Mutagenetix > Incidental Mutation

Incidental Mutation 'R6490:Vps53'

522791

Institutional Source

Beutler Lab

Gene Symbol

Vps53

Ensembl Gene

ENSMUSG00000017288

Gene Name

VPS53 GARP complex subunit

Synonyms

2310040I21Rik, 3100002B05Rik, 2010002A08Rik

MMRRC Submission

044622-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6490 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

75937052-76070464 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 75967881 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 414 (M414K)

Ref Sequence

ENSEMBL: ENSMUSP00000104057 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000056601] [ENSMUST00000094015] [ENSMUST00000108419] [ENSMUST00000166752] [ENSMUST00000167114] [ENSMUST00000169734]

AlphaFold

Q8CCB4

Predicted Effect

probably benign
Transcript: ENSMUST00000056601
AA Change: M591K

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000061317
Gene: ENSMUSG00000017288
AA Change: M591K

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:DUF2450	25	225	5.9e-11	PFAM
Pfam:Vps53_N	39	453	1.9e-176	PFAM
low complexity region	520	533	N/A	INTRINSIC
low complexity region	820	832	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000094015
AA Change: M562K

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000091554
Gene: ENSMUSG00000017288
AA Change: M562K

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:Vps53_N	39	96	6.2e-21	PFAM
Pfam:Vps53_N	93	424	1.4e-133	PFAM
low complexity region	491	504	N/A	INTRINSIC
low complexity region	791	803	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000108419
AA Change: M414K

PolyPhen 2 Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)

SMART Domains

Protein: ENSMUSP00000104057
Gene: ENSMUSG00000017288
AA Change: M414K

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:DUF2450	25	224	4e-11	PFAM
Pfam:Vps53_N	39	233	5.2e-87	PFAM
Pfam:Vps53_N	226	276	1.6e-14	PFAM
low complexity region	343	356	N/A	INTRINSIC
low complexity region	643	655	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000143163

Predicted Effect

probably benign
Transcript: ENSMUST00000166752

SMART Domains

Protein: ENSMUSP00000129159
Gene: ENSMUSG00000017288

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:DUF2450	25	225	8.2e-12	PFAM
Pfam:Vps53_N	39	230	6e-87	PFAM
Pfam:Vps53_N	226	405	1.4e-60	PFAM
low complexity region	472	485	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000167114
AA Change: M314K

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000131663
Gene: ENSMUSG00000017288
AA Change: M314K

Domain	Start	End	E-Value	Type
low complexity region	3	19	N/A	INTRINSIC
Pfam:Vps53_N	39	101	1.2e-21	PFAM
Pfam:Vps53_N	104	176	3.1e-15	PFAM
low complexity region	243	256	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000169734

SMART Domains

Protein: ENSMUSP00000130499
Gene: ENSMUSG00000017288

Domain	Start	End	E-Value	Type
Pfam:DUF2450	5	225	5.1e-12	PFAM
Pfam:Vps53_N	39	329	1e-137	PFAM

