Mutagenetix > Incidental Mutation

Incidental Mutation 'R1789:Vps16'

201583

Institutional Source

Beutler Lab

Gene Symbol

Vps16

Ensembl Gene

ENSMUSG00000027411

Gene Name

VSP16 CORVET/HOPS core subunit

Synonyms

1810074M16Rik

MMRRC Submission

039820-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.970) question?

Stock #

R1789 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

130266259-130286189 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 130285520 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 821 (T821I)

Ref Sequence

ENSEMBL: ENSMUSP00000028900 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028900] [ENSMUST00000128994]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000028900
AA Change: T821I

PolyPhen 2 Score 0.418 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000028900
Gene: ENSMUSG00000027411
AA Change: T821I

Domain	Start	End	E-Value	Type
Pfam:Vps16_N	4	420	1e-166	PFAM
low complexity region	452	462	N/A	INTRINSIC
Pfam:Vps16_C	517	835	5.5e-150	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000125098

Predicted Effect

probably benign
Transcript: ENSMUST00000128994

SMART Domains

Protein: ENSMUSP00000115899
Gene: ENSMUSG00000027411

Domain	Start	End	E-Value	Type
Pfam:Vps16_N	4	212	3.2e-74	PFAM
Pfam:Vps16_N	205	316	1e-45	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130258

