Mutagenetix > Incidental Mutation

Incidental Mutation 'R7378:Vps16'

572438

Institutional Source

Beutler Lab

Gene Symbol

Vps16

Ensembl Gene

ENSMUSG00000027411

Gene Name

VSP16 CORVET/HOPS core subunit

Synonyms

1810074M16Rik

MMRRC Submission

045460-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.971) question?

Stock #

R7378 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

130266259-130286189 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 130280099 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glycine at position 108 (V108G)

Ref Sequence

ENSEMBL: ENSMUSP00000028900 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000028900
AA Change: V108G

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000028900
Gene: ENSMUSG00000027411
AA Change: V108G

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 damaging
Transcript: ENSMUST00000128994
AA Change: V108G

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000115899
Gene: ENSMUSG00000027411
AA Change: V108G

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: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.0%

Validation Efficiency

99% (138/140)

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: 142 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2ml1	A	C	6: 128,523,210 (GRCm39)		probably null	Het
Aars1	A	G	8: 111,768,974 (GRCm39)	Y258C	probably damaging	Het
Acaa2	A	T	18: 74,938,943 (GRCm39)	Y376F	probably benign	Het
Adcy1	C	T	11: 7,119,543 (GRCm39)	S1062F	possibly damaging	Het
Adgrb3	A	T	1: 25,571,000 (GRCm39)	C492*	probably null	Het
Adgrg6	A	G	10: 14,411,636 (GRCm39)	F22S	probably benign	Het
Adh1	A	G	3: 137,994,648 (GRCm39)		probably null	Het
Afm	T	A	5: 90,699,259 (GRCm39)	C568S	probably benign	Het
Ago4	C	T	4: 126,405,257 (GRCm39)	E439K	probably benign	Het
Aifm2	T	G	10: 61,563,496 (GRCm39)	V122G	possibly damaging	Het
Akap6	A	G	12: 53,189,357 (GRCm39)	N2257S	probably benign	Het
Ap3m2	A	G	8: 23,294,026 (GRCm39)	I8T	probably benign	Het
Apc2	C	A	10: 80,147,228 (GRCm39)	L761I	probably damaging	Het
Asap2	A	G	12: 21,162,052 (GRCm39)	D3G	probably benign	Het
Asxl1	T	C	2: 153,243,913 (GRCm39)	C1489R	probably damaging	Het
Atm	T	G	9: 53,364,737 (GRCm39)		probably null	Het
Bmal1	C	A	7: 112,898,415 (GRCm39)	T281K	probably benign	Het
Bpifa6	C	A	2: 153,828,353 (GRCm39)	A153E	probably damaging	Het
Cav2	A	G	6: 17,282,059 (GRCm39)	T106A	probably benign	Het
Cavin4	A	G	4: 48,663,631 (GRCm39)	N4D	probably benign	Het
Cenpc1	T	C	5: 86,194,358 (GRCm39)	N136S	probably benign	Het
Cfap45	T	A	1: 172,365,910 (GRCm39)		probably null	Het
