Mutagenetix > Incidental Mutation

Incidental Mutation 'R4580:Vps39'

343565

Institutional Source

Beutler Lab

Gene Symbol

Vps39

Ensembl Gene

ENSMUSG00000027291

Gene Name

VPS39 HOPS complex subunit

Synonyms

Vam6, Vam6P, A230065P22Rik, mVam6

MMRRC Submission

041599-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.950) question?

Stock #

R4580 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

120146942-120183618 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 120169814 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Asparagine at position 246 (I246N)

Ref Sequence

ENSEMBL: ENSMUSP00000099559 (fasta)

Gene Model

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

AlphaFold

Q8R5L3

Predicted Effect

probably benign
Transcript: ENSMUST00000028752
AA Change: I235N

PolyPhen 2 Score 0.158 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: I235N

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

probably benign
Transcript: ENSMUST00000102501
AA Change: I246N

PolyPhen 2 Score 0.352 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: I246N

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: ENSMUST00000129857

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000138854

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147085

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156296

Coding Region Coverage

1x: 99.3%
3x: 98.6%
10x: 97.1%
20x: 94.9%

Validation Efficiency

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: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2810408A11Rik	T	C	11: 69,791,237 (GRCm39)	Y114C	probably damaging	Het
Abcc2	T	C	19: 43,799,558 (GRCm39)	S556P	probably damaging	Het
Arl6ip1	AAAATAAATAAATAAATAAATAAATA	AAAATAAATAAATAAATAAATAAATAAATA	7: 117,721,122 (GRCm39)		probably benign	Het
Atp6v1g1	A	G	4: 63,468,269 (GRCm39)	N91D	probably benign	Het
BC005537	G	T	13: 24,987,394 (GRCm39)	A11S	probably benign	Het
Bltp1	A	T	3: 37,084,174 (GRCm39)	T3864S	probably benign	Het
Bub1	A	C	2: 127,671,596 (GRCm39)		probably null	Het
Ccdc162	T	C	10: 41,437,136 (GRCm39)	T1758A	probably benign	Het
Cdh15	T	C	8: 123,591,897 (GRCm39)	L594P	probably damaging	Het
Cobll1	C	T	2: 64,981,417 (GRCm39)	V90I	probably benign	Het
Cog2	T	C	8: 125,271,875 (GRCm39)	V463A	probably benign	Het
Cpeb4	T	A	11: 31,877,757 (GRCm39)		probably null	Het
Creb5	G	A	6: 53,581,519 (GRCm39)	M172I	possibly damaging	Het
Cyp4a32	T	C	4: 115,460,126 (GRCm39)		silent	Het
Dnah8	T	A	17: 30,881,026 (GRCm39)	S588T	probably benign	Het
Ecpas	T	C	4: 58,840,751 (GRCm39)	Y669C	probably damaging	Het
Esd	T	C	14: 74,979,517 (GRCm39)	V120A	possibly damaging	Het
Fbxo5	T	C	10: 5,755,255 (GRCm39)		probably null	Het
Gm4922	T	C	10: 18,659,432 (GRCm39)	D430G	probably benign	Het
Golga4	C	A	9: 118,386,327 (GRCm39)	Q1150K	probably benign	Het
Grb14	T	C	2: 64,783,947 (GRCm39)	N60S	probably benign	Het
Grk4	A	G	5: 34,818,325 (GRCm39)	N2S	probably damaging	Het
Henmt1	T	A	3: 108,850,081 (GRCm39)	S21R	probably benign	Het
Ifngr2	A	G	16: 91,354,906 (GRCm39)	K113E	probably benign	Het
Ighv15-2	T	A	12: 114,528,590 (GRCm39)	T15S	probably benign	Het
Kif24	A	G	4: 41,395,287 (GRCm39)	S529P	probably damaging	Het
Large2	T	C	2: 92,200,957 (GRCm39)	N51S	possibly damaging	Het
