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

Essential gene?

Probably essential (E-score: 0.971) 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 (GRCm38)	H739Q	probably benign	Het
Abca3	C	T	17: 24,374,300 (GRCm38)	R224C	probably damaging	Het
Abca8b	A	G	11: 109,974,988 (GRCm38)		probably null	Het
Adam1b	C	T	5: 121,501,159 (GRCm38)	V608M	probably damaging	Het
Ank2	A	G	3: 126,941,871 (GRCm38)		probably benign	Het
Ankrd17	A	C	5: 90,282,868 (GRCm38)	L1019R	probably damaging	Het
Arih1	T	C	9: 59,486,232 (GRCm38)	N39S	unknown	Het
Best3	G	A	10: 116,988,742 (GRCm38)	V38I	probably benign	Het
Bicc1	A	G	10: 70,947,883 (GRCm38)	S393P	possibly damaging	Het
C1d	T	A	11: 17,266,674 (GRCm38)	N135K	probably benign	Het
Cage1	G	T	13: 38,011,411 (GRCm38)	S778*	probably null	Het
Capn7	T	A	14: 31,352,426 (GRCm38)	V262E	probably damaging	Het
Ccdc190	A	G	1: 169,933,087 (GRCm38)	R95G	probably damaging	Het
Cd163	C	T	6: 124,325,288 (GRCm38)	T937I	probably damaging	Het
Cdh18	G	A	15: 23,259,666 (GRCm38)	S194N	probably damaging	Het
Clec4b2	A	T	6: 123,200,956 (GRCm38)	S77C	probably null	Het
Ctsw	T	A	19: 5,466,049 (GRCm38)	D237V	probably damaging	Het
Cyp2c68	G	A	19: 39,712,507 (GRCm38)	T289I	probably benign	Het
Cyp4f39	A	G	17: 32,481,104 (GRCm38)	Y133C	probably damaging	Het
Dlg5	T	C	14: 24,136,622 (GRCm38)	E1847G	probably damaging	Het
Dnah7a	C	A	1: 53,647,248 (GRCm38)	E248*	probably null	Het
Eef2kmt	T	A	16: 5,247,599 (GRCm38)	D248V	probably damaging	Het
Ewsr1	T	C	11: 5,088,054 (GRCm38)	T113A	possibly damaging	Het
Fbxo4	A	G	15: 3,977,756 (GRCm38)		probably null	Het
Fbxo43	A	T	15: 36,162,929 (GRCm38)	M44K	probably benign	Het
Fchsd1	A	G	18: 37,964,810 (GRCm38)	I340T	possibly damaging	Het
Fgf5	C	A	5: 98,262,015 (GRCm38)	A141E	probably damaging	Het
Gfm1	T	C	3: 67,473,544 (GRCm38)	V664A	probably damaging	Het
Glp2r	T	C	11: 67,741,032 (GRCm38)	T121A	possibly damaging	Het
Gm10803	A	C	2: 93,564,172 (GRCm38)	L96F	probably damaging	Het
Gm12169	T	A	11: 46,528,532 (GRCm38)	D58E	probably damaging	Het
Gm14569	T	C	X: 36,430,817 (GRCm38)	D1413G	probably benign	Het
Gm15455	T	C	1: 33,837,351 (GRCm38)		noncoding transcript	Het
Gm1818	G	C	12: 48,555,535 (GRCm38)		noncoding transcript	Het
Gm4907	G	A	X: 23,907,241 (GRCm38)	G327E	probably damaging	Het
Gm5155	A	T	7: 17,902,706 (GRCm38)	D236V	probably damaging	Het
Gm7030	A	G	17: 36,109,415 (GRCm38)		probably benign	Het
Gnb2	G	A	5: 137,529,940 (GRCm38)		probably null	Het
Gpc4	G	A	X: 52,074,563 (GRCm38)	R148C	probably damaging	Het
Gpx5	C	T	13: 21,288,745 (GRCm38)	V140I	probably damaging	Het
Gtpbp1	A	T	15: 79,719,221 (GRCm38)	Q637L	possibly damaging	Het
Herc1	A	T	9: 66,470,326 (GRCm38)	K3458M	possibly damaging	Het
Hhat	A	T	1: 192,727,339 (GRCm38)	L138Q	probably damaging	Het
