Mutagenetix > Incidental Mutation

Incidental Mutation 'R6867:Vps50'

535970

Institutional Source

Beutler Lab

Gene Symbol

Vps50

Ensembl Gene

ENSMUSG00000001376

Gene Name

VPS50 EARP/GARPII complex subunit

Synonyms

Ccdc132, 1700034M03Rik, 8430415E05Rik

MMRRC Submission

045028-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.890) question?

Stock #

R6867 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

3498393-3603531 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 3517835 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 91 (D91G)

Ref Sequence

ENSEMBL: ENSMUSP00000001412 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000001412] [ENSMUST00000164052] [ENSMUST00000170873]

AlphaFold

Q8CI71

Predicted Effect

probably benign
Transcript: ENSMUST00000001412
AA Change: D91G

PolyPhen 2 Score 0.159 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000001412
Gene: ENSMUSG00000001376
AA Change: D91G

Domain	Start	End	E-Value	Type
Pfam:DUF2450	54	345	2.5e-112	PFAM
low complexity region	659	676	N/A	INTRINSIC
Pfam:DUF2451	723	957	2.2e-98	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000164052
AA Change: D91G

PolyPhen 2 Score 0.131 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000125872
Gene: ENSMUSG00000001376
AA Change: D91G

Domain	Start	End	E-Value	Type
Pfam:DUF2450	54	345	5.2e-111	PFAM
low complexity region	659	676	N/A	INTRINSIC
Pfam:DUF2451	723	929	1.1e-90	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000170873
AA Change: D91G

PolyPhen 2 Score 0.131 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000128323
Gene: ENSMUSG00000001376
AA Change: D91G

Domain	Start	End	E-Value	Type
Pfam:DUF2450	54	345	5.3e-111	PFAM
low complexity region	659	676	N/A	INTRINSIC
Pfam:DUF2451	723	933	2.6e-90	PFAM

Meta Mutation Damage Score

0.1810

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.4%
20x: 98.0%

Validation Efficiency

100% (43/43)

Allele List at MGI

Other mutations in this stock

Total: 42 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Apold1	T	C	6: 134,961,019 (GRCm39)	S158P	possibly damaging	Het
Cep162	A	T	9: 87,099,134 (GRCm39)	L788*	probably null	Het
Cyp7b1	T	C	3: 18,151,394 (GRCm39)	Y273C	probably damaging	Het
Dlx1	C	A	2: 71,361,353 (GRCm39)	N122K	probably damaging	Het
Dock10	A	T	1: 80,508,976 (GRCm39)	I1605K	probably damaging	Het
Enox1	T	C	14: 77,936,739 (GRCm39)		probably null	Het
F3	T	C	3: 121,523,020 (GRCm39)	S77P	possibly damaging	Het
Fam186a	T	A	15: 99,843,731 (GRCm39)	I838L	unknown	Het
Flrt2	T	C	12: 95,746,156 (GRCm39)	F165L	probably damaging	Het
Gcgr	T	A	11: 120,427,295 (GRCm39)	V135E	possibly damaging	Het
Gm6741	T	C	17: 91,544,339 (GRCm39)	L34P	probably benign	Het
Gna13	T	C	11: 109,286,948 (GRCm39)	M257T	possibly damaging	Het
Hsd11b2	G	A	8: 106,248,949 (GRCm39)	R147H	probably benign	Het
Hydin	A	G	8: 111,266,434 (GRCm39)	Y2865C	probably benign	Het
Igdcc3	A	G	9: 65,090,320 (GRCm39)	N610D	probably damaging	Het
Ipp	T	A	4: 116,367,606 (GRCm39)		probably null	Het
Kdm5d	A	G	Y: 927,425 (GRCm39)	T682A	probably benign	Het
Megf8	A	G	7: 25,030,460 (GRCm39)	Y471C	probably benign	Het
Mprip	T	C	11: 59,640,456 (GRCm39)		probably null	Het
Mtres1	ACTGCACCACCT	ACT	10: 43,408,721 (GRCm39)		probably benign	Het
Myrfl	T	A	10: 116,684,187 (GRCm39)	R179*	probably null	Het
Nek1	C	A	8: 61,525,364 (GRCm39)	Q601K	possibly damaging	Het
Neurod4	C	G	10: 130,106,583 (GRCm39)	K230N	probably damaging	Het
Or1ab2	C	T	8: 72,863,707 (GRCm39)	T99I	possibly damaging	Het
Or8u10	A	G	2: 85,916,082 (GRCm39)	I13T	possibly damaging	Het
Orc3	A	G	4: 34,605,539 (GRCm39)	L114P	probably damaging	Het
Rag1	T	C	2: 101,472,292 (GRCm39)	D950G	probably damaging	Het
Rasgrp2	G	A	19: 6,463,213 (GRCm39)	S504N	probably benign	Het
Rgl2	A	G	17: 34,151,661 (GRCm39)	D235G	probably benign	Het
Slc35e2	A	G	4: 155,703,157 (GRCm39)	E390G	probably benign	Het
Slc39a1	T	A	3: 90,156,759 (GRCm39)	V105E	probably damaging	Het
Tesk2	T	A	4: 116,658,995 (GRCm39)	C291S	probably damaging	Het
Tmco3	T	A	8: 13,363,927 (GRCm39)	F83Y	probably damaging	Het
Trim25	T	C	11: 88,901,713 (GRCm39)	I336T	probably benign	Het
Ush2a	A	G	1: 188,643,170 (GRCm39)	I4177M	probably damaging	Het
Veph1	T	A	3: 66,162,458 (GRCm39)	T67S	probably damaging	Het
Vmn2r43	A	G	7: 8,258,125 (GRCm39)	F363L	probably benign	Het
Vps28	A	T	15: 76,506,871 (GRCm39)	I109N	probably damaging	Het
Wdr20	T	C	12: 110,760,133 (GRCm39)	F340L	probably benign	Het
Wdr95	A	G	5: 149,504,388 (GRCm39)		probably null	Het
Zfand6	A	G	7: 84,265,122 (GRCm39)	V193A	probably damaging	Het
Zfp703	C	A	8: 27,468,668 (GRCm39)	P111T	probably damaging	Het

