Mutagenetix > Incidental Mutation

Incidental Mutation 'R0364:Vps39'

261851

Institutional Source

Beutler Lab

Gene Symbol

Vps39

Ensembl Gene

ENSMUSG00000027291

Gene Name

VPS39 HOPS complex subunit

Synonyms

Vam6, Vam6P, A230065P22Rik, mVam6

MMRRC Submission

038570-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.950) question?

Stock #

R0364 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

120146942-120183618 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 120176119 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Lysine to Threonine at position 76 (K76T)

Ref Sequence

ENSEMBL: ENSMUSP00000028752 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028752] [ENSMUST00000102501]

AlphaFold

Q8R5L3

Predicted Effect

probably damaging
Transcript: ENSMUST00000028752
AA Change: K76T

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: K76T

Domain	Start	End	E-Value	Type
Pfam:CNH	19	280	8.3e-53	PFAM
Pfam:Clathrin	410	536	3.9e-9	PFAM
Pfam:Vps39_1	449	551	1.7e-35	PFAM
Pfam:Clathrin	570	740	2.3e-8	PFAM
Pfam:Vps39_2	761	869	5.1e-36	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000102501
AA Change: K87T

PolyPhen 2 Score 0.896 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: K87T

Domain	Start	End	E-Value	Type
Pfam:CNH	20	291	1.3e-32	PFAM
Pfam:Clathrin	421	547	2e-9	PFAM
Pfam:Vps39_1	460	562	6.7e-36	PFAM
Pfam:Clathrin	582	751	2.3e-8	PFAM
Pfam:Vps39_2	772	880	6.6e-36	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126526

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000129857

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138854

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147085

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156296

Meta Mutation Damage Score

0.1338

Coding Region Coverage

1x: 99.0%
3x: 98.0%
10x: 95.3%
20x: 89.3%

Validation Efficiency

99% (86/87)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that may promote clustering and fusion of late endosomes and lysosomes. The protein may also act as an adaptor protein that modulates the transforming growth factor-beta response by coupling the transforming growth factor-beta receptor complex to the Smad pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

