Mutagenetix > Incidental Mutation

Incidental Mutation 'R6302:Vps52'

509316

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

044467-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6302 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

34174786-34186009 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 34182189 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Serine at position 589 (F589S)

Ref Sequence

ENSEMBL: ENSMUSP00000025178 (fasta)

Gene Model

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

AlphaFold

Q8C754

Predicted Effect

probably damaging
Transcript: ENSMUST00000025178
AA Change: F589S

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

SMART Domains

Protein: ENSMUSP00000025178
Gene: ENSMUSG00000024319
AA Change: F589S

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: ENSMUST00000172558

Predicted Effect

probably damaging
Transcript: ENSMUST00000173196
AA Change: F521S

PolyPhen 2 Score 0.959 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000133926
Gene: ENSMUSG00000024319
AA Change: F521S

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: ENSMUST00000173318

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173445

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000174588

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadacl4fm4	G	T	4: 144,396,760 (GRCm39)	S324*	probably null	Het
Actl11	T	G	9: 107,806,772 (GRCm39)	V365G	probably benign	Het
Adgrg6	T	A	10: 14,317,227 (GRCm39)	D531V	probably benign	Het
Ankrd11	A	G	8: 123,616,728 (GRCm39)	S2354P	probably benign	Het
Ano9	A	T	7: 140,684,221 (GRCm39)	W514R	probably damaging	Het
Arfgef3	A	T	10: 18,528,589 (GRCm39)	V266E	probably damaging	Het
Bahcc1	T	C	11: 120,167,634 (GRCm39)	I1345T	probably damaging	Het
Bpifb4	G	A	2: 153,801,587 (GRCm39)	M355I	probably benign	Het
Catsperb	T	C	12: 101,554,402 (GRCm39)	S699P	possibly damaging	Het
Cdh23	T	G	10: 60,140,872 (GRCm39)	I3161L	possibly damaging	Het
Chd3	T	C	11: 69,244,604 (GRCm39)	T1257A	probably damaging	Het
Cnnm4	C	T	1: 36,539,036 (GRCm39)	T638I	probably benign	Het
Cspg4b	A	G	13: 113,504,646 (GRCm39)	D1925G	probably damaging	Het
Cyp26c1	A	G	19: 37,674,936 (GRCm39)	T86A	probably damaging	Het
Cyp3a63-ps	A	G	5: 145,564,847 (GRCm39)		noncoding transcript	Het
Dnah14	T	A	1: 181,428,771 (GRCm39)	I259N	possibly damaging	Het
Dnah17	T	C	11: 118,019,981 (GRCm39)	D22G	probably benign	Het
Epn2	T	G	11: 61,437,312 (GRCm39)	T87P	probably damaging	Het
Fbxl18	A	G	5: 142,874,578 (GRCm39)	L81P	probably damaging	Het
Gas1	A	T	13: 60,323,970 (GRCm39)	D221E	probably damaging	Het
Gm8356	T	C	14: 17,691,275 (GRCm39)	Y130C	probably damaging	Het
Gpr151	T	G	18: 42,712,459 (GRCm39)	K73T	probably damaging	Het
Helq	A	C	5: 100,946,305 (GRCm39)	V12G	probably damaging	Het
Inpp4b	A	G	8: 82,494,806 (GRCm39)	T74A	probably benign	Het