Col3a1	G	A	1: 45,366,807 (GRCm39)		probably null	Het
Crocc2	C	T	1: 93,121,809 (GRCm39)	L653F	probably damaging	Het
Cry2	A	G	2: 92,244,009 (GRCm39)	L388P	probably damaging	Het
Cstb	T	C	10: 78,262,822 (GRCm39)	F43S	probably damaging	Het
Ctcfl	A	G	2: 172,954,051 (GRCm39)	Y349H	probably damaging	Het
Ctu2	T	A	8: 123,208,238 (GRCm39)	V485D	probably damaging	Het
Cwc25	A	C	11: 97,638,823 (GRCm39)	L367R	possibly damaging	Het
Dock4	T	A	12: 40,838,243 (GRCm39)	H1061Q	possibly damaging	Het
Dpy19l3	C	A	7: 35,452,067 (GRCm39)	V26L	probably benign	Het
Efcab3	T	C	11: 104,605,528 (GRCm39)	I298T	probably benign	Het
Elmo1	A	T	13: 20,465,105 (GRCm39)	I225F	probably benign	Het
Ep300	T	C	15: 81,534,746 (GRCm39)	S2268P	probably damaging	Het
F2r	C	T	13: 95,754,836 (GRCm39)	C16Y	probably damaging	Het
Fbxo33	C	A	12: 59,251,157 (GRCm39)	E453*	probably null	Het
Flot1	A	T	17: 36,136,405 (GRCm39)	D186V	probably damaging	Het
Fmn2	CCCTCCTCTCCCTGGAATGGGAATACCTCCCCCACCTCCTCTCCCTGGAATGGGAATACCTCCCCCACCTCCTCTCCCTGGAATGGGAATATCTCCCCTACCTCCTCTCCCTGGAATGGGAATACCTCC	CCCTCCTCTCCCTGGAATGGGAATACCTCCCCCACCTCCTCTCCCTGGAATGGGAATATCTCCCCTACCTCCTCTCCCTGGAATGGGAATACCTCC	1: 174,436,769 (GRCm39)		probably benign	Het
Fras1	T	C	5: 96,744,644 (GRCm39)	C560R	probably damaging	Het
Get3	A	T	8: 85,746,492 (GRCm39)	F119I	probably benign	Het
Gfi1	A	T	5: 107,871,095 (GRCm39)	S165T	possibly damaging	Het
Gli2	T	C	1: 118,776,222 (GRCm39)	D400G	probably damaging	Het
Gm37240	T	A	3: 84,879,944 (GRCm39)		probably null	Het
Gml	C	T	15: 74,688,970 (GRCm39)	V27I	possibly damaging	Het
Htt	A	T	5: 34,961,143 (GRCm39)	I257F	probably benign	Het
Hycc2	T	C	1: 58,569,193 (GRCm39)	K462R	probably benign	Het
Ier5	C	T	1: 154,974,438 (GRCm39)	V247M	probably damaging	Het
Ift46	C	T	9: 44,689,892 (GRCm39)		probably benign	Het
Il12b	A	G	11: 44,298,721 (GRCm39)	T59A	probably benign	Het
Insr	A	G	8: 3,248,231 (GRCm39)	L438P	probably damaging	Het
Iqgap2	C	T	13: 95,869,398 (GRCm39)		probably null	Het
Irx4	A	T	13: 73,415,672 (GRCm39)	T154S	possibly damaging	Het
Itgbl1	A	G	14: 124,094,901 (GRCm39)	K309E	probably benign	Het
Kcns2	T	A	15: 34,839,849 (GRCm39)	L404*	probably null	Het
Kif2c	T	C	4: 117,019,226 (GRCm39)	E644G	possibly damaging	Het
Klhl22	T	C	16: 17,594,669 (GRCm39)	L266P	probably damaging	Het
Krt71	T	A	15: 101,646,764 (GRCm39)	K315*	probably null	Het
Lca5	T	C	9: 83,277,583 (GRCm39)	N587S	probably benign	Het
Lrp1b	T	A	2: 41,185,681 (GRCm39)	M1459L		Het
Lrrtm2	T	C	18: 35,346,645 (GRCm39)	K219R	probably damaging	Het
Mcmbp	T	C	7: 128,306,241 (GRCm39)	D459G	probably damaging	Het
Megf8	A	G	7: 25,048,367 (GRCm39)	H1680R	probably damaging	Het