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131220

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132388

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000134677

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137084

Coding Region Coverage

1x: 97.4%
3x: 96.8%
10x: 95.2%
20x: 92.1%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human homolog of yeast class C Vps16 protein. The mammalian class C Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2009]
PHENOTYPE: Mice with a homozygous point mutation in exon 3 display impaired motor function. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 100 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc5	G	A	16: 20,184,701 (GRCm39)	P986L	probably damaging	Het
Acad10	A	T	5: 121,769,456 (GRCm39)	Y667N	possibly damaging	Het
Ahi1	G	A	10: 20,839,014 (GRCm39)	G121D	probably benign	Het
Ampd1	T	A	3: 103,006,442 (GRCm39)	I690N	possibly damaging	Het
Amy1	C	A	3: 113,351,814 (GRCm39)	W425L	possibly damaging	Het
Arhgap27	A	T	11: 103,223,831 (GRCm39)	V823E	probably damaging	Het
Arhgef17	A	G	7: 100,579,077 (GRCm39)	S624P	probably damaging	Het
Arid5b	T	C	10: 68,021,897 (GRCm39)	H231R	probably damaging	Het
Aspscr1	C	A	11: 120,579,386 (GRCm39)	T78N	probably damaging	Het
Auts2	T	A	5: 131,501,288 (GRCm39)	T42S	probably damaging	Het
Ccdc171	A	G	4: 83,473,045 (GRCm39)	D158G	probably damaging	Het
Ces4a	G	A	8: 105,864,729 (GRCm39)	G69S	probably damaging	Het
Cfap61	T	C	2: 145,781,913 (GRCm39)		probably null	Het
Chrna5	T	C	9: 54,911,935 (GRCm39)	V245A	possibly damaging	Het
Cntnap5c	G	A	17: 58,320,916 (GRCm39)	G163R	probably damaging	Het
Col5a2	A	G	1: 45,417,465 (GRCm39)		probably null	Het
Col5a2	T	C	1: 45,433,936 (GRCm39)	Q759R	probably damaging	Het
Comp	A	G	8: 70,829,796 (GRCm39)	D340G	probably benign	Het
Cyfip1	T	A	7: 55,576,143 (GRCm39)	D1104E	probably damaging	Het
Dnah11	A	T	12: 118,002,515 (GRCm39)	S308T	probably damaging	Het
Dnah5	A	G	15: 28,270,572 (GRCm39)	H958R	probably benign	Het
Elp3	A	G	14: 65,785,368 (GRCm39)	Y478H	probably damaging	Het
Fam237b	A	T	5: 5,625,652 (GRCm39)	Q116L	possibly damaging	Het
Fat3	T	C	9: 16,288,281 (GRCm39)	Y414C	probably benign	Het
Fbxo10	C	A	4: 45,046,389 (GRCm39)	A574S	probably damaging	Het
Fsip2	G	T	2: 82,807,906 (GRCm39)	L1408F	probably benign	Het
Fubp3	T	C	2: 31,501,747 (GRCm39)	V425A	possibly damaging	Het
Gm7168	A	T	17: 14,169,846 (GRCm39)	R404S	probably benign	Het
Gpd1	T	G	15: 99,621,083 (GRCm39)	F299C	probably damaging	Het
Gpr137	C	T	19: 6,919,425 (GRCm39)		probably benign	Het
Grin3b	T	C	10: 79,809,242 (GRCm39)	S331P	probably benign	Het
Grk3	T	A	5: 113,089,584 (GRCm39)	I281F	probably damaging	Het
Hoxb7	T	A	11: 96,177,607 (GRCm39)	S18R	probably damaging	Het
Igf1r	C	T	7: 67,864,681 (GRCm39)	R1160*	probably null	Het
Itfg1	A	G	8: 86,452,141 (GRCm39)		probably null	Het
Itgb8	T	C	12: 119,166,190 (GRCm39)	I114V	probably benign	Het
Kcnk1	A	G	8: 126,752,123 (GRCm39)	E243G	possibly damaging	Het
Kif27	A	G	13: 58,491,822 (GRCm39)	L439P	probably damaging	Het
Kif2c	T	A	4: 117,024,558 (GRCm39)	Q279L	probably benign	Het
Kmt2d	A	T	15: 98,749,955 (GRCm39)		probably benign	Het
L3mbtl1	A	G	2: 162,816,422 (GRCm39)	T821A	probably benign	Het
Lrrc24	A	T	15: 76,606,778 (GRCm39)	M206K	probably benign	Het
Mamdc4	T	G	2: 25,457,634 (GRCm39)	K460Q	possibly damaging	Het
Maml2	C	G	9: 13,608,641 (GRCm39)	L30V	probably damaging	Het