Hipk1	G	T	3: 103,777,507 (GRCm38)	T264N	probably damaging	Het
Hjurp	A	T	1: 88,275,050 (GRCm38)	Y71N	possibly damaging	Het
Hnf4g	G	T	3: 3,644,587 (GRCm38)	A144S	probably damaging	Het
Hook3	TAGAG	TAG	8: 26,032,019 (GRCm38)		probably null	Het
Ifi204	G	A	1: 173,751,740 (GRCm38)	T513I	possibly damaging	Het
Ino80b	G	T	6: 83,125,042 (GRCm38)	S26R	probably damaging	Het
Ints9	T	A	14: 64,980,228 (GRCm38)	L68H	probably damaging	Het
Isx	C	T	8: 74,892,714 (GRCm38)	T178I	probably benign	Het
Kel	A	G	6: 41,688,111 (GRCm38)	L255P	probably damaging	Het
Klf11	T	A	12: 24,655,359 (GRCm38)	S271T	probably benign	Het
Klhl20	A	C	1: 161,109,220 (GRCm38)		probably null	Het
Lama2	G	A	10: 27,190,504 (GRCm38)	T1127I	probably damaging	Het
Larp1b	T	A	3: 41,033,985 (GRCm38)	N81K	possibly damaging	Het
Lsm11	T	C	11: 45,944,839 (GRCm38)	D25G	probably damaging	Het
Map3k20	T	A	2: 72,402,345 (GRCm38)		probably benign	Het
Mbd6	C	T	10: 127,286,441 (GRCm38)	V173I	probably benign	Het
Milr1	A	G	11: 106,766,965 (GRCm38)	D131G	possibly damaging	Het
Mybpc1	T	G	10: 88,543,774 (GRCm38)	D635A	probably damaging	Het
Myh7b	G	C	2: 155,632,373 (GRCm38)	R1669S	possibly damaging	Het
Ndufa7	A	G	17: 33,824,603 (GRCm38)		probably benign	Het
Ndufs3	C	A	2: 90,898,660 (GRCm38)	A161S	probably benign	Het
Neo1	T	C	9: 58,990,271 (GRCm38)	D134G	probably damaging	Het
Nme4	G	A	17: 26,093,668 (GRCm38)	T129I	probably benign	Het
Npffr2	A	T	5: 89,582,687 (GRCm38)	T159S	probably benign	Het
Nup153	A	T	13: 46,681,109 (GRCm38)		probably benign	Het
Olfr139	T	A	11: 74,045,055 (GRCm38)	D73V	probably damaging	Het
Olfr616	A	C	7: 103,565,171 (GRCm38)	M36R	possibly damaging	Het
Pate2	T	C	9: 35,686,111 (GRCm38)		probably benign	Het
Pcca	A	G	14: 122,790,398 (GRCm38)	N73D	probably damaging	Het
Pip5k1c	G	A	10: 81,310,889 (GRCm38)		probably null	Het
Pkhd1l1	G	A	15: 44,582,227 (GRCm38)	M3768I	probably benign	Het
Pkhd1l1	A	T	15: 44,528,191 (GRCm38)	H1551L	probably benign	Het
Ppa2	A	G	3: 133,370,434 (GRCm38)	M275V	probably benign	Het
Ptpn23	G	A	9: 110,388,556 (GRCm38)	T744I	probably benign	Het
Ptprv	A	T	1: 135,124,506 (GRCm38)		noncoding transcript	Het
Rad17	A	T	13: 100,645,063 (GRCm38)	H75Q	possibly damaging	Het
Rbm44	T	C	1: 91,169,098 (GRCm38)		probably null	Het
Rbpj	C	T	5: 53,649,415 (GRCm38)	R201W	probably damaging	Het
Rbpjl	C	A	2: 164,410,289 (GRCm38)	L215I	probably damaging	Het
Ror1	A	G	4: 100,425,932 (GRCm38)	E398G	probably benign	Het
Scamp3	T	A	3: 89,182,293 (GRCm38)		probably benign	Het
Selenot	CATGTATG	CATGTATGTATG	3: 58,588,453 (GRCm38)		probably null	Het
Siglec15	A	G	18: 78,048,675 (GRCm38)	C104R	probably damaging	Het
Sis	T	C	3: 72,934,122 (GRCm38)	I787V	probably benign	Het
Slc17a8	T	C	10: 89,576,560 (GRCm38)	D521G	probably benign	Het
Slc7a10	T	A	7: 35,197,355 (GRCm38)	M172K	possibly damaging	Het
