Mutagenetix > Incidental Mutations

Incidental Mutation 'R5447:Vps39'

429111

Institutional Source

Beutler Lab

Gene Symbol

Vps39

Ensembl Gene

ENSMUSG00000027291

Gene Name

VPS39 HOPS complex subunit

Synonyms

mVam6, Vam6P, Vam6, A230065P22Rik

MMRRC Submission

043012-MU

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.859) question?

Stock #

R5447 (G1)

Quality Score

153

Status

Validated

Chromosome

Chromosomal Location

120316461-120353137 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 120352932 bp

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 19 (D19G)

Ref Sequence

ENSEMBL: ENSMUSP00000099559 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028752] [ENSMUST00000090042] [ENSMUST00000090046] [ENSMUST00000102501]

Predicted Effect

probably benign
Transcript: ENSMUST00000028752
AA Change: D19G

PolyPhen 2 Score 0.430 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: D19G

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: ENSMUST00000090042

SMART Domains

Protein: ENSMUSP00000087496
Gene: ENSMUSG00000033808

Domain	Start	End	E-Value	Type
Pfam:Lung_7-TM_R	184	471	1.1e-87	PFAM
low complexity region	480	486	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000090046

SMART Domains

Protein: ENSMUSP00000087500
Gene: ENSMUSG00000033808

Domain	Start	End	E-Value	Type
Pfam:Lung_7-TM_R	185	472	1.5e-85	PFAM
low complexity region	481	487	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000102501
AA Change: D19G

PolyPhen 2 Score 0.430 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: D19G

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: ENSMUST00000124806

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126526

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000129857

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000136410

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147085

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156296

Meta Mutation Damage Score

0.2146

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.1%

Validation Efficiency

97% (71/73)

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: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5830473C10Rik	C	A	5: 90,584,310	A458E	probably damaging	Het
Abcb5	T	C	12: 118,927,326	I479V	probably damaging	Het
Adam30	A	G	3: 98,161,343	D164G	probably benign	Het
Adgrl3	T	A	5: 81,465,341		probably benign	Het
Adrb1	T	C	19: 56,723,087	I239T	probably benign	Het
B4galnt3	T	C	6: 120,215,057	T572A	probably benign	Het
Baz2b	T	C	2: 59,913,988	E1391G	probably damaging	Het
BC016579	A	G	16: 45,648,889	V72A	probably benign	Het
Btnl10	A	T	11: 58,922,318	I258F	probably benign	Het
Cdh5	A	T	8: 104,129,362	D309V	probably damaging	Het
Cdhr2	A	G	13: 54,733,250	D1042G	probably damaging	Het
Clk2	G	T	3: 89,167,191	V53F	possibly damaging	Het
Cyfip2	T	C	11: 46,291,586	D15G	possibly damaging	Het
Dip2b	C	T	15: 100,211,986	R1451C	probably damaging	Het
Dmbt1	A	G	7: 131,119,511	Y1836C	probably damaging	Het
Dysf	T	C	6: 84,195,263	F1905L	probably damaging	Het
E130114P18Rik	A	G	4: 97,690,718	S7P	unknown	Het
Fam110a	T	C	2: 151,970,709	E47G	probably damaging	Het
Gemin6	T	G	17: 80,227,749	V46G	probably damaging	Het
H2-Ke6	A	T	17: 34,026,912	V202D	probably damaging	Het
Helb	T	A	10: 120,102,901	D556V	possibly damaging	Het
Hoxd4	A	G	2: 74,727,343	E22G	probably damaging	Het
Il1rl2	T	G	1: 40,329,156	I162R	probably damaging	Het
Lhfpl5	A	G	17: 28,576,097	T33A	probably damaging	Het
Mapk8ip3	G	A	17: 24,899,189	A1283V	probably benign	Het
Mettl13	A	G	1: 162,535,880	V227A	probably benign	Het
Mmgt2	T	A	11: 62,664,998	C57*	probably null	Het
Muc4	G	C	16: 32,753,919	R1265P	probably benign	Het
Mylk2	T	C	2: 152,912,510	S175P	probably damaging	Het
Neu4	C	T	1: 94,022,418	T33M	probably damaging	Het
Nfs1	C	T	2: 156,142,136	R107H	probably benign	Het
Nfxl1	C	T	5: 72,529,169	R563Q	probably benign	Het
Nid1	A	G	13: 13,437,910	D70G	probably benign	Het
Nup160	C	A	2: 90,725,615	Q1220K	possibly damaging	Het
Olfr175-ps1	A	T	16: 58,824,483	C75*	probably null	Het
Olfr381	A	G	11: 73,486,176	V216A	probably benign	Het
Olfr51	G	A	11: 51,007,343	V124M	possibly damaging	Het
Olfr605	A	C	7: 103,442,940	M61R	probably damaging	Het
Pdgfrb	T	A	18: 61,068,108	V422E	probably damaging	Het
Pear1	G	A	3: 87,759,142	R85C	probably damaging	Het
Pkhd1	T	A	1: 20,239,385	M2780L	probably benign	Het
Ppp4r4	T	C	12: 103,584,151	V62A	possibly damaging	Het
Prol1	C	T	5: 88,328,266	P172S	unknown	Het
Proz	A	G	8: 13,072,578	I231V	probably benign	Het
Ptch1	T	G	13: 63,527,245	M718L	probably benign	Het
Ptprs	A	G	17: 56,429,128	C102R	possibly damaging	Het
Robo2	A	T	16: 73,973,766	Y490*	probably null	Het
Rptor	G	A	11: 119,843,713	G514D	probably damaging	Het
Scara5	CG	C	14: 65,759,662		probably null	Het
Skint6	T	A	4: 113,105,909	S442C	probably benign	Het
Snw1	T	C	12: 87,455,715	E303G	probably benign	Het
Sp110	C	G	1: 85,589,118	E219D	probably damaging	Het
Stam2	G	A	2: 52,736,293		probably benign	Het
Stk10	C	T	11: 32,604,166	Q618*	probably null	Het
Tmc3	A	T	7: 83,622,361	E907V	possibly damaging	Het
Ttn	A	T	2: 76,811,243	L5176Q	possibly damaging	Het
Ttn	T	A	2: 76,899,107		probably benign	Het
Zan	T	C	5: 137,472,191	S229G	probably damaging	Het
Zfp141	A	T	7: 42,475,559	C496*	probably null	Het
Zgrf1	T	C	3: 127,563,119	S665P	possibly damaging	Het