Mia3	A	G	1: 183,115,629 (GRCm39)	S301P	probably benign	Het
Mtrr	A	G	13: 68,712,521 (GRCm39)	Y622H	probably damaging	Het
Myo7b	T	A	18: 32,099,292 (GRCm39)	Q1710L	probably damaging	Het
Nab1	T	C	1: 52,520,154 (GRCm39)	N276D	probably damaging	Het
Nalcn	C	T	14: 123,540,302 (GRCm39)	R1127H	probably damaging	Het
Nbas	T	A	12: 13,324,220 (GRCm39)	I110N	probably damaging	Het
Nfe2l3	C	T	6: 51,434,276 (GRCm39)	Q279*	probably null	Het
Nlrp9c	C	T	7: 26,064,440 (GRCm39)	E963K	probably benign	Het
Nsmaf	A	G	4: 6,416,586 (GRCm39)	V569A	probably benign	Het
Or10ak14	T	C	4: 118,611,372 (GRCm39)	Y123C	possibly damaging	Het
Or13c3	C	T	4: 52,856,421 (GRCm39)	V31I	probably benign	Het
Or52a5b	T	A	7: 103,417,137 (GRCm39)	I156F	probably benign	Het
Or52n5	A	T	7: 104,588,638 (GRCm39)	I302F	probably benign	Het
Or5ac17	T	A	16: 59,036,283 (GRCm39)	D231V	probably benign	Het
Or5p4	T	C	7: 107,680,399 (GRCm39)	S133P	not run	Het
Or7e166	A	T	9: 19,624,183 (GRCm39)	D20V	probably damaging	Het
Or7g32	T	A	9: 19,408,398 (GRCm39)	M118K	probably damaging	Het
Or8d1b	T	A	9: 38,887,017 (GRCm39)	V15E	probably benign	Het
Or8k28	T	C	2: 86,286,412 (GRCm39)	T68A	probably benign	Het
Paf1	A	G	7: 28,096,353 (GRCm39)	Y322C	probably damaging	Het
Pcdha2	C	A	18: 37,072,438 (GRCm39)	A23D	possibly damaging	Het
Pcdhb6	G	A	18: 37,468,225 (GRCm39)	C382Y	probably damaging	Het
Pdzd7	C	T	19: 45,034,045 (GRCm39)	G13D	probably damaging	Het
Pik3r2	T	C	8: 71,222,025 (GRCm39)	N586S	probably benign	Het
Pik3r3	T	A	4: 116,128,027 (GRCm39)	D119E	probably benign	Het
Pkd2l1	T	A	19: 44,142,154 (GRCm39)	I535F	probably benign	Het
Ppfia3	T	C	7: 45,010,870 (GRCm39)		probably null	Het
Ppl	T	A	16: 4,930,860 (GRCm39)	Q53L	possibly damaging	Het
Rimbp3	T	G	16: 17,029,068 (GRCm39)	S831A	probably benign	Het
Rnps1	A	G	17: 24,637,504 (GRCm39)	T49A	unknown	Het
Rpl7a	T	A	2: 26,802,019 (GRCm39)		probably null	Het
Rrm2b	T	A	15: 37,931,891 (GRCm39)	E248D	probably benign	Het
Sdhaf4	A	G	1: 24,035,439 (GRCm39)	F70L	probably damaging	Het
Sel1l3	A	T	5: 53,273,751 (GRCm39)	S1038R	probably benign	Het
Selenoo	T	A	15: 88,973,681 (GRCm39)	F124I	probably benign	Het
Setbp1	A	T	18: 78,900,701 (GRCm39)	Y989N	probably damaging	Het
Slc1a7	A	G	4: 107,859,400 (GRCm39)	E163G	possibly damaging	Het
Slc22a2	T	C	17: 12,831,278 (GRCm39)	F356S	probably damaging	Het
Slc24a4	C	T	12: 102,205,435 (GRCm39)	P378L	probably benign	Het
Slc4a1ap	A	G	5: 31,684,871 (GRCm39)	D169G	probably benign	Het
Slc4a7	T	A	14: 14,757,421 (GRCm38)	V422D	probably damaging	Het
Slitrk6	T	C	14: 110,987,295 (GRCm39)	Y804C	probably damaging	Het