Lmtk2	A	G	5: 144,111,599 (GRCm39)	E773G	possibly damaging	Het
Lrfn3	A	T	7: 30,059,467 (GRCm39)	C253S	probably damaging	Het
Maea	T	C	5: 33,517,832 (GRCm39)	V130A	possibly damaging	Het
Marchf11	A	T	15: 26,311,189 (GRCm39)	I222F	probably damaging	Het
Mast4	A	T	13: 102,873,766 (GRCm39)	Y1699*	probably null	Het
Mavs	G	T	2: 131,082,370 (GRCm39)	A85S	probably damaging	Het
Mpzl3	T	A	9: 44,979,529 (GRCm39)	V160E	possibly damaging	Het
Myh15	T	C	16: 48,885,388 (GRCm39)	S88P	possibly damaging	Het
Myl2	A	T	5: 122,244,801 (GRCm39)	H157L	probably benign	Het
Myo9b	A	G	8: 71,767,779 (GRCm39)	N284S	probably damaging	Het
Nphp1	A	G	2: 127,610,089 (GRCm39)		probably null	Het
Nrcam	T	C	12: 44,609,323 (GRCm39)		probably null	Het
Nt5c3b	G	T	11: 100,323,885 (GRCm39)	F134L	probably damaging	Het
Or4c120	T	A	2: 89,001,544 (GRCm39)	Q4L	probably benign	Het
Otog	A	G	7: 45,937,225 (GRCm39)	R1645G	possibly damaging	Het
Pask	T	C	1: 93,249,830 (GRCm39)	I523M	probably benign	Het
Pcdhb7	T	A	18: 37,475,188 (GRCm39)	L108Q	probably damaging	Het
Pdp2	C	A	8: 105,321,576 (GRCm39)	T475K	probably damaging	Het
Pgbd1	G	C	13: 21,612,499 (GRCm39)	P113A	probably benign	Het
Plk5	C	T	10: 80,196,301 (GRCm39)	H291Y	possibly damaging	Het
Pmpca	G	T	2: 26,283,347 (GRCm39)	S382I	probably damaging	Het
Prl3b1	A	G	13: 27,433,450 (GRCm39)	T202A	possibly damaging	Het
Ptgs2	A	T	1: 149,979,845 (GRCm39)	T317S	possibly damaging	Het
Ptprc	C	T	1: 137,998,989 (GRCm39)	M1020I	probably benign	Het
Rhbdl3	T	C	11: 80,244,471 (GRCm39)	Y393H	probably damaging	Het
Sema3e	T	C	5: 14,283,717 (GRCm39)	L482P	probably damaging	Het
Setd2	C	T	9: 110,403,311 (GRCm39)	T1984I	probably benign	Het
Slc17a1	T	C	13: 24,071,960 (GRCm39)	Y393H	probably damaging	Het
Slc9a3	C	T	13: 74,307,005 (GRCm39)	R377*	probably null	Het
Slitrk3	A	G	3: 72,958,539 (GRCm39)	S78P	probably damaging	Het
Smim35	G	T	9: 45,155,426 (GRCm39)		probably null	Het
Specc1	T	A	11: 62,110,157 (GRCm39)	V1054E	probably damaging	Het
Tbc1d4	T	C	14: 101,696,219 (GRCm39)	T847A	probably benign	Het
Tcf7l2	G	A	19: 55,907,468 (GRCm39)	G343R	probably damaging	Het
Tex36	A	C	7: 133,189,111 (GRCm39)	Y154D	possibly damaging	Het
Topaz1	T	A	9: 122,576,580 (GRCm39)	M57K	probably null	Het
Trav6-4	T	C	14: 53,692,156 (GRCm39)	Y85H	probably damaging	Het
Trim30d	A	G	7: 104,121,765 (GRCm39)	Y327H	possibly damaging	Het
Ttn	A	G	2: 76,781,740 (GRCm39)	V1056A	probably benign	Het
Usp32	C	A	11: 84,949,953 (GRCm39)		probably null	Het
Vmn1r59	A	T	7: 5,457,136 (GRCm39)	M208K	probably damaging	Het
Vmn2r25	T	C	6: 123,799,982 (GRCm39)	T787A	possibly damaging	Het
Xab2	T	C	8: 3,660,162 (GRCm39)	D855G	probably damaging	Het
Xpc	A	G	6: 91,476,993 (GRCm39)	S369P	probably benign	Het
Ythdc2	T	A	18: 44,991,265 (GRCm39)	C758S	possibly damaging	Het
Zfp62	A	G	11: 49,107,099 (GRCm39)	I397V	possibly damaging	Het
Zscan4d	A	G	7: 10,896,435 (GRCm39)	S312P	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
R0364:Vps39	UTSW	2	120,176,119 (GRCm39)	missense	probably damaging	1.00
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
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'- GTTATGCTGTGCTTTGCTAACATAG -3'
(R):5'- TTCCTGCAGGTGGATGGAAAG -3'

Sequencing Primer
(F):5'- AGCACATCTCTGGGTTCAAG -3'
(R):5'- GGGGTCCATCAAAGAGCTCTTC -3'

Posted On

2015-09-24