Mutagenetix > Incidental Mutation

Incidental Mutation 'R7380:Vps52'

572677

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

045462-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7380 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

34174786-34186009 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 34177283 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 108 (N108K)

Ref Sequence

ENSEMBL: ENSMUSP00000025178 (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: N108K

PolyPhen 2 Score 0.817 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000025178
Gene: ENSMUSG00000024319
AA Change: N108K

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: N108K

PolyPhen 2 Score 0.111 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000133926
Gene: ENSMUSG00000024319
AA Change: N108K

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

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

0.1795

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

98% (79/81)

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: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700030J22Rik	T	C	8: 117,700,376 (GRCm39)	T9A	probably benign	Het
Abcc5	A	T	16: 20,215,784 (GRCm39)	S414R	possibly damaging	Het
Acads	C	A	5: 115,249,057 (GRCm39)	Q365H	probably damaging	Het
Ankib1	G	T	5: 3,772,576 (GRCm39)	Q487K	probably benign	Het
BC034090	T	G	1: 155,108,229 (GRCm39)	S11R	probably damaging	Het
Car12	A	G	9: 66,654,945 (GRCm39)	N125S	probably benign	Het
Casq1	A	G	1: 172,044,416 (GRCm39)	V137A	probably benign	Het
Cfap54	C	A	10: 92,883,840 (GRCm39)	V305F	probably damaging	Het
Clstn3	T	C	6: 124,433,948 (GRCm39)	E404G	probably benign	Het
Copg1	T	G	6: 87,870,824 (GRCm39)	L209R	probably damaging	Het
Cpb2	A	T	14: 75,493,449 (GRCm39)	Q42L	possibly damaging	Het
Cpd	G	A	11: 76,693,151 (GRCm39)	Q712*	probably null	Het
Csmd3	T	A	15: 47,450,361 (GRCm39)	Y2690F		Het
Dchs1	G	T	7: 105,407,835 (GRCm39)	T1999K	probably benign	Het
Ddx10	T	A	9: 53,151,786 (GRCm39)	T80S	probably damaging	Het
Dmtn	G	A	14: 70,854,768 (GRCm39)	T69I	probably damaging	Het
Dnah5	T	A	15: 28,370,524 (GRCm39)	H2821Q	probably damaging	Het
Fam162b	T	A	10: 51,466,572 (GRCm39)		probably benign	Het
Fam193b	A	C	13: 55,690,612 (GRCm39)	S717A	probably benign	Het
Far2	T	C	6: 148,082,493 (GRCm39)	F500L	unknown	Het
Focad	T	A	4: 88,192,435 (GRCm39)	V588D	unknown	Het
Gm12728	T	C	4: 105,651,593 (GRCm39)	F68L	probably damaging	Het
Gm1527	T	A	3: 28,974,621 (GRCm39)	M478K	probably benign	Het
Gm57858	T	A	3: 36,080,070 (GRCm39)	D229V	possibly damaging	Het
Gpd2	A	T	2: 57,230,171 (GRCm39)	I308F	probably damaging	Het
Igf2bp3	T	C	6: 49,085,933 (GRCm39)	T249A	probably benign	Het
Igfn1	C	A	1: 135,889,746 (GRCm39)	V2434F	probably damaging	Het
Inhca	G	A	9: 103,156,680 (GRCm39)	Q127*	probably null	Het
Kdm5a	C	A	6: 120,382,879 (GRCm39)	Q737K	probably benign	Het
Khdrbs2	T	C	1: 32,372,685 (GRCm39)	S120P	unknown	Het
Lmx1a	T	C	1: 167,519,609 (GRCm39)	F46L	probably damaging	Het
Lrba	C	G	3: 86,232,381 (GRCm39)	T776R	probably damaging	Het
Lrrc8c	A	G	5: 105,755,701 (GRCm39)	N492S	possibly damaging	Het
Mapk3	A	T	7: 126,363,967 (GRCm39)	I365F		Het