Allele List at MGI

Other mutations in this stock

Total: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acp7	G	A	7: 28,310,553 (GRCm39)		probably benign	Het
Ano7	A	G	1: 93,316,380 (GRCm39)	D221G	probably benign	Het
Arhgef12	A	T	9: 42,929,697 (GRCm39)	N199K	probably damaging	Het
Arpc2	A	G	1: 74,276,046 (GRCm39)	N26S	probably null	Het
Camta2	G	A	11: 70,574,136 (GRCm39)	T127I	probably damaging	Het
Ccdc13	T	A	9: 121,627,282 (GRCm39)	N665I	probably damaging	Het
Ccdc178	C	T	18: 22,048,119 (GRCm39)	R757H	probably damaging	Het
Cfap52	A	C	11: 67,844,436 (GRCm39)	I93S	possibly damaging	Het
Cmklr1	A	T	5: 113,752,578 (GRCm39)	L141H	probably damaging	Het
Crybb3	T	A	5: 113,223,819 (GRCm39)	I197F	probably damaging	Het
Cryzl1	G	A	16: 91,504,155 (GRCm39)	P97S	probably benign	Het
Cubn	T	C	2: 13,315,318 (GRCm39)		probably benign	Het
Cyp2d37-ps	T	C	15: 82,574,253 (GRCm39)		noncoding transcript	Het
Cyp4a12b	C	A	4: 115,290,117 (GRCm39)	N223K	probably benign	Het
Dennd2a	T	C	6: 39,485,233 (GRCm39)	T349A	probably benign	Het
Dnah12	A	G	14: 26,445,628 (GRCm39)	T730A	probably benign	Het
Dock5	G	A	14: 68,060,129 (GRCm39)		probably benign	Het
Dync2i1	A	G	12: 116,221,097 (GRCm39)		probably benign	Het
Elac2	A	G	11: 64,870,136 (GRCm39)	Y67C	probably damaging	Het
Elmo1	A	T	13: 20,748,663 (GRCm39)	K503*	probably null	Het
Endou	A	T	15: 97,616,854 (GRCm39)		probably benign	Het
Eng	T	C	2: 32,569,149 (GRCm39)	S559P	probably benign	Het
Epc2	T	A	2: 49,427,145 (GRCm39)	V563E	possibly damaging	Het
Fbxw17	T	C	13: 50,586,477 (GRCm39)	S40P	possibly damaging	Het
Flt4	A	T	11: 49,527,818 (GRCm39)	M924L	probably benign	Het
Fyb1	A	G	15: 6,610,272 (GRCm39)	K282E	probably damaging	Het
Gabpa	T	A	16: 84,654,275 (GRCm39)	N317K	possibly damaging	Het
Gli3	G	T	13: 15,899,349 (GRCm39)	G912V	probably benign	Het
Gm10295	C	A	7: 71,000,361 (GRCm39)	C73F	unknown	Het
Gm10382	G	T	5: 125,466,728 (GRCm39)		probably benign	Het
Gp1ba	T	C	11: 70,531,284 (GRCm39)		probably benign	Het
Gpr146	G	A	5: 139,364,933 (GRCm39)		probably benign	Het
Grm5	A	G	7: 87,723,594 (GRCm39)	Y628C	probably damaging	Het
Hexa	A	G	9: 59,471,218 (GRCm39)	N491D	probably benign	Het
Hexd	T	A	11: 121,102,969 (GRCm39)	H62Q	probably benign	Het
Hpx	G	T	7: 105,245,471 (GRCm39)	Q101K	probably benign	Het
Ino80	G	A	2: 119,213,441 (GRCm39)	R1249C	probably damaging	Het
Inpp4b	A	T	8: 82,723,943 (GRCm39)	T492S	probably benign	Het
Iqgap2	A	C	13: 95,867,783 (GRCm39)		probably benign	Het
Islr2	T	C	9: 58,107,027 (GRCm39)	T78A	possibly damaging	Het
Itga9	A	G	9: 118,670,210 (GRCm39)	T177A	probably benign	Het
Itpkc	A	C	7: 26,927,174 (GRCm39)	S247A	possibly damaging	Het
Kirrel1	T	C	3: 86,997,106 (GRCm39)	Y287C	probably damaging	Het