Slco4c1	G	A	1: 96,841,228 (GRCm38)	P303L	probably damaging	Het
Slitrk3	T	C	3: 73,050,648 (GRCm38)	T264A	probably benign	Het
Smg8	A	C	11: 87,086,137 (GRCm38)	V206G	probably damaging	Het
Smg9	A	G	7: 24,405,872 (GRCm38)	K137R	possibly damaging	Het
Srrm2	C	A	17: 23,819,317 (GRCm38)		probably benign	Het
Sult2a2	T	A	7: 13,734,860 (GRCm38)	Y84N	possibly damaging	Het
Syngr2	A	T	11: 117,812,510 (GRCm38)	I34F	probably benign	Het
Tank	G	A	2: 61,578,635 (GRCm38)		probably benign	Het
Tead4	T	C	6: 128,294,171 (GRCm38)		probably benign	Het
Tex36	A	T	7: 133,595,290 (GRCm38)	C33S	probably benign	Het
Timm21	C	A	18: 84,949,414 (GRCm38)	V112L	possibly damaging	Het
Tmem240	T	A	4: 155,739,674 (GRCm38)	L92Q	probably damaging	Het
Tmem268	C	G	4: 63,568,540 (GRCm38)	S100C	probably damaging	Het
Tmod3	G	A	9: 75,511,206 (GRCm38)	P183S	probably damaging	Het
Trappc10	G	T	10: 78,217,160 (GRCm38)	F260L	possibly damaging	Het
Trim16	A	T	11: 62,836,812 (GRCm38)	Y233F	probably benign	Het
Trmt112	T	C	19: 6,910,753 (GRCm38)	V91A	probably benign	Het
Ttc3	A	G	16: 94,429,359 (GRCm38)	E450G	probably benign	Het
Ttk	A	G	9: 83,863,541 (GRCm38)	D647G	probably damaging	Het
Ubash3b	A	G	9: 41,037,459 (GRCm38)	C187R	possibly damaging	Het
Vmn1r29	T	A	6: 58,308,067 (GRCm38)	Y257*	probably null	Het
Vmn1r33	T	C	6: 66,612,105 (GRCm38)	N155S	probably benign	Het
Vmn2r28	T	A	7: 5,486,464 (GRCm38)	I459L	probably benign	Het
Vwde	T	C	6: 13,192,642 (GRCm38)	I421V	possibly damaging	Het
Xiap	T	C	X: 42,094,465 (GRCm38)	F23L	probably benign	Het
Xkr7	A	G	2: 153,054,380 (GRCm38)	T385A	probably benign	Het
Zbtb11	A	G	16: 56,006,065 (GRCm38)	Y819C	probably damaging	Het
Zfp112	A	G	7: 24,126,484 (GRCm38)	T624A	probably damaging	Het
Zfp592	A	G	7: 81,024,347 (GRCm38)	D353G	probably damaging	Het
Zfp62	T	A	11: 49,215,729 (GRCm38)	S216T	probably damaging	Het
Zfp677	A	T	17: 21,397,794 (GRCm38)	H371L	probably damaging	Het
Zfp780b	T	C	7: 27,963,448 (GRCm38)	K561E	possibly damaging	Het
Zfp936	G	A	7: 43,187,257 (GRCm38)	D31N	probably damaging	Het
Znfx1	T	C	2: 167,039,826 (GRCm38)	Y217C	probably damaging	Het
Zpbp	C	T	11: 11,415,248 (GRCm38)	E200K	probably benign	Het

Other mutations in Vps16

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01327:Vps16	APN	2	130,437,696 (GRCm38)	missense	probably benign	0.19
IGL01400:Vps16	APN	2	130,438,353 (GRCm38)	missense	possibly damaging	0.73
IGL01542:Vps16	APN	2	130,438,394 (GRCm38)	missense	probably damaging	0.97
IGL02011:Vps16	APN	2	130,441,479 (GRCm38)	missense	probably benign	0.04
IGL02192:Vps16	APN	2	130,440,932 (GRCm38)	missense	probably damaging	0.98
IGL02220:Vps16	APN	2	130,441,653 (GRCm38)	missense	possibly damaging	0.85
IGL02587:Vps16	APN	2	130,439,716 (GRCm38)	critical splice donor site	probably null
