Mutagenetix > Incidental Mutation

Incidental Mutation 'R9800:Vps16'

735141

Institutional Source

Beutler Lab

Gene Symbol

Vps16

Ensembl Gene

ENSMUSG00000027411

Gene Name

VSP16 CORVET/HOPS core subunit

Synonyms

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.973) question?

Stock #

R9800 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

130424339-130444269 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 130440485 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 413 (F413L)

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: F413L

PolyPhen 2 Score 0.017 (Sensitivity: 0.95; Specificity: 0.80)

SMART Domains

Protein: ENSMUSP00000028900
Gene: ENSMUSG00000027411
AA Change: F413L

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

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

Coding Region Coverage

1x: 99.9%
3x: 99.8%
10x: 99.5%
20x: 98.7%

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: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca16	T	A	7: 120,520,060	I1009N	possibly damaging	Het
Adcy8	T	A	15: 64,699,246	N1213Y	probably benign	Het
Ahctf1	T	C	1: 179,753,868	S1590G	possibly damaging	Het
Ahcyl1	A	T	3: 107,670,272	N277K	probably damaging	Het
Ank2	A	T	3: 126,946,500	S1912T	unknown	Het
Ank3	T	A	10: 69,898,127	N740K	unknown	Het
Atp13a3	A	C	16: 30,340,233	I800S	probably benign	Het
AU041133	T	A	10: 82,150,845	C111S	probably damaging	Het
Azi2	T	A	9: 118,055,856	I211N	probably benign	Het
Btbd11	C	A	10: 85,388,215	A296E	unknown	Het
Camk2b	T	C	11: 5,972,408	N480S	probably damaging	Het
Card6	A	G	15: 5,099,220	V898A	probably benign	Het
Copb2	T	A	9: 98,579,028	M381K	probably damaging	Het
Crisp1	A	T	17: 40,305,180	M102K	probably damaging	Het
Dcxr	A	T	11: 120,727,258		probably benign	Het
Dennd5a	C	A	7: 109,901,167	R917L	probably benign	Het
Egflam	T	A	15: 7,250,044	T494S	probably benign	Het
Fkbpl	T	A	17: 34,645,717	M153K	probably benign	Het
Helz2	A	T	2: 181,240,823	I59N	probably damaging	Het
Ldlrap1	T	C	4: 134,749,992	T194A	probably benign	Het
Lman1l	T	C	9: 57,615,777	D133G	probably damaging	Het
Lrrc27	T	C	7: 139,227,997	M340T	probably benign	Het
Lum	T	A	10: 97,568,295	S17R	probably benign	Het
Malrd1	A	G	2: 15,842,594	K1182E	unknown	Het
Map3k2	A	T	18: 32,200,016	D81V	possibly damaging	Het
Muc5b	A	T	7: 141,861,743	T2809S	possibly damaging	Het
Nle1	C	A	11: 82,903,050	V387L	probably benign	Het
Nr1h4	T	C	10: 89,454,756	D474G	probably benign	Het
Nup205	T	C	6: 35,186,533	I144T	possibly damaging	Het
Olfr1122	G	T	2: 87,388,164	C153F	probably damaging	Het
Olfr1309	G	A	2: 111,983,849	S75L	possibly damaging	Het
Olfr23	C	A	11: 73,941,160	L305I	probably benign	Het
Olfr444	A	T	6: 42,956,157	I220F	probably damaging	Het
Olfr566	T	C	7: 102,856,886	Y132C	probably benign	Het
Olfr732	G	A	14: 50,282,244	T3I	probably benign	Het
Pkn3	C	T	2: 30,083,278	R371*	probably null	Het
Plin2	A	T	4: 86,668,505	S30T	possibly damaging	Het
Ppfibp1	T	C	6: 147,016,271	V475A	probably benign	Het
Ppp2ca	T	C	11: 52,118,083	Y137H	probably damaging	Het
Rasgrf2	T	A	13: 92,131,352	Q48L	probably damaging	Het
Rnf168	G	C	16: 32,298,568	V316L	probably benign	Het
Shank1	G	A	7: 44,312,918	S71N	unknown	Het
Spata31d1d	T	C	13: 59,726,823	H966R	possibly damaging	Het
Speg	C	A	1: 75,422,714	D2268E	probably benign	Het
Srp54c	A	G	12: 55,250,026	I170V	probably benign	Het
Syde2	A	G	3: 145,998,609	R439G	probably benign	Het
Tcof1	T	C	18: 60,816,486	K1155R	unknown	Het
Tmem184c	T	C	8: 77,596,458	I592V	probably benign	Het
Trav6-7-dv9	A	G	14: 53,710,212	Y57C	probably damaging	Het
Trpc1	T	A	9: 95,743,250	I108F	probably damaging	Het
Virma	A	T	4: 11,546,007	H1615L	probably damaging	Het
Vmn2r10	A	T	5: 109,002,538	D213E	probably damaging	Het
Vmn2r116	T	A	17: 23,401,425	V711E	probably damaging	Het
Vwa1	G	A	4: 155,772,879	P154L	probably damaging	Het
Wasf1	T	C	10: 40,936,697	I494T	unknown	Het
Wdr36	A	G	18: 32,852,647	D539G	possibly damaging	Het
Zfp81	A	T	17: 33,335,437	C134*	probably null	Het

