Mutagenetix > Incidental Mutation

Incidental Mutation 'R5540:Vps16'

435860

Institutional Source

Beutler Lab

Gene Symbol

Vps16

Ensembl Gene

ENSMUSG00000027411

Gene Name

VSP16 CORVET/HOPS core subunit

Synonyms

1810074M16Rik

MMRRC Submission

043098-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.970) question?

Stock #

R5540 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

130266259-130286189 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 130284305 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 685 (D685E)

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: D685E

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000028900
Gene: ENSMUSG00000027411
AA Change: D685E

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

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: 99.9%
3x: 99.7%
10x: 98.6%
20x: 96.1%

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: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700008O03Rik	A	G	7: 44,012,371 (GRCm39)	S15P	probably damaging	Het
Actl7a	A	T	4: 56,744,388 (GRCm39)	H305L	probably benign	Het
Adam26b	C	A	8: 43,974,654 (GRCm39)	C116F	probably damaging	Het
Adgrl2	A	G	3: 148,543,198 (GRCm39)		probably null	Het
Akr1b10	A	G	6: 34,371,047 (GRCm39)	T238A	probably damaging	Het
Akr1c18	A	G	13: 4,187,178 (GRCm39)	V186A	probably benign	Het
Alpk3	G	A	7: 80,745,184 (GRCm39)	V1311M	probably damaging	Het
Aox1	A	G	1: 58,143,569 (GRCm39)	N1229S	probably benign	Het
Apobec3	T	A	15: 79,782,120 (GRCm39)	N43K	probably benign	Het
Arid1a	A	C	4: 133,407,765 (GRCm39)	D2247E	unknown	Het
Asph	A	G	4: 9,635,906 (GRCm39)	L77S	probably damaging	Het
Cd300ld	T	A	11: 114,878,231 (GRCm39)	T94S	probably damaging	Het
Celf2	T	C	2: 6,558,743 (GRCm39)	T382A	probably benign	Het
Cfap54	C	T	10: 92,808,470 (GRCm39)	A1402T	possibly damaging	Het
Chrnb1	A	T	11: 69,686,476 (GRCm39)	V48E	probably benign	Het
Col6a5	T	A	9: 105,739,975 (GRCm39)	E2548V	probably benign	Het
Crebrf	A	G	17: 26,961,071 (GRCm39)	D56G	possibly damaging	Het
Dctn5	A	G	7: 121,734,275 (GRCm39)	T40A	probably benign	Het
Dmxl2	A	T	9: 54,301,141 (GRCm39)	N2323K	probably benign	Het
Dync1h1	A	G	12: 110,627,384 (GRCm39)	Q4021R	probably benign	Het
Dyrk1a	T	G	16: 94,486,202 (GRCm39)		probably null	Het
Ephb3	T	A	16: 21,039,610 (GRCm39)	F454Y	probably damaging	Het
Fbxo38	A	G	18: 62,647,864 (GRCm39)		probably null	Het
Flg	T	C	3: 93,184,923 (GRCm39)	F15S	probably damaging	Het
Fndc3b	G	A	3: 27,555,651 (GRCm39)	P301L	probably damaging	Het
Fpr-rs7	C	T	17: 20,334,356 (GRCm39)	G45R	probably damaging	Het
Garin3	A	G	11: 46,295,715 (GRCm39)	N29S	probably damaging	Het
Gfi1	T	A	5: 107,867,991 (GRCm39)	T360S	probably damaging	Het
Grik4	T	C	9: 42,432,243 (GRCm39)	H918R	probably damaging	Het
Hpx	A	G	7: 105,241,119 (GRCm39)	S385P	possibly damaging	Het
Kdm5b	A	G	1: 134,558,979 (GRCm39)	D1501G	probably damaging	Het
Kif20b	A	T	19: 34,915,860 (GRCm39)	M546L	probably benign	Het
Map3k9	G	T	12: 81,819,587 (GRCm39)	N222K	probably damaging	Het