Mcee	A	G	7: 64,061,657 (GRCm39)	I153M	possibly damaging	Het
Mllt3	T	C	4: 87,710,180 (GRCm39)	D415G	possibly damaging	Het
Muc4	A	T	16: 32,575,740 (GRCm39)	T1747S	unknown	Het
Myh14	A	T	7: 44,310,466 (GRCm39)	V139E	probably damaging	Het
Myo10	A	T	15: 25,779,706 (GRCm39)	I772L	probably benign	Het
Naa15	T	G	3: 51,367,268 (GRCm39)		probably null	Het
Nbeal1	T	A	1: 60,283,969 (GRCm39)	I841N	probably damaging	Het
Nf1	C	T	11: 79,437,102 (GRCm39)	T2006I	probably damaging	Het
Npr2	T	A	4: 43,641,254 (GRCm39)	W427R	probably damaging	Het
Nr1h3	A	T	2: 91,020,540 (GRCm39)	F324L	possibly damaging	Het
Obscn	T	C	11: 58,947,740 (GRCm39)	K4430E		Het
Or1e1d-ps1	T	A	11: 73,819,013 (GRCm39)	Y61N	possibly damaging	Het
Or5ac21	A	G	16: 59,124,391 (GRCm39)	R292G	probably damaging	Het
Or6c2	A	T	10: 129,362,530 (GRCm39)	T145S	probably benign	Het
Or6d13	T	C	6: 116,517,894 (GRCm39)	L160P	probably benign	Het
Osgin1	T	A	8: 120,172,170 (GRCm39)	H321Q	probably benign	Het
P4ha1	A	G	10: 59,186,273 (GRCm39)	I251V	probably benign	Het
Padi2	G	A	4: 140,644,997 (GRCm39)	W77*	probably null	Het
Pkd1	T	A	17: 24,800,616 (GRCm39)	I3086N	probably damaging	Het
Plk3	T	C	4: 116,988,350 (GRCm39)	N360S	probably benign	Het
Prr14	A	T	7: 127,075,614 (GRCm39)	S541C	probably null	Het
Ptch2	C	A	4: 116,971,843 (GRCm39)	Q1122K	possibly damaging	Het
Rab3gap1	T	C	1: 127,865,727 (GRCm39)	V764A	possibly damaging	Het
Rad50	T	C	11: 53,586,223 (GRCm39)	I258V	probably benign	Het
Rapgef3	G	T	15: 97,664,672 (GRCm39)	R64S	probably benign	Het
Rbm44	A	G	1: 91,079,938 (GRCm39)	N42S	possibly damaging	Het
Ring1	T	C	17: 34,240,694 (GRCm39)	Y361C	probably damaging	Het
Robo3	T	C	9: 37,329,852 (GRCm39)	T1155A	probably damaging	Het
Rsf1	GGCGG	GGCGGTGGCCGCGG	7: 97,229,122 (GRCm39)		probably benign	Het
Ryr3	T	C	2: 112,470,502 (GRCm39)	T4682A	probably damaging	Het
Scart1	A	T	7: 139,804,790 (GRCm39)	N598Y	possibly damaging	Het
Sema7a	T	C	9: 57,868,847 (GRCm39)	V653A	unknown	Het
Slc16a13	T	C	11: 70,110,105 (GRCm39)	Y132C	probably damaging	Het
Slc24a1	A	G	9: 64,855,815 (GRCm39)	V364A	unknown	Het
Slc8a2	C	T	7: 15,868,278 (GRCm39)	A170V	probably damaging	Het
Slfn8	C	T	11: 82,894,566 (GRCm39)	R691Q	not run	Het
Snx2	T	C	18: 53,327,640 (GRCm39)	V122A	probably benign	Het
Sstr1	A	T	12: 58,260,066 (GRCm39)	M230L	probably benign	Het
Themis2	C	T	4: 132,513,528 (GRCm39)	V233I	possibly damaging	Het
Tmem106b	T	C	6: 13,078,167 (GRCm39)	S121P	probably damaging	Het
Tmem63c	A	G	12: 87,124,722 (GRCm39)	I529V	probably benign	Het
Tmem94	T	C	11: 115,686,971 (GRCm39)		probably null	Het
Trmt10c	A	T	16: 55,854,619 (GRCm39)	W339R	probably damaging	Het
Ugt2b1	A	T	5: 87,065,578 (GRCm39)	F487Y	not run	Het
Vmn2r91	T	A	17: 18,356,838 (GRCm39)	L835*	probably null	Het
Wdpcp	T	A	11: 21,661,585 (GRCm39)	C286S	possibly damaging	Het
Zfp959	T	A	17: 56,205,551 (GRCm39)	H529Q	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
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
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'- AAGTCAATCCGGGACTGTATCC -3'
(R):5'- ATCATCACTTGTCCAAGGGG -3'

Sequencing Primer
(F):5'- CCAAGATGGCTGCTATTGGC -3'
(R):5'- TCAGATTTGGGGCAACAG -3'

Posted On

2019-09-13