Mutagenetix > Incidental Mutation

Incidental Mutation 'R2109:Vps50'

232361

Institutional Source

Beutler Lab

Gene Symbol

Vps50

Ensembl Gene

ENSMUSG00000001376

Gene Name

VPS50 EARP/GARPII complex subunit

Synonyms

Ccdc132, 1700034M03Rik, 8430415E05Rik

MMRRC Submission

040113-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.890) question?

Stock #

R2109 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

3498393-3603531 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 3555379 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 425 (V425A)

Ref Sequence

ENSEMBL: ENSMUSP00000128323 (fasta)

Gene Model

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

AlphaFold

Q8CI71

Predicted Effect

probably damaging
Transcript: ENSMUST00000001412
AA Change: V425A

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000001412
Gene: ENSMUSG00000001376
AA Change: V425A

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 damaging
Transcript: ENSMUST00000164052
AA Change: V425A

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000125872
Gene: ENSMUSG00000001376
AA Change: V425A

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 damaging
Transcript: ENSMUST00000170873
AA Change: V425A

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000128323
Gene: ENSMUSG00000001376
AA Change: V425A

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184461

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.4%
20x: 95.4%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2410002F23Rik	G	T	7: 43,900,435 (GRCm39)	R113S	probably benign	Het
Ackr2	A	T	9: 121,738,026 (GRCm39)	I134F	probably damaging	Het
Actr3b	T	A	5: 26,036,709 (GRCm39)	I174N	possibly damaging	Het
Akap9	T	A	5: 4,094,847 (GRCm39)	S2214T	possibly damaging	Het
Arhgef12	C	A	9: 42,890,768 (GRCm39)	R986L	possibly damaging	Het
Brap	G	T	5: 121,801,422 (GRCm39)	S59I	possibly damaging	Het
Btnl1	C	T	17: 34,598,578 (GRCm39)	H65Y	probably damaging	Het
C1s2	T	C	6: 124,612,004 (GRCm39)	T121A	probably damaging	Het
Capn1	T	A	19: 6,064,388 (GRCm39)	Y37F	probably benign	Het
Ccdc39	T	C	3: 33,869,650 (GRCm39)	K726E	probably damaging	Het
Cd300lb	G	A	11: 114,816,865 (GRCm39)	S195F	probably damaging	Het
Cenpf	T	C	1: 189,411,264 (GRCm39)	K307E	probably damaging	Het
Chodl	A	C	16: 78,738,251 (GRCm39)	N73T	possibly damaging	Het
Cimip2c	G	A	5: 30,637,851 (GRCm39)	G66E	probably damaging	Het
Crnn	A	T	3: 93,055,747 (GRCm39)	M178L	probably benign	Het
Cyp4a12b	A	G	4: 115,290,110 (GRCm39)	D221G	probably damaging	Het
Dipk2a	A	T	9: 94,406,498 (GRCm39)	I303N	probably damaging	Het
Dmxl2	A	G	9: 54,301,097 (GRCm39)	V2338A	probably benign	Het
Dnah9	G	T	11: 65,928,411 (GRCm39)	P2086Q	probably damaging	Het
Dsg2	A	G	18: 20,725,346 (GRCm39)	I486V	probably benign	Het
E2f8	A	G	7: 48,524,855 (GRCm39)	S265P	probably damaging	Het
Eif1b	A	G	9: 120,323,296 (GRCm39)	D52G	probably benign	Het
Etl4	A	T	2: 20,790,153 (GRCm39)	T602S	probably benign	Het
Exoc3l2	A	T	7: 19,223,059 (GRCm39)		probably benign	Het
Fbxl6	C	A	15: 76,421,173 (GRCm39)	V297F	probably damaging	Het
Fgr	T	A	4: 132,725,786 (GRCm39)	N398K	probably benign	Het
G3bp1	A	G	11: 55,379,986 (GRCm39)	R107G	probably damaging	Het
Gp2	A	T	7: 119,052,155 (GRCm39)	N186K	probably benign	Het
Hbs1l	T	A	10: 21,217,831 (GRCm39)	L249*	probably null	Het
Hmgcs2	T	A	3: 98,204,337 (GRCm39)	L246*	probably null	Het
Hsp90ab1	G	T	17: 45,880,254 (GRCm39)	H96Q	probably benign	Het
Ibtk	C	T	9: 85,588,603 (GRCm39)	V1078I	probably benign	Het
Ltn1	T	C	16: 87,212,530 (GRCm39)	D677G	probably benign	Het
Lyst	C	T	13: 13,887,405 (GRCm39)	T3078I	possibly damaging	Het
