Mutagenetix > Incidental Mutation

Incidental Mutation 'R8535:Vps50'

659200

Institutional Source

Beutler Lab

Gene Symbol

Vps50

Ensembl Gene

ENSMUSG00000001376

Gene Name

VPS50 EARP/GARPII complex subunit

Synonyms

Ccdc132, 1700034M03Rik, 8430415E05Rik

MMRRC Submission

068504-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.902) question?

Stock #

R8535 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

3498393-3603531 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 3565612 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 517 (Y517H)

Ref Sequence

ENSEMBL: ENSMUSP00000001412 (fasta)

Gene Model

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

AlphaFold

Q8CI71

Predicted Effect

possibly damaging
Transcript: ENSMUST00000001412
AA Change: Y517H

PolyPhen 2 Score 0.947 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000001412
Gene: ENSMUSG00000001376
AA Change: Y517H

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

possibly damaging
Transcript: ENSMUST00000164052
AA Change: Y517H

PolyPhen 2 Score 0.933 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000125872
Gene: ENSMUSG00000001376
AA Change: Y517H

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

possibly damaging
Transcript: ENSMUST00000170873
AA Change: Y517H

PolyPhen 2 Score 0.933 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000128323
Gene: ENSMUSG00000001376
AA Change: Y517H

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

Validation Efficiency

100% (34/34)

Allele List at MGI

Other mutations in this stock

Total: 35 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acsl6	A	T	11: 54,229,328 (GRCm39)	I362F	probably damaging	Het
Anks1b	T	A	10: 90,784,493 (GRCm39)	S1154T	probably benign	Het
Bsn	G	A	9: 107,988,651 (GRCm39)	A2367V	probably benign	Het
Chd7	T	A	4: 8,859,211 (GRCm39)	S2434T	possibly damaging	Het
Crybg2	T	C	4: 133,808,514 (GRCm39)	S1372P	probably damaging	Het
Dock5	A	G	14: 68,031,425 (GRCm39)	Y1002H	probably benign	Het
Dst	T	C	1: 34,225,082 (GRCm39)	S1163P	probably damaging	Het
Fah	A	T	7: 84,250,305 (GRCm39)	S14T	probably benign	Het
Gcnt7	T	C	2: 172,296,466 (GRCm39)	I119M	possibly damaging	Het
Gja10	G	A	4: 32,602,274 (GRCm39)	L37F	probably damaging	Het
Gm10750	A	G	2: 148,857,888 (GRCm39)	V121A	unknown	Het
Klhl25	G	A	7: 75,515,843 (GRCm39)	V250I	probably benign	Het
Kmt2a	A	C	9: 44,730,812 (GRCm39)	S200R	possibly damaging	Het
Map1b	T	A	13: 99,571,662 (GRCm39)	D353V	probably damaging	Het
Myh8	G	A	11: 67,169,741 (GRCm39)	R20Q	probably damaging	Het
Or4c127	G	A	2: 89,833,511 (GRCm39)	V254M	probably benign	Het
Or6c200-ps1	T	C	10: 128,869,892 (GRCm39)	Y273C	probably damaging	Het
Pcnt	G	A	10: 76,256,039 (GRCm39)	R734W	probably damaging	Het
Pkn3	A	T	2: 29,969,936 (GRCm39)		probably null	Het
Ptpn21	T	A	12: 98,646,285 (GRCm39)	T1058S	probably damaging	Het
Ryr3	A	G	2: 112,779,433 (GRCm39)		probably null	Het
Sardh	T	A	2: 27,129,657 (GRCm39)	I263F	probably damaging	Het
Scart1	G	A	7: 139,804,634 (GRCm39)	V546M	probably benign	Het
Sh3bp5	A	G	14: 31,139,375 (GRCm39)	V66A	probably benign	Het
Styxl2	T	C	1: 165,928,730 (GRCm39)	D294G	probably benign	Het
Taf4b	T	A	18: 14,955,195 (GRCm39)	S583T	probably damaging	Het
Tbcb	G	A	7: 29,926,421 (GRCm39)	P132L	probably benign	Het
Tcirg1	A	G	19: 3,946,324 (GRCm39)	I791T	probably damaging	Het
Tmeff2	T	A	1: 51,220,985 (GRCm39)	V320D	probably damaging	Het
Tnfrsf19	T	C	14: 61,208,417 (GRCm39)	E368G	probably benign	Het
Trdv2-1	T	A	14: 54,183,972 (GRCm39)	I67N	probably damaging	Het
Unc13c	G	A	9: 73,447,653 (GRCm39)	T1849I	probably benign	Het
Vav2	G	A	2: 27,161,841 (GRCm39)	T655I	probably damaging	Het
Wdr27	G	A	17: 15,123,799 (GRCm39)	T558I	possibly damaging	Het
Yeats2	C	T	16: 19,977,926 (GRCm39)	R137W	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
R6867:Vps50	UTSW	6	3,517,835 (GRCm39)	missense	probably benign	0.16
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
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'- TTTAGGGAAGGCCACCGTTG -3'
(R):5'- GGTTAACAGATAAGCAATCCAGC -3'

Sequencing Primer
(F):5'- GCGAGGCCATTCTGACTTAAG -3'
(R):5'- TCCAGCAAACTAACAACTCACTTCAG -3'

Posted On

2021-01-18