Mutagenetix > Incidental Mutation

Incidental Mutation 'R5023:Vps16'

391080

Institutional Source

Beutler Lab

Gene Symbol

Vps16

Ensembl Gene

ENSMUSG00000027411

Gene Name

VSP16 CORVET/HOPS core subunit

Synonyms

MMRRC Submission

042614-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.967) question?

Stock #

R5023 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

130424339-130444269 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 130439452 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Glycine at position 235 (S235G)

Ref Sequence

ENSEMBL: ENSMUSP00000115899 (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: S276G

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000028900
Gene: ENSMUSG00000027411
AA Change: S276G

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

noncoding transcript
Transcript: ENSMUST00000125973

Predicted Effect

probably benign
Transcript: ENSMUST00000128994
AA Change: S235G

PolyPhen 2 Score 0.073 (Sensitivity: 0.93; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000115899
Gene: ENSMUSG00000027411
AA Change: S235G

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

Meta Mutation Damage Score

0.1014

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.2%

Validation Efficiency

98% (127/129)

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: 124 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933427D14Rik	A	T	11: 72,166,755	H739Q	probably benign	Het
Abca3	C	T	17: 24,374,300	R224C	probably damaging	Het
Abca8b	A	G	11: 109,974,988		probably null	Het
Adam1b	C	T	5: 121,501,159	V608M	probably damaging	Het
Ank2	A	G	3: 126,941,871		probably benign	Het
Ankrd17	A	C	5: 90,282,868	L1019R	probably damaging	Het
Arih1	T	C	9: 59,486,232	N39S	unknown	Het
Best3	G	A	10: 116,988,742	V38I	probably benign	Het
Bicc1	A	G	10: 70,947,883	S393P	possibly damaging	Het
C1d	T	A	11: 17,266,674	N135K	probably benign	Het
Cage1	G	T	13: 38,011,411	S778*	probably null	Het
Capn7	T	A	14: 31,352,426	V262E	probably damaging	Het
Ccdc190	A	G	1: 169,933,087	R95G	probably damaging	Het
Cd163	C	T	6: 124,325,288	T937I	probably damaging	Het
Cdh18	G	A	15: 23,259,666	S194N	probably damaging	Het
Clec4b2	A	T	6: 123,200,956	S77C	probably null	Het
Ctsw	T	A	19: 5,466,049	D237V	probably damaging	Het
Cyp2c68	G	A	19: 39,712,507	T289I	probably benign	Het
Cyp4f39	A	G	17: 32,481,104	Y133C	probably damaging	Het
Dlg5	T	C	14: 24,136,622	E1847G	probably damaging	Het
Dnah7a	C	A	1: 53,647,248	E248*	probably null	Het
Eef2kmt	T	A	16: 5,247,599	D248V	probably damaging	Het
Ewsr1	T	C	11: 5,088,054	T113A	possibly damaging	Het
Fbxo4	A	G	15: 3,977,756		probably null	Het
Fbxo43	A	T	15: 36,162,929	M44K	probably benign	Het
Fchsd1	A	G	18: 37,964,810	I340T	possibly damaging	Het
Fgf5	C	A	5: 98,262,015	A141E	probably damaging	Het
Gfm1	T	C	3: 67,473,544	V664A	probably damaging	Het
Glp2r	T	C	11: 67,741,032	T121A	possibly damaging	Het
Gm10803	A	C	2: 93,564,172	L96F	probably damaging	Het
Gm12169	T	A	11: 46,528,532	D58E	probably damaging	Het
Gm14569	T	C	X: 36,430,817	D1413G	probably benign	Het
Gm15455	T	C	1: 33,837,351		noncoding transcript	Het
Gm1818	G	C	12: 48,555,535		noncoding transcript	Het
Gm4907	G	A	X: 23,907,241	G327E	probably damaging	Het
Gm5155	A	T	7: 17,902,706	D236V	probably damaging	Het
Gm7030	A	G	17: 36,109,415		probably benign	Het
Gnb2	G	A	5: 137,529,940		probably null	Het
Gpc4	G	A	X: 52,074,563	R148C	probably damaging	Het
Gpx5	C	T	13: 21,288,745	V140I	probably damaging	Het
Gtpbp1	A	T	15: 79,719,221	Q637L	possibly damaging	Het
Herc1	A	T	9: 66,470,326	K3458M	possibly damaging	Het
Hhat	A	T	1: 192,727,339	L138Q	probably damaging	Het
Hipk1	G	T	3: 103,777,507	T264N	probably damaging	Het
Hjurp	A	T	1: 88,275,050	Y71N	possibly damaging	Het
Hnf4g	G	T	3: 3,644,587	A144S	probably damaging	Het
Hook3	TAGAG	TAG	8: 26,032,019		probably null	Het
Ifi204	G	A	1: 173,751,740	T513I	possibly damaging	Het
Ino80b	G	T	6: 83,125,042	S26R	probably damaging	Het
Ints9	T	A	14: 64,980,228	L68H	probably damaging	Het
Isx	C	T	8: 74,892,714	T178I	probably benign	Het