Me1	A	G	9: 86,561,926 (GRCm39)	L53P	possibly damaging	Het
Mis18bp1	T	C	12: 65,195,520 (GRCm39)	E748G	possibly damaging	Het
Morc3	T	A	16: 93,644,268 (GRCm39)	N186K	probably benign	Het
Mtor	A	G	4: 148,539,165 (GRCm39)	T221A	probably benign	Het
Muc6	A	G	7: 141,235,850 (GRCm39)		probably null	Het
Myh8	C	A	11: 67,177,266 (GRCm39)	T444N	probably benign	Het
Myo7b	A	G	18: 32,140,143 (GRCm39)	Y216H	probably damaging	Het
Myom1	G	A	17: 71,416,782 (GRCm39)	V1382M	probably damaging	Het
Nbeal2	A	T	9: 110,460,801 (GRCm39)	Y1718N	probably damaging	Het
Npc1l1	A	G	11: 6,164,546 (GRCm39)	S1168P	probably damaging	Het
Or4c58	A	G	2: 89,675,011 (GRCm39)	F102S	probably damaging	Het
Or4d2	T	A	11: 87,784,511 (GRCm39)	K80*	probably null	Het
Or51f5	C	T	7: 102,424,136 (GRCm39)	A135V	probably benign	Het
Or5an9	T	A	19: 12,187,824 (GRCm39)	I298N	probably damaging	Het
Or6c8b	G	T	10: 128,882,364 (GRCm39)	D189E	probably damaging	Het
Pcdha4	C	A	18: 37,087,890 (GRCm39)	A691E	probably benign	Het
Pde6a	T	G	18: 61,364,438 (GRCm39)	F165V	probably damaging	Het
Ptpn14	A	T	1: 189,578,561 (GRCm39)	M340L	probably benign	Het
Rnasel	G	T	1: 153,630,890 (GRCm39)	E469*	probably null	Het
Rsph3a	T	G	17: 8,164,790 (GRCm39)	L50R	probably benign	Het
Rusc2	A	G	4: 43,423,975 (GRCm39)	Y1043C	probably damaging	Het
Serpinb6b	A	T	13: 33,161,541 (GRCm39)	K86*	probably null	Het
Serpine1	T	C	5: 137,092,063 (GRCm39)	T392A	probably benign	Het
Shcbp1	A	T	8: 4,794,529 (GRCm39)	D421E	probably damaging	Het
Slc24a1	A	G	9: 64,855,863 (GRCm39)	V348A	unknown	Het
Slc26a7	A	G	4: 14,506,621 (GRCm39)	F605L	probably benign	Het
Slc66a1	A	T	4: 139,027,655 (GRCm39)	L229Q	probably damaging	Het
Spag17	A	C	3: 99,963,588 (GRCm39)	E1102A	possibly damaging	Het
Stab2	A	G	10: 86,683,989 (GRCm39)	V2390A	probably benign	Het
Stk11	A	G	10: 79,961,883 (GRCm39)	I35V	probably benign	Het
Stk24	T	C	14: 121,531,693 (GRCm39)	D321G	possibly damaging	Het
Tbx4	A	T	11: 85,801,994 (GRCm39)	N209I	possibly damaging	Het
Tmem225	T	C	9: 40,060,681 (GRCm39)	L80P	probably damaging	Het
Tnfrsf4	C	T	4: 156,098,380 (GRCm39)	T17I	probably benign	Het
Traf3ip1	G	A	1: 91,429,037 (GRCm39)	R268Q	probably benign	Het
Trhde	T	A	10: 114,636,497 (GRCm39)	I237F	probably benign	Het
Ugt2a1	A	T	5: 87,633,915 (GRCm39)	W231R	probably damaging	Het
Vash1	ACTGCTGCTGCTGCTGCTGC	ACTGCTGCTGCTGCTGC	12: 86,726,831 (GRCm39)		probably benign	Het
Washc4	A	G	10: 83,409,657 (GRCm39)	D602G	probably damaging	Het
Wdr59	A	G	8: 112,211,816 (GRCm39)	L377P	possibly damaging	Het
Wdr81	T	C	11: 75,339,896 (GRCm39)	E1364G	probably damaging	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
R1789:Vps16	UTSW	2	130,285,520 (GRCm39)	missense	probably benign	0.42
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
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'- CAGCTGATGCCTTCTACAAAGC -3'
(R):5'- GCCAGCTTTAACCACCATAGTC -3'

Sequencing Primer
(F):5'- GCCAAGAATGAATTTGCAGCC -3'
(R):5'- TCTGCAGGAAAGCTGTACTC -3'

Posted On

2016-10-24