Mutagenetix > Incidental Mutation

Incidental Mutation 'R5715:Vps39'

451087

Institutional Source

Beutler Lab

Gene Symbol

Vps39

Ensembl Gene

ENSMUSG00000027291

Gene Name

VPS39 HOPS complex subunit

Synonyms

Vam6, Vam6P, A230065P22Rik, mVam6

MMRRC Submission

043336-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.950) question?

Stock #

R5715 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

120146942-120183618 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 120155717 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Serine at position 519 (N519S)

Ref Sequence

ENSEMBL: ENSMUSP00000028752 (fasta)

Gene Model

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

AlphaFold

Q8R5L3

Predicted Effect

possibly damaging
Transcript: ENSMUST00000028752
AA Change: N519S

PolyPhen 2 Score 0.728 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: N519S

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: N530S

PolyPhen 2 Score 0.605 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: N530S

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: ENSMUST00000132476

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145193

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147085

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.4%
20x: 95.7%

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: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9930111J21Rik2	T	A	11: 48,910,777 (GRCm39)	Y552F	probably damaging	Het
Asprv1	T	A	6: 86,605,596 (GRCm39)	D147E	probably benign	Het
Atg4c	G	T	4: 99,146,639 (GRCm39)	L405F	probably damaging	Het
Birc6	C	T	17: 74,938,615 (GRCm39)	L2670F	probably damaging	Het
Cdc20	T	C	4: 118,292,015 (GRCm39)	D379G	probably damaging	Het
Chd6	T	C	2: 160,791,798 (GRCm39)	M2520V	probably benign	Het
Clca4b	A	G	3: 144,619,018 (GRCm39)	V707A	probably benign	Het
Cmtm1	CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT	CGGCACGTACTGAAGGTCGCTGACTGGATGGTGTGGCACGTACTGAAGGTCGCTGACTGGATGGT	8: 105,036,102 (GRCm39)		probably benign	Het
Col12a1	A	T	9: 79,523,347 (GRCm39)	C2743*	probably null	Het
Coq6	C	A	12: 84,413,681 (GRCm39)	D70E	probably benign	Het
Cspg4	T	A	9: 56,798,335 (GRCm39)	V1450D	possibly damaging	Het
Dnah7a	A	G	1: 53,452,937 (GRCm39)	L3847P	probably damaging	Het
Drd2	T	A	9: 49,316,189 (GRCm39)	H316Q	probably benign	Het
Dusp19	T	A	2: 80,461,330 (GRCm39)	N206K	probably benign	Het
Fam13c	T	G	10: 70,370,670 (GRCm39)	F270C	probably damaging	Het
Fam20a	T	C	11: 109,569,257 (GRCm39)	E246G	probably damaging	Het
Fbxo31	A	G	8: 122,305,302 (GRCm39)	F65L	probably damaging	Het
Fshr	T	A	17: 89,293,824 (GRCm39)		probably null	Het
Fstl4	T	C	11: 52,891,243 (GRCm39)	V127A	possibly damaging	Het
Gdpd4	A	T	7: 97,610,804 (GRCm39)	I75F	probably benign	Het
Grm5	C	A	7: 87,779,464 (GRCm39)	A968E	probably benign	Het
Gucy2g	A	C	19: 55,221,587 (GRCm39)	F305V	possibly damaging	Het
Hivep3	T	C	4: 119,953,570 (GRCm39)	F629L	probably benign	Het
Hoxb1	A	G	11: 96,257,152 (GRCm39)	E167G	probably benign	Het
Hoxd4	T	C	2: 74,557,708 (GRCm39)	L29P	probably damaging	Het
Ikbkb	A	G	8: 23,168,866 (GRCm39)	L211P	probably damaging	Het
Insc	T	C	7: 114,449,076 (GRCm39)	V499A	probably benign	Het
Irak3	A	T	10: 119,978,641 (GRCm39)	H511Q	possibly damaging	Het