Mamdc4	A	G	2: 25,459,402 (GRCm39)	F199S	probably damaging	Het
Megf6	G	T	4: 154,261,578 (GRCm39)	V68L	probably benign	Het
Mki67	G	A	7: 135,299,592 (GRCm39)	T1814I	probably damaging	Het
Msantd5l	T	A	11: 51,145,264 (GRCm39)	I108F	possibly damaging	Het
Mttp	A	T	3: 137,800,763 (GRCm39)	F766I	probably benign	Het
Nbl1	T	A	4: 138,810,915 (GRCm39)		probably null	Het
Nmrk1	T	A	19: 18,618,802 (GRCm39)	L118Q	probably damaging	Het
Nopchap1	C	T	10: 83,201,656 (GRCm39)	S143L	probably damaging	Het
Oog3	A	T	4: 143,886,082 (GRCm39)	L172H	probably damaging	Het
Or2y11	T	G	11: 49,443,260 (GRCm39)	S229A	probably damaging	Het
Osbpl1a	T	G	18: 12,892,457 (GRCm39)	Q332P	probably damaging	Het
Pik3cg	A	G	12: 32,243,709 (GRCm39)	F921L	possibly damaging	Het
Plch2	T	C	4: 155,069,054 (GRCm39)	S1086G	possibly damaging	Het
Plekha5	A	G	6: 140,369,942 (GRCm39)	T18A	possibly damaging	Het
Pogz	T	A	3: 94,786,276 (GRCm39)	S955T	probably benign	Het
Pot1b	A	T	17: 55,960,413 (GRCm39)	I639N	probably benign	Het
Prkdc	T	C	16: 15,505,254 (GRCm39)	I852T	probably benign	Het
Prps1l1	A	G	12: 35,035,521 (GRCm39)	K212R	probably benign	Het
Ptpn5	A	G	7: 46,735,807 (GRCm39)	Y304H	probably damaging	Het
Ralgapa1	A	G	12: 55,822,973 (GRCm39)	I281T	possibly damaging	Het
Rgs22	A	T	15: 36,099,880 (GRCm39)	Y278*	probably null	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Rnf213	T	A	11: 119,333,489 (GRCm39)	Y2899*	probably null	Het
Rttn	C	T	18: 89,004,197 (GRCm39)	T397I	possibly damaging	Het
Sacs	G	T	14: 61,410,902 (GRCm39)		probably null	Het
Sbf2	G	T	7: 110,060,419 (GRCm39)	Q182K	probably damaging	Het
Sec14l5	C	T	16: 4,984,968 (GRCm39)	R105*	probably null	Het
Sh2b1	A	T	7: 126,071,536 (GRCm39)	D216E	possibly damaging	Het
Sh3gl3	A	G	7: 81,920,008 (GRCm39)	N72S	possibly damaging	Het
Slc12a1	A	T	2: 125,015,619 (GRCm39)	I391F	probably damaging	Het
Slc36a2	G	A	11: 55,072,381 (GRCm39)	A77V	probably damaging	Het
Smc2	A	T	4: 52,474,987 (GRCm39)	I888L	probably benign	Het
Smoc1	C	T	12: 81,197,450 (GRCm39)	T194M	probably damaging	Het
Sorcs1	C	T	19: 50,666,630 (GRCm39)	G93R	probably benign	Het
Sox30	T	G	11: 45,882,595 (GRCm39)	F542V	probably damaging	Het
Svep1	A	G	4: 58,206,030 (GRCm39)	V116A	possibly damaging	Het
Synj2	A	G	17: 6,063,966 (GRCm39)	D330G	probably benign	Het
Tenm3	A	C	8: 48,796,384 (GRCm39)	S202A	possibly damaging	Het
Tg	C	T	15: 66,601,443 (GRCm39)	T151I	probably benign	Het
Tnfaip2	A	G	12: 111,414,527 (GRCm39)	E361G	probably damaging	Het
Tnk1	A	T	11: 69,746,009 (GRCm39)	D305E	probably damaging	Het
Tpp1	A	G	7: 105,399,177 (GRCm39)	L133P	probably damaging	Het
Trappc1	T	A	11: 69,215,243 (GRCm39)	M41K	probably damaging	Het
Tsen54	A	G	11: 115,706,549 (GRCm39)	D9G	probably damaging	Het
Ttn	T	A	2: 76,804,598 (GRCm39)	I225F	probably damaging	Het
Ube4b	T	C	4: 149,457,298 (GRCm39)	K313R	probably benign	Het
Wbp2	A	T	11: 115,971,445 (GRCm39)	Y153*	probably null	Het
Xrn1	A	G	9: 95,861,273 (GRCm39)	S478G	probably benign	Het
Zfp354c	T	C	11: 50,707,969 (GRCm39)	E77G	probably benign	Het
Zfp462	T	C	4: 55,008,496 (GRCm39)	M154T	probably benign	Het
Zfp704	A	G	3: 9,539,585 (GRCm39)	V255A	probably damaging	Het
Zfp763	G	T	17: 33,238,752 (GRCm39)	A131E	probably benign	Het
Zfp931	A	T	2: 177,711,651 (GRCm39)	V32E	probably null	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
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
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'- GGATCTGGGCTTGAAGGATC -3'
(R):5'- TCCAGTATGTTCAACCCAATCC -3'

Sequencing Primer
(F):5'- ATCTGGGCTTGAAGGATCTTTTTC -3'
(R):5'- TCTTGATGAAGTATCCCTAAC -3'

Posted On

2014-09-18