Meta Mutation Damage Score

0.0676

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.1%
20x: 94.6%

Validation Efficiency

99% (69/70)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein with sequence similarity to the yeast Vps53p protein. Vps53p is involved in retrograde vesicle trafficking in late Golgi. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit embryonic lethality prior to E12.5 with trophoblast cell hyperplasia. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700018B08Rik	T	G	8: 122,267,293 (GRCm39)	K38T	probably benign	Het
Abca13	A	G	11: 9,248,661 (GRCm39)	T2803A	probably benign	Het
Adam23	A	G	1: 63,596,613 (GRCm39)	D565G	probably damaging	Het
Adcy3	A	G	12: 4,262,150 (GRCm39)	T1067A	probably damaging	Het
Agrn	A	T	4: 156,251,819 (GRCm39)	Y1921*	probably null	Het
Apc2	A	G	10: 80,149,757 (GRCm39)	N1604D	probably benign	Het
Atxn7	A	T	14: 14,089,446 (GRCm38)	R321*	probably null	Het
Axin1	T	A	17: 26,361,968 (GRCm39)	I104N	probably damaging	Het
Bahd1	T	C	2: 118,747,619 (GRCm39)	S413P	probably benign	Het
Baz2b	C	T	2: 59,732,073 (GRCm39)	C2024Y	probably damaging	Het
Cacna1i	T	A	15: 80,262,448 (GRCm39)	V1388E	probably damaging	Het
Ces4a	G	A	8: 105,876,090 (GRCm39)	V544M	probably benign	Het
Cntn3	G	A	6: 102,255,301 (GRCm39)	T199I	probably damaging	Het
Col6a4	A	T	9: 105,952,191 (GRCm39)	L569*	probably null	Het
Ctnna2	A	G	6: 77,120,892 (GRCm39)	I12T	probably benign	Het
Dhx37	A	G	5: 125,496,196 (GRCm39)	M754T	probably benign	Het
Dmrt1	T	A	19: 25,523,395 (GRCm39)	S249T	possibly damaging	Het
Ell	G	T	8: 71,025,553 (GRCm39)	S59I	probably damaging	Het
Fam89a	G	A	8: 125,467,982 (GRCm39)	S110F	probably damaging	Het
Fer1l4	A	C	2: 155,889,834 (GRCm39)	F278V	possibly damaging	Het
Fyn	T	C	10: 39,427,398 (GRCm39)	I427T	probably damaging	Het
Galnt14	T	C	17: 73,832,365 (GRCm39)	D250G	probably damaging	Het
Glp1r	T	C	17: 31,143,546 (GRCm39)	V194A	probably damaging	Het
Glt1d1	T	A	5: 127,721,360 (GRCm39)		probably null	Het
Gm7995	A	G	14: 42,133,327 (GRCm39)	K69R	probably benign	Het
Grip1	A	G	10: 119,822,329 (GRCm39)	T379A	possibly damaging	Het
Gtpbp2	G	T	17: 46,479,147 (GRCm39)	A570S	probably benign	Het
Hmcn1	T	C	1: 150,459,029 (GRCm39)	I5192V	probably benign	Het
Igfl3	A	T	7: 17,913,844 (GRCm39)	I65F	possibly damaging	Het
Igsf10	G	T	3: 59,236,992 (GRCm39)	T1063K	probably benign	Het
Itfg1	A	G	8: 86,466,930 (GRCm39)	V381A	probably benign	Het
Itprid1	A	G	6: 55,953,405 (GRCm39)	D907G	probably damaging	Het
Jmjd8	T	A	17: 26,048,086 (GRCm39)	V16E	probably benign	Het
Kank1	A	G	19: 25,387,449 (GRCm39)	Y374C	probably damaging	Het
Kcnma1	C	T	14: 23,386,165 (GRCm39)	V891I	possibly damaging	Het
Kif20a	C	A	18: 34,762,543 (GRCm39)	T472K	possibly damaging	Het
Klhl32	A	T	4: 24,711,578 (GRCm39)		probably benign	Het
Lrrc37a	A	G	11: 103,347,486 (GRCm39)	S3070P	unknown	Het
Mettl21e	T	G	1: 44,249,425 (GRCm39)	Y77S	probably damaging	Het
Mlst8	G	T	17: 24,696,935 (GRCm39)	D82E	probably benign	Het
Mrgprx2	A	T	7: 48,132,617 (GRCm39)	L67Q	probably damaging	Het
Mylk	T	A	16: 34,750,237 (GRCm39)	L1192Q	possibly damaging	Het
Myt1l	A	T	12: 29,882,365 (GRCm39)	Y520F	unknown	Het
Naip2	A	T	13: 100,297,193 (GRCm39)	W948R	probably benign	Het
Nlrp9a	A	C	7: 26,250,311 (GRCm39)	K25N	probably damaging	Het
Nsd3	T	C	8: 26,204,212 (GRCm39)	C414R	probably damaging	Het
Oit3	A	T	10: 59,274,374 (GRCm39)	V142D	possibly damaging	Het
Or2aj6	C	T	16: 19,443,194 (GRCm39)	V219M	probably benign	Het
P2ry6	T	C	7: 100,587,580 (GRCm39)	T260A	probably damaging	Het
Papola	A	G	12: 105,771,196 (GRCm39)	Q87R	probably benign	Het
Pla2g4a	T	A	1: 149,727,086 (GRCm39)	R557*	probably null	Het
Rgs13	G	T	1: 144,016,576 (GRCm39)	H56N	probably damaging	Het
Sbf1	T	C	15: 89,189,111 (GRCm39)	S537G	probably benign	Het
Sntg1	A	C	1: 8,653,508 (GRCm39)	L243R	possibly damaging	Het
Spata31h1	A	T	10: 82,125,138 (GRCm39)	L2624Q	possibly damaging	Het
Stam2	T	C	2: 52,610,954 (GRCm39)	T23A	probably benign	Het
Tbl1xr1	C	A	3: 22,258,141 (GRCm39)	H467Q	probably damaging	Het
Tmem131l	A	G	3: 83,820,587 (GRCm39)	S1222P	possibly damaging	Het
Tmem43	G	T	6: 91,455,759 (GRCm39)	Q123H	probably damaging	Het
Tmem43	T	A	6: 91,463,862 (GRCm39)	I379N	possibly damaging	Het
Trim43c	A	T	9: 88,727,003 (GRCm39)	I277F	possibly damaging	Het
Ttn	A	G	2: 76,703,211 (GRCm39)		probably benign	Het
Vmn1r75	T	A	7: 11,615,003 (GRCm39)	V245D	probably damaging	Het
Vmn2r111	T	C	17: 22,778,032 (GRCm39)	N549S	possibly damaging	Het
Wrn	T	G	8: 33,809,248 (GRCm39)	L249F	probably benign	Het
Zc3h13	TGATGTCCGGGATGTCCGGGATGTCCGGGATGTCCGGGATGT	TGATGTCCGGGATGTCCGGGATGTCCGGGATGT	14: 75,560,998 (GRCm39)		probably benign	Het
Zfp454	T	C	11: 50,764,950 (GRCm39)	N161D	probably benign	Het
Zfp619	G	A	7: 39,183,586 (GRCm39)	G60R	probably benign	Het
Zfp623	T	A	15: 75,820,308 (GRCm39)	H421Q	probably damaging	Het
Zfp827	A	G	8: 79,916,606 (GRCm39)		probably benign	Het