Itpripl1	T	C	2: 126,983,927 (GRCm39)	E65G	probably damaging	Het
Lurap1l	T	A	4: 80,871,958 (GRCm39)	S150R	possibly damaging	Het
Mab21l3	C	T	3: 101,730,723 (GRCm39)	R172Q	probably benign	Het
Macf1	T	C	4: 123,577,807 (GRCm39)	D59G	probably damaging	Het
Mettl21a	A	T	1: 64,654,314 (GRCm39)	S68T	probably benign	Het
Mlxip	T	A	5: 123,578,121 (GRCm39)	W146R	probably damaging	Het
Mpp2	T	A	11: 101,953,087 (GRCm39)	N285I	probably damaging	Het
Mrgprb4	T	C	7: 47,848,787 (GRCm39)	N47S	probably damaging	Het
Msi2	A	G	11: 88,276,889 (GRCm39)	Y237H	probably damaging	Het
Muc4	C	T	16: 32,570,734 (GRCm39)	T598I	possibly damaging	Het
Musk	A	T	4: 58,333,663 (GRCm39)	I253F	probably damaging	Het
Myo5b	G	T	18: 74,875,246 (GRCm39)	C1550F	possibly damaging	Het
Nckap5l	T	C	15: 99,321,457 (GRCm39)	T1137A	probably benign	Het
Neb	T	C	2: 52,141,780 (GRCm39)	D3009G	probably damaging	Het
Nxph1	T	A	6: 9,247,740 (GRCm39)	V237E	probably damaging	Het
Or52a33	A	C	7: 103,289,009 (GRCm39)	S113A	probably damaging	Het
Pla2g12a	A	G	3: 129,688,591 (GRCm39)	K150E	probably damaging	Het
Potegl	T	C	2: 23,097,989 (GRCm39)	Y56H	possibly damaging	Het
Pramel30	A	G	4: 144,057,870 (GRCm39)	D159G	possibly damaging	Het
Ptpn23	G	A	9: 110,216,143 (GRCm39)	R1238W	probably damaging	Het
Pts	C	T	9: 50,433,578 (GRCm39)	G124R	probably damaging	Het
Rfk	A	T	19: 17,376,002 (GRCm39)	I99F	probably benign	Het
Rictor	A	T	15: 6,780,197 (GRCm39)	R151*	probably null	Het
Scn2a	T	A	2: 65,547,928 (GRCm39)	I1040N	probably benign	Het
Serinc5	A	C	13: 92,842,710 (GRCm39)	T387P	probably damaging	Het
Sh3bp5l	A	G	11: 58,236,841 (GRCm39)	Q266R	possibly damaging	Het
Slc14a2	T	C	18: 78,201,551 (GRCm39)	Y656C	probably damaging	Het
Slc26a3	T	A	12: 31,498,842 (GRCm39)		probably null	Het
Slc3a2	G	T	19: 8,685,594 (GRCm39)	H168Q	probably benign	Het
Smarca2	A	T	19: 26,626,522 (GRCm39)	I449L	probably benign	Het
Smarcc1	T	C	9: 110,025,435 (GRCm39)	V704A	possibly damaging	Het
Sox13	A	G	1: 133,313,921 (GRCm39)		probably null	Het
Sptbn5	T	C	2: 119,902,985 (GRCm39)	E7G	probably damaging	Het
Stard10	A	G	7: 100,971,110 (GRCm39)	D26G	probably damaging	Het
Tap1	A	T	17: 34,411,868 (GRCm39)	R91*	probably null	Het
Tgfbrap1	A	T	1: 43,099,097 (GRCm39)	V239D	possibly damaging	Het
Tmem209	A	T	6: 30,497,922 (GRCm39)	Y124*	probably null	Het
Tmprss2	T	A	16: 97,370,183 (GRCm39)	E327V	possibly damaging	Het
Ttbk1	T	C	17: 46,790,133 (GRCm39)	Y104C	probably damaging	Het
Ttll10	A	T	4: 156,129,848 (GRCm39)	F154I	probably damaging	Het
Ubn2	T	A	6: 38,438,412 (GRCm39)	Y40*	probably null	Het
Ubr5	A	T	15: 38,002,477 (GRCm39)	S1519T	probably benign	Het
Ugt3a1	A	C	15: 9,306,430 (GRCm39)	D193A	probably damaging	Het
Upf1	A	T	8: 70,805,628 (GRCm39)	Y6N	probably damaging	Het
Vmn2r103	A	T	17: 20,015,201 (GRCm39)	D447V	probably benign	Het
Zfp109	T	C	7: 23,928,995 (GRCm39)	E138G	possibly damaging	Het
Znrf3	A	C	11: 5,236,239 (GRCm39)	V157G	possibly damaging	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
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
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'- CTATACAAGCAGGAGCCTCC -3'
(R):5'- CTGTATGAGAAGAAGGGGCTCC -3'

Sequencing Primer
(F):5'- GGAAGCACGTGTCTTCAATC -3'
(R):5'- CTCCATGAGAAAGGTGACCTG -3'

Posted On

2017-01-03