Kel	A	G	6: 41,688,111	L255P	probably damaging	Het
Klf11	T	A	12: 24,655,359	S271T	probably benign	Het
Klhl20	A	C	1: 161,109,220		probably null	Het
Lama2	G	A	10: 27,190,504	T1127I	probably damaging	Het
Larp1b	T	A	3: 41,033,985	N81K	possibly damaging	Het
Lsm11	T	C	11: 45,944,839	D25G	probably damaging	Het
Map3k20	T	A	2: 72,402,345		probably benign	Het
Mbd6	C	T	10: 127,286,441	V173I	probably benign	Het
Milr1	A	G	11: 106,766,965	D131G	possibly damaging	Het
Mybpc1	T	G	10: 88,543,774	D635A	probably damaging	Het
Myh7b	G	C	2: 155,632,373	R1669S	possibly damaging	Het
Ndufa7	A	G	17: 33,824,603		probably benign	Het
Ndufs3	C	A	2: 90,898,660	A161S	probably benign	Het
Neo1	T	C	9: 58,990,271	D134G	probably damaging	Het
Nme4	G	A	17: 26,093,668	T129I	probably benign	Het
Npffr2	A	T	5: 89,582,687	T159S	probably benign	Het
Nup153	A	T	13: 46,681,109		probably benign	Het
Olfr139	T	A	11: 74,045,055	D73V	probably damaging	Het
Olfr616	A	C	7: 103,565,171	M36R	possibly damaging	Het
Pate2	T	C	9: 35,686,111		probably benign	Het
Pcca	A	G	14: 122,790,398	N73D	probably damaging	Het
Pip5k1c	G	A	10: 81,310,889		probably null	Het
Pkhd1l1	A	T	15: 44,528,191	H1551L	probably benign	Het
Pkhd1l1	G	A	15: 44,582,227	M3768I	probably benign	Het
Ppa2	A	G	3: 133,370,434	M275V	probably benign	Het
Ptpn23	G	A	9: 110,388,556	T744I	probably benign	Het
Ptprv	A	T	1: 135,124,506		noncoding transcript	Het
Rad17	A	T	13: 100,645,063	H75Q	possibly damaging	Het
Rbm44	T	C	1: 91,169,098		probably null	Het
Rbpj	C	T	5: 53,649,415	R201W	probably damaging	Het
Rbpjl	C	A	2: 164,410,289	L215I	probably damaging	Het
Ror1	A	G	4: 100,425,932	E398G	probably benign	Het
Scamp3	T	A	3: 89,182,293		probably benign	Het
Selenot	CATGTATG	CATGTATGTATG	3: 58,588,453		probably null	Het
Siglec15	A	G	18: 78,048,675	C104R	probably damaging	Het
Sis	T	C	3: 72,934,122	I787V	probably benign	Het
Slc17a8	T	C	10: 89,576,560	D521G	probably benign	Het
Slc7a10	T	A	7: 35,197,355	M172K	possibly damaging	Het
Slco4c1	G	A	1: 96,841,228	P303L	probably damaging	Het
Slitrk3	T	C	3: 73,050,648	T264A	probably benign	Het
Smg8	A	C	11: 87,086,137	V206G	probably damaging	Het
Smg9	A	G	7: 24,405,872	K137R	possibly damaging	Het
Srrm2	C	A	17: 23,819,317		probably benign	Het
Sult2a2	T	A	7: 13,734,860	Y84N	possibly damaging	Het
Syngr2	A	T	11: 117,812,510	I34F	probably benign	Het
Tank	G	A	2: 61,578,635		probably benign	Het
Tead4	T	C	6: 128,294,171		probably benign	Het
Tex36	A	T	7: 133,595,290	C33S	probably benign	Het
Timm21	C	A	18: 84,949,414	V112L	possibly damaging	Het
Tmem240	T	A	4: 155,739,674	L92Q	probably damaging	Het
Tmem268	C	G	4: 63,568,540	S100C	probably damaging	Het
Tmod3	G	A	9: 75,511,206	P183S	probably damaging	Het
Trappc10	G	T	10: 78,217,160	F260L	possibly damaging	Het
Trim16	A	T	11: 62,836,812	Y233F	probably benign	Het
Trmt112	T	C	19: 6,910,753	V91A	probably benign	Het
Ttc3	A	G	16: 94,429,359	E450G	probably benign	Het
Ttk	A	G	9: 83,863,541	D647G	probably damaging	Het
Ubash3b	A	G	9: 41,037,459	C187R	possibly damaging	Het
Vmn1r29	T	A	6: 58,308,067	Y257*	probably null	Het
Vmn1r33	T	C	6: 66,612,105	N155S	probably benign	Het
Vmn2r28	T	A	7: 5,486,464	I459L	probably benign	Het
Vwde	T	C	6: 13,192,642	I421V	possibly damaging	Het
Xiap	T	C	X: 42,094,465	F23L	probably benign	Het
Xkr7	A	G	2: 153,054,380	T385A	probably benign	Het
Zbtb11	A	G	16: 56,006,065	Y819C	probably damaging	Het
Zfp112	A	G	7: 24,126,484	T624A	probably damaging	Het
Zfp592	A	G	7: 81,024,347	D353G	probably damaging	Het
Zfp62	T	A	11: 49,215,729	S216T	probably damaging	Het
Zfp677	A	T	17: 21,397,794	H371L	probably damaging	Het
Zfp780b	T	C	7: 27,963,448	K561E	possibly damaging	Het
Zfp936	G	A	7: 43,187,257	D31N	probably damaging	Het
Znfx1	T	C	2: 167,039,826	Y217C	probably damaging	Het
Zpbp	C	T	11: 11,415,248	E200K	probably benign	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
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'- AACTTTGTCCTCTATGGGCC -3'
(R):5'- CATCGAGCACAAACCTGAGTTC -3'

Sequencing Primer
(F):5'- CCACTTGACTGGTAGTGTAAGAGC -3'
(R):5'- CCTGAGTTCAGTCAAGGCTACTAAG -3'

Posted On

2016-06-06