGGGG	8: 106,210,376 (GRCm39)		probably null	Het
Zic2	A	G	14: 122,713,227 (GRCm39)	N47S	probably 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
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
R6888:Vps52	UTSW	17	34,182,180 (GRCm39)	missense	probably benign	0.06
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'- CCAAGATGGCTGCTATTGGC -3'
(R):5'- GTCTCTGTGCAAATCCCTGGTAC -3'

Sequencing Primer
(F):5'- GCTATTGGCATGGGCTCTTG -3'
(R):5'- TGGGAGATCATCACTTGTCCAAG -3'

Posted On

2016-08-04