Mutagenetix > Incidental Mutation

Incidental Mutation 'R8385:Vps52'

647143

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

067751-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R8385 (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 34181791 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 539 (L539P)

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: L539P

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

SMART Domains

Protein: ENSMUSP00000025178
Gene: ENSMUSG00000024319
AA Change: L539P

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 damaging
Transcript: ENSMUST00000173196
AA Change: L471P

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

SMART Domains

Protein: ENSMUSP00000133926
Gene: ENSMUSG00000024319
AA Change: L471P

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: 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: 51 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Brap	C	T	5: 121,823,197 (GRCm39)	T473I	probably benign	Het
Cacna1e	T	A	1: 154,319,687 (GRCm39)	M1400L	probably damaging	Het
Catsper2	A	G	2: 121,240,621 (GRCm39)	I127T	possibly damaging	Het
Dbt	A	T	3: 116,317,039 (GRCm39)	I72F	probably damaging	Het
Ddhd2	T	C	8: 26,225,041 (GRCm39)	H592R	probably damaging	Het
Disp2	T	A	2: 118,620,891 (GRCm39)	M541K	probably damaging	Het
Dnai7	C	T	6: 145,120,918 (GRCm39)	E685K	probably damaging	Het
Dnmbp	T	C	19: 43,878,090 (GRCm39)	D327G	probably benign	Het
Dvl1	A	G	4: 155,940,037 (GRCm39)	S390G	possibly damaging	Het
Fbxo22	A	G	9: 55,121,233 (GRCm39)	D106G	probably damaging	Het
Gfm2	A	G	13: 97,301,519 (GRCm39)	T441A	probably benign	Het
Gm5431	T	C	11: 48,780,347 (GRCm39)	I192V	probably damaging	Het
Gosr1	T	A	11: 76,620,967 (GRCm39)	T241S	possibly damaging	Het
Hk2	T	C	6: 82,706,527 (GRCm39)	S792G	probably benign	Het
Itsn1	A	C	16: 91,690,699 (GRCm39)	K1302Q	unknown	Het
Kif16b	T	C	2: 142,554,258 (GRCm39)	K847E	probably benign	Het
Lfng	G	A	5: 140,598,981 (GRCm39)	E297K	probably damaging	Het
Mark3	A	G	12: 111,621,808 (GRCm39)	D650G	possibly damaging	Het
Mgat4f	A	G	1: 134,318,376 (GRCm39)	K383E	probably benign	Het
Mob3b	T	C	4: 34,985,980 (GRCm39)	Y186C	probably damaging	Het
Mphosph9	T	C	5: 124,450,785 (GRCm39)	K329E	probably benign	Het
Mta1	A	T	12: 113,095,085 (GRCm39)	M448L	probably benign	Het
Mterf1a	A	T	5: 3,941,384 (GRCm39)	N161K	probably damaging	Het
Myo10	T	A	15: 25,804,484 (GRCm39)	I1593N	probably damaging	Het
Naca	A	G	10: 127,878,307 (GRCm39)	N1113S	unknown	Het
Or2w4	T	C	13: 21,795,522 (GRCm39)	I206V	probably benign	Het
Or5e1	T	G	7: 108,354,511 (GRCm39)	Y149*	probably null	Het
Pcdhga1	A	T	18: 37,795,149 (GRCm39)	D51V	probably damaging	Het
Peg3	T	C	7: 6,711,082 (GRCm39)	E1380G	probably damaging	Het
Pkd1	G	A	17: 24,794,702 (GRCm39)	V2130M	possibly damaging	Het
Pla2g4c	C	T	7: 13,063,589 (GRCm39)	P19S	probably benign	Het
Popdc2	G	A	16: 38,183,262 (GRCm39)	V82I	probably benign	Het
Ppfibp2	A	G	7: 107,296,894 (GRCm39)	R203G	probably benign	Het
Rab19	T	A	6: 39,360,892 (GRCm39)	N13K	probably benign	Het
Raet1d	T	A	10: 22,246,817 (GRCm39)	D48E	probably benign	Het
Rell1	T	A	5: 64,087,861 (GRCm39)	K136*	probably null	Het
Slc38a4	A	G	15: 96,897,393 (GRCm39)	I474T	probably damaging	Het
Slf1	T	C	13: 77,254,109 (GRCm39)	M243V	probably benign	Het
Spata31f1a	C	T	4: 42,850,509 (GRCm39)	R549H	possibly damaging	Het
Speer4c2	A	T	5: 15,857,669 (GRCm39)	S203T	unknown	Het
Spg11	A	T	2: 121,927,802 (GRCm39)	S661T	probably benign	Het
Thra	C	G	11: 98,659,177 (GRCm39)	S435R	probably benign	Het
Tmem181a	T	C	17: 6,339,274 (GRCm39)	I61T	probably benign	Het
Ttpa	G	A	4: 20,028,483 (GRCm39)	G247S	probably damaging	Het
Usp17lb	C	T	7: 104,489,830 (GRCm39)	V366I	possibly damaging	Het
Vit	A	T	17: 78,927,066 (GRCm39)	Q337L	probably benign	Het
Vmn2r102	A	G	17: 19,914,088 (GRCm39)	Y551C	possibly damaging	Het
Ythdc1	C	A	5: 86,975,961 (GRCm39)	P529T	possibly damaging	Het
Zdhhc13	T	C	7: 48,455,444 (GRCm39)		probably null	Het
Zfp282	A	T	6: 47,882,023 (GRCm39)	Y570F	possibly damaging	Het
Zfp872	A	T	9: 22,111,407 (GRCm39)	K295N	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
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
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
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'- CAACATCTGTTCTGACTGGTGAC -3'
(R):5'- AGGAGCAGCATTACCATCAGC -3'

Sequencing Primer
(F):5'- CAGAACTTGCAGGGGTATCTG -3'
(R):5'- ACCCCGAGCATCATGTCATAGTTG -3'

Posted On

2020-09-02