Other mutations in Vps50

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00338:Vps50	APN	6	3,602,670 (GRCm39)	missense	probably benign	0.00
IGL00764:Vps50	APN	6	3,532,177 (GRCm39)	nonsense	probably null
IGL00844:Vps50	APN	6	3,532,177 (GRCm39)	nonsense	probably null
IGL00845:Vps50	APN	6	3,532,177 (GRCm39)	nonsense	probably null
IGL00850:Vps50	APN	6	3,532,177 (GRCm39)	nonsense	probably null
IGL01417:Vps50	APN	6	3,522,377 (GRCm39)	splice site	probably benign
IGL01648:Vps50	APN	6	3,498,545 (GRCm39)	missense	probably benign	0.25
IGL03238:Vps50	APN	6	3,594,771 (GRCm39)	missense	possibly damaging	0.60
IGL03285:Vps50	APN	6	3,555,011 (GRCm39)	missense	possibly damaging	0.71
R0309:Vps50	UTSW	6	3,536,853 (GRCm39)	missense	possibly damaging	0.90
R0513:Vps50	UTSW	6	3,520,210 (GRCm39)	missense	probably damaging	1.00
R0714:Vps50	UTSW	6	3,571,105 (GRCm39)	missense	probably benign	0.05
R1066:Vps50	UTSW	6	3,533,565 (GRCm39)	missense	probably damaging	1.00
R1210:Vps50	UTSW	6	3,594,884 (GRCm39)	missense	probably damaging	0.99
R1420:Vps50	UTSW	6	3,588,007 (GRCm39)	nonsense	probably null
R1437:Vps50	UTSW	6	3,517,852 (GRCm39)	nonsense	probably null
R1451:Vps50	UTSW	6	3,565,628 (GRCm39)	missense	possibly damaging	0.77
R1470:Vps50	UTSW	6	3,517,777 (GRCm39)	splice site	probably benign
R1576:Vps50	UTSW	6	3,545,568 (GRCm39)	missense	possibly damaging	0.60
R1599:Vps50	UTSW	6	3,565,537 (GRCm39)	missense	probably benign	0.00
R1860:Vps50	UTSW	6	3,520,279 (GRCm39)	critical splice donor site	probably null
R2055:Vps50	UTSW	6	3,522,265 (GRCm39)	missense	probably benign	0.01
R2109:Vps50	UTSW	6	3,555,379 (GRCm39)	missense	probably damaging	0.99
R3408:Vps50	UTSW	6	3,600,212 (GRCm39)	missense	probably damaging	1.00
R3732:Vps50	UTSW	6	3,519,243 (GRCm39)	synonymous	silent
R3764:Vps50	UTSW	6	3,588,063 (GRCm39)	missense	probably damaging	1.00
R3828:Vps50	UTSW	6	3,533,500 (GRCm39)	missense	probably benign
R4092:Vps50	UTSW	6	3,551,037 (GRCm39)	missense	probably benign
R4385:Vps50	UTSW	6	3,516,694 (GRCm39)	missense	probably benign	0.00
R4588:Vps50	UTSW	6	3,562,306 (GRCm39)	missense	probably damaging	1.00
R4843:Vps50	UTSW	6	3,536,974 (GRCm39)	critical splice donor site	probably null
R4978:Vps50	UTSW	6	3,517,808 (GRCm39)	missense	probably benign
R5368:Vps50	UTSW	6	3,567,739 (GRCm39)	missense	possibly damaging	0.88
R5867:Vps50	UTSW	6	3,536,965 (GRCm39)	missense	probably damaging	1.00
R6591:Vps50	UTSW	6	3,504,939 (GRCm39)	critical splice donor site	probably null
R6626:Vps50	UTSW	6	3,551,101 (GRCm39)	nonsense	probably null
R6691:Vps50	UTSW	6	3,504,939 (GRCm39)	critical splice donor site	probably null