R0427:Vps16	UTSW	2	130,438,850 (GRCm38)	missense	probably benign	0.00
R0507:Vps16	UTSW	2	130,437,712 (GRCm38)	critical splice donor site	probably null
R1550:Vps16	UTSW	2	130,440,340 (GRCm38)	missense	probably benign	0.09
R1789:Vps16	UTSW	2	130,443,600 (GRCm38)	missense	probably benign	0.42
R3895:Vps16	UTSW	2	130,438,676 (GRCm38)	missense	possibly damaging	0.96
R3981:Vps16	UTSW	2	130,442,594 (GRCm38)	missense	possibly damaging	0.77
R4092:Vps16	UTSW	2	130,439,912 (GRCm38)	missense	probably damaging	1.00
R4555:Vps16	UTSW	2	130,443,576 (GRCm38)	missense	probably damaging	1.00
R4569:Vps16	UTSW	2	130,442,204 (GRCm38)	missense	probably benign
R4803:Vps16	UTSW	2	130,438,110 (GRCm38)	missense	probably benign	0.27
R4835:Vps16	UTSW	2	130,438,300 (GRCm38)	splice site	probably benign
R5022:Vps16	UTSW	2	130,439,452 (GRCm38)	missense	probably benign	0.07
R5057:Vps16	UTSW	2	130,439,452 (GRCm38)	missense	probably benign	0.07
R5158:Vps16	UTSW	2	130,441,279 (GRCm38)	missense	probably damaging	1.00
R5177:Vps16	UTSW	2	130,443,368 (GRCm38)	nonsense	probably null
R5540:Vps16	UTSW	2	130,442,385 (GRCm38)	missense	probably benign	0.00
R5680:Vps16	UTSW	2	130,440,324 (GRCm38)	missense	possibly damaging	0.64
R5689:Vps16	UTSW	2	130,439,091 (GRCm38)	nonsense	probably null
R5690:Vps16	UTSW	2	130,439,091 (GRCm38)	nonsense	probably null
R5926:Vps16	UTSW	2	130,443,556 (GRCm38)	missense	probably damaging	0.97
R5992:Vps16	UTSW	2	130,424,449 (GRCm38)	critical splice donor site	probably null
R6135:Vps16	UTSW	2	130,438,653 (GRCm38)	missense	possibly damaging	0.57
R6370:Vps16	UTSW	2	130,443,384 (GRCm38)	missense	probably damaging	1.00
R6898:Vps16	UTSW	2	130,437,681 (GRCm38)	missense	possibly damaging	0.74
R7378:Vps16	UTSW	2	130,438,179 (GRCm38)	missense	probably damaging	1.00
R7487:Vps16	UTSW	2	130,439,057 (GRCm38)	nonsense	probably null
R7641:Vps16	UTSW	2	130,440,528 (GRCm38)	missense	probably benign	0.28
R7720:Vps16	UTSW	2	130,441,703 (GRCm38)	nonsense	probably null
R8246:Vps16	UTSW	2	130,438,873 (GRCm38)	missense	probably damaging	1.00
R8363:Vps16	UTSW	2	130,442,241 (GRCm38)	missense	probably benign	0.08
R9092:Vps16	UTSW	2	130,439,673 (GRCm38)	missense	probably damaging	0.99
R9128:Vps16	UTSW	2	130,424,399 (GRCm38)	missense	possibly damaging	0.51
R9352:Vps16	UTSW	2	130,441,903 (GRCm38)	critical splice donor site	probably null
R9406:Vps16	UTSW	2	130,441,505 (GRCm38)	critical splice donor site	probably null
R9508:Vps16	UTSW	2	130,442,441 (GRCm38)	missense	possibly damaging	0.94
R9800:Vps16	UTSW	2	130,440,485 (GRCm38)	missense	probably benign	0.02
RF021:Vps16	UTSW	2	130,438,209 (GRCm38)	missense	probably benign	0.09
Z1177:Vps16	UTSW	2	130,441,426 (GRCm38)	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