Other mutations in Vps16

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01327:Vps16	APN	2	130437696	missense	probably benign	0.19
IGL01400:Vps16	APN	2	130438353	missense	possibly damaging	0.73
IGL01542:Vps16	APN	2	130438394	missense	probably damaging	0.97
IGL02011:Vps16	APN	2	130441479	missense	probably benign	0.04
IGL02192:Vps16	APN	2	130440932	missense	probably damaging	0.98
IGL02220:Vps16	APN	2	130441653	missense	possibly damaging	0.85
IGL02587:Vps16	APN	2	130439716	critical splice donor site	probably null
R0427:Vps16	UTSW	2	130438850	missense	probably benign	0.00
R0507:Vps16	UTSW	2	130437712	critical splice donor site	probably null
R1550:Vps16	UTSW	2	130440340	missense	probably benign	0.09
R1789:Vps16	UTSW	2	130443600	missense	probably benign	0.42
R3895:Vps16	UTSW	2	130438676	missense	possibly damaging	0.96
R3981:Vps16	UTSW	2	130442594	missense	possibly damaging	0.77
R4092:Vps16	UTSW	2	130439912	missense	probably damaging	1.00
R4555:Vps16	UTSW	2	130443576	missense	probably damaging	1.00
R4569:Vps16	UTSW	2	130442204	missense	probably benign
R4803:Vps16	UTSW	2	130438110	missense	probably benign	0.27
R4835:Vps16	UTSW	2	130438300	splice site	probably benign
R5022:Vps16	UTSW	2	130439452	missense	probably benign	0.07
R5023:Vps16	UTSW	2	130439452	missense	probably benign	0.07
R5057:Vps16	UTSW	2	130439452	missense	probably benign	0.07
R5158:Vps16	UTSW	2	130441279	missense	probably damaging	1.00
R5177:Vps16	UTSW	2	130443368	nonsense	probably null
R5540:Vps16	UTSW	2	130442385	missense	probably benign	0.00
R5680:Vps16	UTSW	2	130440324	missense	possibly damaging	0.64
R5689:Vps16	UTSW	2	130439091	nonsense	probably null
R5690:Vps16	UTSW	2	130439091	nonsense	probably null
R5926:Vps16	UTSW	2	130443556	missense	probably damaging	0.97
R5992:Vps16	UTSW	2	130424449	critical splice donor site	probably null
R6135:Vps16	UTSW	2	130438653	missense	possibly damaging	0.57
R6370:Vps16	UTSW	2	130443384	missense	probably damaging	1.00
R6898:Vps16	UTSW	2	130437681	missense	possibly damaging	0.74
R7378:Vps16	UTSW	2	130438179	missense	probably damaging	1.00
R7487:Vps16	UTSW	2	130439057	nonsense	probably null
R7641:Vps16	UTSW	2	130440528	missense	probably benign	0.28
R7720:Vps16	UTSW	2	130441703	nonsense	probably null
R8246:Vps16	UTSW	2	130438873	missense	probably damaging	1.00
R8363:Vps16	UTSW	2	130442241	missense	probably benign	0.08
R9092:Vps16	UTSW	2	130439673	missense	probably damaging	0.99
R9128:Vps16	UTSW	2	130424399	missense	possibly damaging	0.51
R9352:Vps16	UTSW	2	130441903	critical splice donor site	probably null
R9406:Vps16	UTSW	2	130441505	critical splice donor site	probably null
R9508:Vps16	UTSW	2	130442441	missense	possibly damaging	0.94
RF021:Vps16	UTSW	2	130438209	missense	probably benign	0.09
Z1177:Vps16	UTSW	2	130441426	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ATGAGTACCTGCGGGAGATC -3'
(R):5'- GGATCTGCAGACCACATCTC -3'

Sequencing Primer
(F):5'- CAGCAGTGCATTGAGGCTG -3'
(R):5'- GCAGACCACATCTCCTGCC -3'

Posted On

2022-11-14