R6707:Vps50	UTSW	6	3,545,583 (GRCm39)	missense	probably damaging	1.00
R6751:Vps50	UTSW	6	3,600,274 (GRCm39)	missense	probably damaging	1.00
R6773:Vps50	UTSW	6	3,592,560 (GRCm39)	missense	probably benign	0.25
R6883:Vps50	UTSW	6	3,498,513 (GRCm39)	unclassified	probably benign
R6963:Vps50	UTSW	6	3,592,577 (GRCm39)	critical splice donor site	probably null
R7147:Vps50	UTSW	6	3,567,750 (GRCm39)	nonsense	probably null
R7150:Vps50	UTSW	6	3,578,854 (GRCm39)	missense	possibly damaging	0.89
R7167:Vps50	UTSW	6	3,600,256 (GRCm39)	missense	probably damaging	1.00
R7235:Vps50	UTSW	6	3,588,078 (GRCm39)	missense	probably benign	0.01
R7385:Vps50	UTSW	6	3,602,708 (GRCm39)	missense	probably benign	0.00
R7662:Vps50	UTSW	6	3,562,304 (GRCm39)	missense	probably damaging	1.00
R7782:Vps50	UTSW	6	3,532,202 (GRCm39)	critical splice donor site	probably null
R8188:Vps50	UTSW	6	3,562,297 (GRCm39)	nonsense	probably null
R8232:Vps50	UTSW	6	3,600,139 (GRCm39)	missense	probably damaging	1.00
R8535:Vps50	UTSW	6	3,565,612 (GRCm39)	missense	possibly damaging	0.95
R8808:Vps50	UTSW	6	3,522,338 (GRCm39)	nonsense	probably null
R8845:Vps50	UTSW	6	3,504,926 (GRCm39)	missense	probably benign
R8889:Vps50	UTSW	6	3,536,967 (GRCm39)	missense	probably damaging	1.00
R8892:Vps50	UTSW	6	3,536,967 (GRCm39)	missense	probably damaging	1.00
R8911:Vps50	UTSW	6	3,516,710 (GRCm39)	missense	probably benign
R9089:Vps50	UTSW	6	3,536,884 (GRCm39)	missense	probably benign	0.02
R9116:Vps50	UTSW	6	3,588,091 (GRCm39)	splice site	probably benign
R9381:Vps50	UTSW	6	3,592,433 (GRCm39)	missense	probably benign
R9440:Vps50	UTSW	6	3,516,724 (GRCm39)	missense	probably benign	0.01
R9485:Vps50	UTSW	6	3,592,557 (GRCm39)	missense	probably damaging	0.99
R9585:Vps50	UTSW	6	3,600,348 (GRCm39)	missense	probably benign	0.03
R9645:Vps50	UTSW	6	3,516,706 (GRCm39)	missense	possibly damaging	0.94
R9761:Vps50	UTSW	6	3,519,218 (GRCm39)	missense	probably damaging	1.00
R9796:Vps50	UTSW	6	3,562,300 (GRCm39)	missense	probably damaging	1.00
X0025:Vps50	UTSW	6	3,571,012 (GRCm39)	missense	probably benign	0.02
X0062:Vps50	UTSW	6	3,594,833 (GRCm39)	missense	probably benign
Z1176:Vps50	UTSW	6	3,578,792 (GRCm39)	critical splice acceptor site	probably null
Z1177:Vps50	UTSW	6	3,562,312 (GRCm39)	missense	probably damaging	1.00
Z1177:Vps50	UTSW	6	3,555,367 (GRCm39)	critical splice acceptor site	probably null

Predicted Primers

PCR Primer
(F):5'- TGACAGCGTGGAAGCATTGG -3'
(R):5'- GGTCACATCTAAGGACCTGAGAG -3'

Sequencing Primer
(F):5'- CGTGGAAGCATTGGAGGAC -3'
(R):5'- CATCTAAGGACCTGAGAGAATCTC -3'

Posted On

2018-10-18