Mc5r	C	G	18: 68,471,741 (GRCm39)		probably null	Het
Myo10	T	G	15: 25,726,611 (GRCm39)		probably null	Het
Myo1e	T	A	9: 70,246,066 (GRCm39)	L419Q	probably damaging	Het
Myo6	C	A	9: 80,207,854 (GRCm39)	H1115Q	probably damaging	Het
Myo7a	A	G	7: 97,756,302 (GRCm39)	V10A	probably damaging	Het
Myoz2	C	T	3: 122,819,776 (GRCm39)	R61H	probably damaging	Het
Ncdn	G	A	4: 126,645,796 (GRCm39)	R38C	probably damaging	Het
Nckap1	T	A	2: 80,350,900 (GRCm39)	T736S	probably benign	Het
Ncor2	G	A	5: 125,096,954 (GRCm39)	A2325V	probably damaging	Het
Nid2	T	A	14: 19,802,499 (GRCm39)	V140E	possibly damaging	Het
Nlrp9c	C	A	7: 26,079,915 (GRCm39)	D704Y	probably benign	Het
Notch3	T	A	17: 32,377,699 (GRCm39)	S126C	probably damaging	Het
Or2g7	T	C	17: 38,378,839 (GRCm39)	I259T	probably damaging	Het
Or5p60	A	G	7: 107,724,122 (GRCm39)	F116S	probably benign	Het
Or5w10	A	T	2: 87,375,327 (GRCm39)	L187H	probably damaging	Het
Or6c219	A	T	10: 129,781,451 (GRCm39)	L160*	probably null	Het
Or6c6c	T	C	10: 129,541,476 (GRCm39)	M243T	possibly damaging	Het
Or6d15	A	C	6: 116,559,658 (GRCm39)	F83C	probably damaging	Het
Pdzd7	A	G	19: 45,027,667 (GRCm39)	I269T	probably damaging	Het
Phf3	A	T	1: 30,845,287 (GRCm39)	D1299E	probably damaging	Het
Pitx2	T	A	3: 129,012,403 (GRCm39)	Y271N	probably damaging	Het
Polk	T	C	13: 96,633,140 (GRCm39)	E301G	probably damaging	Het
Prkdc	C	A	16: 15,557,388 (GRCm39)	N2230K	probably damaging	Het
Prlr	A	G	15: 10,322,622 (GRCm39)	E170G	probably benign	Het
Prss55	A	G	14: 64,313,179 (GRCm39)	I235T	probably damaging	Het
Psd3	T	C	8: 68,413,217 (GRCm39)	I724V	probably benign	Het
Rabep2	A	G	7: 126,037,971 (GRCm39)	T248A	possibly damaging	Het
Rbm26	T	A	14: 105,354,509 (GRCm39)	K949N	probably benign	Het
Rnf213	T	A	11: 119,331,047 (GRCm39)	D2085E	probably damaging	Het
Serpinb7	A	T	1: 107,378,003 (GRCm39)	H232L	possibly damaging	Het
Slu7	A	G	11: 43,336,069 (GRCm39)	Q484R	probably benign	Het
Smg1	A	G	7: 117,745,021 (GRCm39)	S3044P	possibly damaging	Het
Snrnp48	A	G	13: 38,405,336 (GRCm39)	D248G	possibly damaging	Het
Snrpc	C	A	17: 28,064,193 (GRCm39)	P66Q	unknown	Het
Snrpn	T	A	7: 59,633,207 (GRCm39)		probably benign	Het
Spag17	T	A	3: 99,846,672 (GRCm39)	S65R	possibly damaging	Het
Srsf6	C	A	2: 162,776,408 (GRCm39)		probably benign	Het
Stil	T	A	4: 114,898,979 (GRCm39)	M1203K	probably benign	Het
Syt17	T	C	7: 118,036,061 (GRCm39)	T106A	probably benign	Het
Tbx15	C	T	3: 99,259,562 (GRCm39)	Q478*	probably null	Het
Tg	A	T	15: 66,609,397 (GRCm39)	Q319L	probably benign	Het
Thada	A	G	17: 84,755,461 (GRCm39)	L243P	probably damaging	Het
Thada	G	T	17: 84,755,462 (GRCm39)	L243I	probably damaging	Het
Tnnt3	A	G	7: 142,066,101 (GRCm39)	R211G	probably damaging	Het
Togaram1	A	T	12: 65,049,409 (GRCm39)	Q1282L	possibly damaging	Het
Tpm3-rs7	T	G	14: 113,552,379 (GRCm39)	M91R	probably damaging	Het
Trappc9	G	A	15: 72,897,816 (GRCm39)	R377W	probably damaging	Het
Ttll7	T	G	3: 146,621,535 (GRCm39)	L378R	probably damaging	Het
Tyw1	T	G	5: 130,287,834 (GRCm39)	I22R	probably damaging	Het
Ubr3	T	C	2: 69,846,711 (GRCm39)	S1645P	possibly damaging	Het
Ubr4	T	C	4: 139,120,364 (GRCm39)	L263P	probably damaging	Het
Unc13c	T	C	9: 73,663,621 (GRCm39)	E1071G	possibly damaging	Het
Vmn2r44	G	T	7: 8,383,122 (GRCm39)	D157E	possibly damaging	Het
Washc4	T	C	10: 83,415,389 (GRCm39)	V793A	possibly damaging	Het
Wdr35	G	T	12: 9,027,435 (GRCm39)		probably null	Het
Zfp277	A	G	12: 40,414,084 (GRCm39)	F254L	probably benign	Het