Kirrel3	G	A	9: 34,919,045 (GRCm39)	V234I	probably damaging	Het
Kxd1	T	A	8: 70,972,713 (GRCm39)		probably null	Het
Lif	T	C	11: 4,218,924 (GRCm39)	Y68H	probably damaging	Het
Map6	A	G	7: 98,985,314 (GRCm39)	Q406R	probably damaging	Het
Mcoln3	A	T	3: 145,830,527 (GRCm39)	M86L	probably benign	Het
Mei1	T	A	15: 81,987,439 (GRCm39)	Y834*	probably null	Het
Mroh1	T	C	15: 76,320,319 (GRCm39)		probably null	Het
Myo15b	T	C	11: 115,777,065 (GRCm39)	I2319T	possibly damaging	Het
Myo7b	T	G	18: 32,127,439 (GRCm39)	D621A	probably damaging	Het
Naip5	C	T	13: 100,359,674 (GRCm39)	A521T	possibly damaging	Het
Nek7	T	C	1: 138,426,351 (GRCm39)	D254G	probably damaging	Het
Nsd2	A	G	5: 34,024,921 (GRCm39)	R560G	possibly damaging	Het
Or2t46	T	C	11: 58,472,464 (GRCm39)	F265L	probably benign	Het
Or52x1	A	T	7: 104,852,926 (GRCm39)	L208H	probably damaging	Het
Pbx1	T	A	1: 168,018,910 (GRCm39)	T312S	probably benign	Het
Peg10	GAT	GATCAT	6: 4,756,449 (GRCm39)		probably benign	Het
Pitrm1	A	G	13: 6,610,097 (GRCm39)	S390G	probably damaging	Het
Plcxd3	C	T	15: 4,546,239 (GRCm39)	T81M	probably damaging	Het
Pmf1	C	T	3: 88,307,017 (GRCm39)		probably null	Het
Rabep1	T	C	11: 70,825,947 (GRCm39)	V739A	probably damaging	Het
Rex2	A	G	4: 147,142,451 (GRCm39)	D313G	possibly damaging	Het
Rpia	C	T	6: 70,750,485 (GRCm39)	V216I	probably damaging	Het
Rsf1	CG	CGACGGCGGTG	7: 97,229,115 (GRCm39)		probably benign	Het
Sec13	T	A	6: 113,712,167 (GRCm39)	H56L	probably damaging	Het
Sec16a	A	T	2: 26,315,817 (GRCm39)	V1733D	probably damaging	Het
Sim2	G	A	16: 93,898,089 (GRCm39)	A108T	probably damaging	Het
Slc27a5	T	C	7: 12,722,479 (GRCm39)	D665G	probably damaging	Het
Slc38a6	T	A	12: 73,383,849 (GRCm39)	V180E	probably damaging	Het
Smarcad1	T	G	6: 65,052,122 (GRCm39)	N38K	possibly damaging	Het
Spem2	T	C	11: 69,709,091 (GRCm39)	T45A	possibly damaging	Het
Svil	T	C	18: 5,057,432 (GRCm39)	S714P	probably benign	Het
Taar7b	T	A	10: 23,876,158 (GRCm39)	S108T	possibly damaging	Het
Tbl3	T	C	17: 24,923,645 (GRCm39)	K256E	probably benign	Het
Tcam1	T	G	11: 106,177,276 (GRCm39)	C423G	probably damaging	Het
Trpm4	A	T	7: 44,977,143 (GRCm39)		probably null	Het
Ttyh2	T	C	11: 114,592,662 (GRCm39)	C231R	probably damaging	Het
Ugt3a1	C	T	15: 9,365,397 (GRCm39)	P337S	probably damaging	Het
Vmn2r83	A	C	10: 79,304,837 (GRCm39)	T16P	possibly damaging	Het
Xkr4	T	C	1: 3,286,961 (GRCm39)	T410A	probably damaging	Het
Xkr9	A	G	1: 13,742,726 (GRCm39)	T4A	probably damaging	Het
Yars2	T	C	16: 16,122,438 (GRCm39)	L268P	probably damaging	Het
Zbtb41	C	A	1: 139,357,027 (GRCm39)	N427K	possibly damaging	Het
Zeb2	T	C	2: 44,887,771 (GRCm39)	T414A	probably benign	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
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'- TGATGGTAATGCTGCTCCTCC -3'
(R):5'- GGGCTATAGTACATGCACACAC -3'

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

Posted On

2018-04-02