Kiz	T	G	2: 146,784,076 (GRCm39)	S536R	probably benign	Het
Klhl9	T	G	4: 88,638,527 (GRCm39)	K571N	probably benign	Het
Kprp	A	T	3: 92,731,642 (GRCm39)	Y469*	probably null	Het
Ksr1	A	T	11: 78,919,851 (GRCm39)		probably benign	Het
Lrrc37a	C	T	11: 103,391,466 (GRCm39)	V1320I	possibly damaging	Het
Ltf	A	T	9: 110,854,235 (GRCm39)	N350I	probably benign	Het
Msl3l2	G	A	10: 55,991,947 (GRCm39)	R224Q	possibly damaging	Het
Myh6	A	T	14: 55,185,804 (GRCm39)	Y1490*	probably null	Het
Necap1	A	G	6: 122,857,728 (GRCm39)		probably benign	Het
Nf1	A	T	11: 79,332,783 (GRCm39)	K810*	probably null	Het
Nkx6-3	A	G	8: 23,647,722 (GRCm39)	E227G	possibly damaging	Het
Nlrp1a	T	A	11: 71,004,830 (GRCm39)		probably benign	Het
Obscn	G	A	11: 59,019,107 (GRCm39)	A969V	probably benign	Het
Or11a4	T	C	17: 37,536,934 (GRCm39)	L306P	possibly damaging	Het
Or7g32	G	A	9: 19,389,268 (GRCm39)	Q90*	probably null	Het
Or8b40	A	G	9: 38,027,325 (GRCm39)	T78A	probably benign	Het
Or8k33	A	T	2: 86,384,123 (GRCm39)	L115Q	probably damaging	Het
Pcdhb17	C	A	18: 37,618,888 (GRCm39)	A226E	possibly damaging	Het
Phldb1	A	T	9: 44,610,632 (GRCm39)		probably benign	Het
Plekha5	G	A	6: 140,537,473 (GRCm39)	R646K	possibly damaging	Het
Pon2	G	A	6: 5,266,156 (GRCm39)	Q288*	probably null	Het
Prr14	G	A	7: 127,073,751 (GRCm39)	R205H	probably benign	Het
Ptpn13	C	A	5: 103,681,214 (GRCm39)	R805S	probably damaging	Het
Pyroxd2	A	T	19: 42,735,992 (GRCm39)	V62D	probably damaging	Het
Rab37	G	T	11: 115,047,790 (GRCm39)	C44F	probably damaging	Het
Rbm44	T	C	1: 91,080,069 (GRCm39)	S52P	probably benign	Het
Rusf1	C	T	7: 127,889,786 (GRCm39)	R1H	probably damaging	Het
Scn5a	T	C	9: 119,351,665 (GRCm39)	D772G	probably damaging	Het
Slc7a5	A	G	8: 122,611,754 (GRCm39)	F425L	probably benign	Het
Slk	T	A	19: 47,608,628 (GRCm39)	L527*	probably null	Het
Stpg4	T	A	17: 87,697,142 (GRCm39)		probably null	Het
Taar6	C	A	10: 23,861,046 (GRCm39)	V167L	probably benign	Het
Tas2r123	T	A	6: 132,824,644 (GRCm39)	S180R	probably benign	Het
Tmc2	C	T	2: 130,044,023 (GRCm39)	R86W	probably benign	Het
Tmem200c	T	A	17: 69,147,543 (GRCm39)	V42E	probably damaging	Het
Trhde	T	C	10: 114,338,887 (GRCm39)		probably benign	Het
Tshz1	A	T	18: 84,034,249 (GRCm39)	I53N	probably benign	Het
Tshz3	A	G	7: 36,469,958 (GRCm39)	E649G	probably benign	Het
Ttll7	C	A	3: 146,650,936 (GRCm39)	R719S	possibly damaging	Het
Utp4	T	C	8: 107,625,169 (GRCm39)		probably benign	Het
Vmn1r35	A	G	6: 66,655,827 (GRCm39)	I281T	probably damaging	Het
Whamm	A	G	7: 81,243,799 (GRCm39)	T674A	probably benign	Het
Zbtb16	A	G	9: 48,654,876 (GRCm39)		probably benign	Het
Zfp623	T	C	15: 75,820,510 (GRCm39)	S489P	probably benign	Het