Other mutations in Vps16

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01327:Vps16	APN	2	130,279,616 (GRCm39)	missense	probably benign	0.19
IGL01400:Vps16	APN	2	130,280,273 (GRCm39)	missense	possibly damaging	0.73
IGL01542:Vps16	APN	2	130,280,314 (GRCm39)	missense	probably damaging	0.97
IGL02011:Vps16	APN	2	130,283,399 (GRCm39)	missense	probably benign	0.04
IGL02192:Vps16	APN	2	130,282,852 (GRCm39)	missense	probably damaging	0.98
IGL02220:Vps16	APN	2	130,283,573 (GRCm39)	missense	possibly damaging	0.85
IGL02587:Vps16	APN	2	130,281,636 (GRCm39)	critical splice donor site	probably null
R0427:Vps16	UTSW	2	130,280,770 (GRCm39)	missense	probably benign	0.00
R0507:Vps16	UTSW	2	130,279,632 (GRCm39)	critical splice donor site	probably null
R1550:Vps16	UTSW	2	130,282,260 (GRCm39)	missense	probably benign	0.09
R3895:Vps16	UTSW	2	130,280,596 (GRCm39)	missense	possibly damaging	0.96
R3981:Vps16	UTSW	2	130,284,514 (GRCm39)	missense	possibly damaging	0.77
R4092:Vps16	UTSW	2	130,281,832 (GRCm39)	missense	probably damaging	1.00
R4555:Vps16	UTSW	2	130,285,496 (GRCm39)	missense	probably damaging	1.00
R4569:Vps16	UTSW	2	130,284,124 (GRCm39)	missense	probably benign
R4803:Vps16	UTSW	2	130,280,030 (GRCm39)	missense	probably benign	0.27
R4835:Vps16	UTSW	2	130,280,220 (GRCm39)	splice site	probably benign
R5022:Vps16	UTSW	2	130,281,372 (GRCm39)	missense	probably benign	0.07
R5023:Vps16	UTSW	2	130,281,372 (GRCm39)	missense	probably benign	0.07
R5057:Vps16	UTSW	2	130,281,372 (GRCm39)	missense	probably benign	0.07
R5158:Vps16	UTSW	2	130,283,199 (GRCm39)	missense	probably damaging	1.00
R5177:Vps16	UTSW	2	130,285,288 (GRCm39)	nonsense	probably null
R5540:Vps16	UTSW	2	130,284,305 (GRCm39)	missense	probably benign	0.00
R5680:Vps16	UTSW	2	130,282,244 (GRCm39)	missense	possibly damaging	0.64
R5689:Vps16	UTSW	2	130,281,011 (GRCm39)	nonsense	probably null
R5690:Vps16	UTSW	2	130,281,011 (GRCm39)	nonsense	probably null
R5926:Vps16	UTSW	2	130,285,476 (GRCm39)	missense	probably damaging	0.97
R5992:Vps16	UTSW	2	130,266,369 (GRCm39)	critical splice donor site	probably null
R6135:Vps16	UTSW	2	130,280,573 (GRCm39)	missense	possibly damaging	0.57
R6370:Vps16	UTSW	2	130,285,304 (GRCm39)	missense	probably damaging	1.00
R6898:Vps16	UTSW	2	130,279,601 (GRCm39)	missense	possibly damaging	0.74
R7378:Vps16	UTSW	2	130,280,099 (GRCm39)	missense	probably damaging	1.00
R7487:Vps16	UTSW	2	130,280,977 (GRCm39)	nonsense	probably null
R7641:Vps16	UTSW	2	130,282,448 (GRCm39)	missense	probably benign	0.28
R7720:Vps16	UTSW	2	130,283,623 (GRCm39)	nonsense	probably null
R8246:Vps16	UTSW	2	130,280,793 (GRCm39)	missense	probably damaging	1.00
R8363:Vps16	UTSW	2	130,284,161 (GRCm39)	missense	probably benign	0.08
R9092:Vps16	UTSW	2	130,281,593 (GRCm39)	missense	probably damaging	0.99
R9128:Vps16	UTSW	2	130,266,319 (GRCm39)	missense	possibly damaging	0.51
R9352:Vps16	UTSW	2	130,283,823 (GRCm39)	critical splice donor site	probably null
R9406:Vps16	UTSW	2	130,283,425 (GRCm39)	critical splice donor site	probably null
R9508:Vps16	UTSW	2	130,284,361 (GRCm39)	missense	possibly damaging	0.94
R9800:Vps16	UTSW	2	130,282,405 (GRCm39)	missense	probably benign	0.02
RF021:Vps16	UTSW	2	130,280,129 (GRCm39)	missense	probably benign	0.09
Z1177:Vps16	UTSW	2	130,283,346 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AAAAGGTCAAGGCTTTGCTTC -3'
(R):5'- CAGTTTTGCCTCAAAGCCTGC -3'

Sequencing Primer
(F):5'- AAGTTAGATGAAGGCCTCTGTG -3'
(R):5'- CTTTTCTTAAGCCAGACAGCATAC -3'

Posted On

2014-06-23