Other mutations in Vps39

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01393:Vps39	APN	2	120350238	splice site	probably benign
IGL01629:Vps39	APN	2	120323598	missense	probably benign	0.11
IGL01812:Vps39	APN	2	120320790	splice site	probably benign
IGL01936:Vps39	APN	2	120323128	missense	probably benign	0.23
IGL02379:Vps39	APN	2	120323608	missense	probably benign	0.17
IGL02892:Vps39	APN	2	120323171	splice site	probably benign
IGL02943:Vps39	APN	2	120339487	missense	possibly damaging	0.77
R0001:Vps39	UTSW	2	120318053	missense	probably benign	0.09
R0329:Vps39	UTSW	2	120338787	missense	possibly damaging	0.89
R0330:Vps39	UTSW	2	120338787	missense	possibly damaging	0.89
R0364:Vps39	UTSW	2	120345638	missense	probably damaging	1.00
R1483:Vps39	UTSW	2	120323648	missense	probably damaging	1.00
R1625:Vps39	UTSW	2	120323625	missense	probably damaging	1.00
R1837:Vps39	UTSW	2	120325397	missense	probably damaging	1.00
R1839:Vps39	UTSW	2	120325397	missense	probably damaging	1.00
R1934:Vps39	UTSW	2	120318077	missense	probably damaging	1.00
R2018:Vps39	UTSW	2	120343227	missense	probably damaging	1.00
R2019:Vps39	UTSW	2	120343227	missense	probably damaging	1.00
R2178:Vps39	UTSW	2	120323679	nonsense	probably null
R2513:Vps39	UTSW	2	120338787	missense	probably damaging	1.00
R3771:Vps39	UTSW	2	120342016	missense	possibly damaging	0.85
R3952:Vps39	UTSW	2	120350175	missense	probably benign	0.15
R4580:Vps39	UTSW	2	120339333	missense	probably benign	0.35
R4815:Vps39	UTSW	2	120338559	missense	probably benign	0.37
R4851:Vps39	UTSW	2	120321831	intron	probably benign
R4894:Vps39	UTSW	2	120352959	missense	probably damaging	1.00
R5483:Vps39	UTSW	2	120323083	missense	probably benign	0.08
R5715:Vps39	UTSW	2	120325236	missense	possibly damaging	0.73
R5886:Vps39	UTSW	2	120321572	intron	probably benign
R5949:Vps39	UTSW	2	120328668	missense	probably benign	0.23
R5954:Vps39	UTSW	2	120324662	missense	probably damaging	1.00
R5973:Vps39	UTSW	2	120328705	missense	probably damaging	0.99
R6004:Vps39	UTSW	2	120345650	missense	possibly damaging	0.89
R6208:Vps39	UTSW	2	120333416	missense	probably damaging	0.98
R6705:Vps39	UTSW	2	120320676	missense	probably benign	0.00
R6915:Vps39	UTSW	2	120321031	nonsense	probably null
R7535:Vps39	UTSW	2	120324695	missense	probably damaging	1.00
R7780:Vps39	UTSW	2	120325199	nonsense	probably null

Predicted Primers

PCR Primer
(F):5'- ATGTGAGCTCAGCCTCCAAC -3'
(R):5'- AGTTGTTGCTGAAGGCCCTG -3'

Sequencing Primer
(F):5'- AAATGGACTGTCCTTAGCAATCACG -3'
(R):5'- TTGCTGAAGGCCCTGTAGCAG -3'

Posted On

2016-09-06