Other mutations in Vps39

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01393:Vps39	APN	2	120,180,719 (GRCm39)	splice site	probably benign
IGL01629:Vps39	APN	2	120,154,079 (GRCm39)	missense	probably benign	0.11
IGL01812:Vps39	APN	2	120,151,271 (GRCm39)	splice site	probably benign
IGL01936:Vps39	APN	2	120,153,609 (GRCm39)	missense	probably benign	0.23
IGL02379:Vps39	APN	2	120,154,089 (GRCm39)	missense	probably benign	0.17
IGL02892:Vps39	APN	2	120,153,652 (GRCm39)	splice site	probably benign
IGL02943:Vps39	APN	2	120,169,968 (GRCm39)	missense	possibly damaging	0.77
Jigsaw	UTSW	2	120,163,897 (GRCm39)	missense	probably damaging	0.98
matryoshka	UTSW	2	120,155,176 (GRCm39)	missense	probably damaging	1.00
R0001:Vps39	UTSW	2	120,148,534 (GRCm39)	missense	probably benign	0.09
R0329:Vps39	UTSW	2	120,169,268 (GRCm39)	missense	possibly damaging	0.89
R0330:Vps39	UTSW	2	120,169,268 (GRCm39)	missense	possibly damaging	0.89
R1483:Vps39	UTSW	2	120,154,129 (GRCm39)	missense	probably damaging	1.00
R1625:Vps39	UTSW	2	120,154,106 (GRCm39)	missense	probably damaging	1.00
R1837:Vps39	UTSW	2	120,155,878 (GRCm39)	missense	probably damaging	1.00
R1839:Vps39	UTSW	2	120,155,878 (GRCm39)	missense	probably damaging	1.00
R1934:Vps39	UTSW	2	120,148,558 (GRCm39)	missense	probably damaging	1.00
R2018:Vps39	UTSW	2	120,173,708 (GRCm39)	missense	probably damaging	1.00
R2019:Vps39	UTSW	2	120,173,708 (GRCm39)	missense	probably damaging	1.00
R2178:Vps39	UTSW	2	120,154,160 (GRCm39)	nonsense	probably null
R2513:Vps39	UTSW	2	120,169,268 (GRCm39)	missense	probably damaging	1.00
R3771:Vps39	UTSW	2	120,172,497 (GRCm39)	missense	possibly damaging	0.85
R3952:Vps39	UTSW	2	120,180,656 (GRCm39)	missense	probably benign	0.15
R4580:Vps39	UTSW	2	120,169,814 (GRCm39)	missense	probably benign	0.35
R4815:Vps39	UTSW	2	120,169,040 (GRCm39)	missense	probably benign	0.37
R4851:Vps39	UTSW	2	120,152,312 (GRCm39)	intron	probably benign
R4894:Vps39	UTSW	2	120,183,440 (GRCm39)	missense	probably damaging	1.00
R5447:Vps39	UTSW	2	120,183,413 (GRCm39)	missense	probably benign	0.43
R5483:Vps39	UTSW	2	120,153,564 (GRCm39)	missense	probably benign	0.08
R5715:Vps39	UTSW	2	120,155,717 (GRCm39)	missense	possibly damaging	0.73
R5886:Vps39	UTSW	2	120,152,053 (GRCm39)	intron	probably benign
R5949:Vps39	UTSW	2	120,159,149 (GRCm39)	missense	probably benign	0.23
R5954:Vps39	UTSW	2	120,155,143 (GRCm39)	missense	probably damaging	1.00
R5973:Vps39	UTSW	2	120,159,186 (GRCm39)	missense	probably damaging	0.99
R6004:Vps39	UTSW	2	120,176,131 (GRCm39)	missense	possibly damaging	0.89
R6208:Vps39	UTSW	2	120,163,897 (GRCm39)	missense	probably damaging	0.98
R6705:Vps39	UTSW	2	120,151,157 (GRCm39)	missense	probably benign	0.00
R6915:Vps39	UTSW	2	120,151,512 (GRCm39)	nonsense	probably null
R7535:Vps39	UTSW	2	120,155,176 (GRCm39)	missense	probably damaging	1.00
R7780:Vps39	UTSW	2	120,155,680 (GRCm39)	nonsense	probably null
R7869:Vps39	UTSW	2	120,169,875 (GRCm39)	missense	possibly damaging	0.89
R8061:Vps39	UTSW	2	120,174,692 (GRCm39)	missense	probably benign	0.00
R8770:Vps39	UTSW	2	120,153,548 (GRCm39)	missense	probably benign
R8787:Vps39	UTSW	2	120,172,506 (GRCm39)	missense	probably damaging	1.00
R8933:Vps39	UTSW	2	120,169,066 (GRCm39)	missense	probably benign	0.00
R8962:Vps39	UTSW	2	120,174,687 (GRCm39)	nonsense	probably null
R9302:Vps39	UTSW	2	120,151,525 (GRCm39)	splice site	probably benign
R9573:Vps39	UTSW	2	120,155,179 (GRCm39)	missense	possibly damaging	0.89
R9610:Vps39	UTSW	2	120,172,485 (GRCm39)	missense	probably damaging	0.99
R9611:Vps39	UTSW	2	120,172,485 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- TTCCTGTGAAGTGTGTCAGCCTCC -3'
(R):5'- TGCCCGAATCTTCTGTCACAAGC -3'

Sequencing Primer
(F):5'- TCGGCATGATGATCACTAAACAG -3'
(R):5'- GAATCTTCTGTCACAAGCAGAAAC -3'

Posted On

2015-02-04