Other mutations in Vps53

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00475:Vps53	APN	11	75,967,861 (GRCm39)	splice site	probably null
IGL01596:Vps53	APN	11	75,953,863 (GRCm39)	missense	probably damaging	1.00
IGL01655:Vps53	APN	11	75,953,860 (GRCm39)	missense	probably damaging	0.97
IGL02275:Vps53	APN	11	75,937,949 (GRCm39)	missense	probably benign	0.03
IGL02321:Vps53	APN	11	75,939,364 (GRCm39)	missense	possibly damaging	0.60
IGL02581:Vps53	APN	11	75,992,883 (GRCm39)	missense	probably damaging	0.99
IGL02821:Vps53	APN	11	76,027,143 (GRCm39)	splice site	probably benign
IGL02958:Vps53	APN	11	76,008,537 (GRCm39)	missense	probably damaging	1.00
IGL03001:Vps53	APN	11	76,029,150 (GRCm39)	missense	probably damaging	1.00
PIT4519001:Vps53	UTSW	11	76,007,999 (GRCm39)	missense	probably damaging	1.00
R0257:Vps53	UTSW	11	76,068,211 (GRCm39)	intron	probably benign
R0391:Vps53	UTSW	11	76,012,405 (GRCm39)	missense	probably benign	0.31
R0421:Vps53	UTSW	11	75,973,496 (GRCm39)	missense	probably damaging	1.00
R0882:Vps53	UTSW	11	75,973,485 (GRCm39)	missense	probably damaging	1.00
R2509:Vps53	UTSW	11	75,957,661 (GRCm39)	missense	possibly damaging	0.49
R3622:Vps53	UTSW	11	76,008,609 (GRCm39)	missense	probably benign	0.00
R5137:Vps53	UTSW	11	76,057,074 (GRCm39)	missense	probably damaging	1.00
R5338:Vps53	UTSW	11	75,972,034 (GRCm39)	missense	probably damaging	1.00
R5756:Vps53	UTSW	11	75,983,156 (GRCm39)	splice site	probably benign
R5786:Vps53	UTSW	11	75,953,833 (GRCm39)	missense	probably benign	0.08
R5961:Vps53	UTSW	11	75,939,316 (GRCm39)	missense	probably damaging	1.00
R6059:Vps53	UTSW	11	75,957,693 (GRCm39)	missense	possibly damaging	0.57
R6273:Vps53	UTSW	11	75,992,844 (GRCm39)	missense	probably benign	0.16
R6657:Vps53	UTSW	11	76,025,253 (GRCm39)	missense	probably damaging	1.00
R6671:Vps53	UTSW	11	76,025,332 (GRCm39)	missense	probably damaging	1.00
R6772:Vps53	UTSW	11	76,070,324 (GRCm39)	start codon destroyed	probably null
R7378:Vps53	UTSW	11	75,967,900 (GRCm39)	missense	possibly damaging	0.88
R7735:Vps53	UTSW	11	75,937,962 (GRCm39)	missense	probably damaging	1.00
R8066:Vps53	UTSW	11	76,027,133 (GRCm39)	missense	probably damaging	1.00
Z1177:Vps53	UTSW	11	76,027,024 (GRCm39)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- CTCCCATAGCTGCTAATTCCAG -3'
(R):5'- GTCATGCCTAGAACTGTCTGG -3'

Sequencing Primer
(F):5'- CCATAGCTGCTAATTCCAGATCTC -3'
(R):5'- CTAGAACTGTCTGGGTCGTCAC -3'

Posted On

2018-06-06