Smarcad1	T	A	6: 65,087,360 (GRCm39)	H906Q	probably benign	Het
Smn1	A	G	13: 100,264,373 (GRCm39)	T109A	probably damaging	Het
Sntb2	A	G	8: 107,707,944 (GRCm39)	N236S	probably damaging	Het
Spag9	T	A	11: 94,005,177 (GRCm39)		probably null	Het
Spg11	C	A	2: 121,888,910 (GRCm39)	G2154W	probably damaging	Het
Srsf6	T	C	2: 162,776,489 (GRCm39)	S278P	unknown	Het
Stag3	G	A	5: 138,280,222 (GRCm39)	R29H	probably benign	Het
Stambp	C	T	6: 83,540,888 (GRCm39)	V98I	not run	Het
Styxl2	G	T	1: 165,939,632 (GRCm39)	S58*	probably null	Het
Suco	T	C	1: 161,689,780 (GRCm39)	D89G	possibly damaging	Het
Suox	C	T	10: 128,506,910 (GRCm39)	V373I	probably benign	Het
Sv2b	T	A	7: 74,797,476 (GRCm39)		probably null	Het
Tatdn2	T	C	6: 113,681,662 (GRCm39)	L565P	probably damaging	Het
Tbpl2	T	A	2: 23,984,712 (GRCm39)	E145V	probably benign	Het
Tlr1	T	C	5: 65,082,571 (GRCm39)	I669V	not run	Het
Tmc1	A	T	19: 20,845,753 (GRCm39)	F157I	probably damaging	Het
Tmem26	T	G	10: 68,559,922 (GRCm39)		probably null	Het
Tmem33	A	T	5: 67,443,476 (GRCm39)	I218F	probably benign	Het
Tmem94	T	A	11: 115,685,000 (GRCm39)	D862E	probably damaging	Het
Tnr	T	C	1: 159,712,432 (GRCm39)		probably null	Het
Tnrc6c	T	C	11: 117,632,606 (GRCm39)	S1103P	probably benign	Het
Tomm70a	T	A	16: 56,966,407 (GRCm39)	Y453*	probably null	Het
Trabd	C	A	15: 88,969,493 (GRCm39)	R229S	possibly damaging	Het
Trappc10	T	C	10: 78,029,252 (GRCm39)	D1095G	probably damaging	Het
Trim27	A	G	13: 21,376,631 (GRCm39)	T460A	possibly damaging	Het
Tsen54	T	G	11: 115,712,531 (GRCm39)	D433E	probably benign	Het
Ubap2	A	G	4: 41,235,515 (GRCm39)		probably null	Het
Vat1l	A	T	8: 115,016,132 (GRCm39)	N341Y	possibly damaging	Het
Vmn2r82	C	G	10: 79,232,276 (GRCm39)	Y758*	probably null	Het
Vps53	T	A	11: 75,967,900 (GRCm39)	I585F	possibly damaging	Het
Wrnip1	G	A	13: 33,000,264 (GRCm39)	V424M	probably benign	Het
Yif1a	G	A	19: 5,139,818 (GRCm39)	V88M	possibly damaging	Het
Zfat	T	C	15: 68,052,969 (GRCm39)	Y275C	probably damaging	Het
Zfhx3	A	G	8: 109,519,880 (GRCm39)	E334G	probably damaging	Het
Zfp277	T	C	12: 40,365,852 (GRCm39)	D539G	possibly damaging	Het
Zfp292	A	T	4: 34,808,384 (GRCm39)	N1558K	probably benign	Het
Zfp3	A	G	11: 70,662,899 (GRCm39)	K286R	probably benign	Het
Zfp366	T	C	13: 99,366,023 (GRCm39)	C395R	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
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
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'- TCTGGCTTACCACTGGCTAG -3'
(R):5'- ATTGGCACTCAGAGTAAAGCG -3'

Sequencing Primer
(F):5'- ACTGGCTAGCCTGCTGGTAAG -3'
(R):5'- TCCTGTAAGGATGGCCACC -3'

Posted On

2019-09-13