Mutagenetix > Incidental Mutation

Incidental Mutation 'R1839:Vps39'

205568

Institutional Source

Beutler Lab

Gene Symbol

Vps39

Ensembl Gene

ENSMUSG00000027291

Gene Name

VPS39 HOPS complex subunit

Synonyms

mVam6, Vam6P, Vam6, A230065P22Rik

MMRRC Submission

045015-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.955) question?

Stock #

R1839 (G1)

Quality Score

224

Status

Validated

Chromosome

Chromosomal Location

120316461-120353137 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 120325397 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Histidine at position 514 (L514H)

Ref Sequence

ENSEMBL: ENSMUSP00000099559 (fasta)

Gene Model

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

AlphaFold

Q8R5L3

Predicted Effect

probably damaging
Transcript: ENSMUST00000028752
AA Change: L503H

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

SMART Domains

Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: L503H

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 damaging
Transcript: ENSMUST00000102501
AA Change: L514H

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

SMART Domains

Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: L514H

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

Meta Mutation Damage Score

0.4632

Coding Region Coverage

1x: 97.4%
3x: 96.7%
10x: 94.7%
20x: 90.6%

Validation Efficiency

98% (90/92)

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: 84 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700006A11Rik	T	C	3: 124,409,720	T403A	probably damaging	Het
Acat3	T	A	17: 12,928,606	R175*	probably null	Het
Adam1b	C	A	5: 121,501,041	C647F	probably damaging	Het
Adam28	T	C	14: 68,639,210	N197S	possibly damaging	Het
Adcy2	C	T	13: 68,689,261		probably null	Het
Adcy5	A	T	16: 35,248,940	N426I	probably damaging	Het
Adgre1	T	C	17: 57,441,299	S500P	probably benign	Het
Aloxe3	A	G	11: 69,130,085	Y212C	probably damaging	Het
Ap3d1	A	G	10: 80,727,108	S180P	probably damaging	Het
Arhgap20	C	T	9: 51,849,326	R790W	probably damaging	Het
Atp8b4	C	A	2: 126,361,782	A757S	possibly damaging	Het
Begain	G	A	12: 109,035,323		probably benign	Het
Ccdc141	T	C	2: 77,011,665	E1474G	probably benign	Het
Ccdc88b	A	G	19: 6,854,109		probably benign	Het
Ccnk	A	G	12: 108,195,074	T195A	probably damaging	Het
Cd55b	C	A	1: 130,414,105	C265F	probably damaging	Het
Celsr3	A	G	9: 108,829,906	H1196R	probably benign	Het
Cenpt	T	C	8: 105,849,014	S190G	possibly damaging	Het
Chd8	T	C	14: 52,204,883	S2077G	probably benign	Het
Col6a5	G	A	9: 105,864,833	H2296Y	probably benign	Het
Cxxc4	C	A	3: 134,240,653	H332N	probably damaging	Het
Cyp24a1	T	C	2: 170,496,741	I12V	probably benign	Het
Cyp3a57	T	A	5: 145,381,301	L364Q	probably damaging	Het
Ddi2	T	C	4: 141,713,526	I47V	probably benign	Het
Ddx5	A	T	11: 106,784,897	D322E	probably benign	Het
Dhx40	A	G	11: 86,789,297	C405R	possibly damaging	Het
Emc1	T	C	4: 139,360,485	F100S	probably damaging	Het
Exoc2	T	C	13: 30,906,497		probably benign	Het
Gm10110	A	T	14: 89,897,836		noncoding transcript	Het
Gm17332	T	C	11: 31,182,386	H26R	possibly damaging	Het
Gna12	T	C	5: 140,762,612	N183S	probably benign	Het
Gpx6	A	G	13: 21,312,327	N24D	probably benign	Het
Gsdma3	C	T	11: 98,629,858	A105V	probably benign	Het
Hsd3b5	T	C	3: 98,619,728	Y134C	probably benign	Het
Ifi213	T	C	1: 173,589,600	I415M	probably damaging	Het
Ints9	C	A	14: 65,016,530	P278T	probably damaging	Het
Krt79	C	T	15: 101,937,938	E192K	possibly damaging	Het
Lrrk2	A	G	15: 91,683,134	N132S	probably benign	Het
Ltn1	T	A	16: 87,416,264	K470*	probably null	Het
Magi2	A	T	5: 20,465,827	T163S	probably damaging	Het
Mcm9	A	G	10: 53,541,553	M18T	probably damaging	Het
Med12l	A	G	3: 59,068,319	T212A	probably benign	Het
Mfhas1	T	C	8: 35,590,858	L829P	possibly damaging	Het
Mgme1	T	A	2: 144,279,487	C288S	probably benign	Het
Muc4	G	C	16: 32,753,919	R1265P	probably benign	Het
Myh7	T	C	14: 54,973,180	N1725S	possibly damaging	Het
Nat6	G	A	9: 107,583,017	R37H	possibly damaging	Het
Nme4	A	T	17: 26,092,097	W165R	probably damaging	Het
Nup205	T	A	6: 35,219,714	D1128E	probably benign	Het
Olfr291	T	C	7: 84,856,548	Y60H	probably damaging	Het
Olfr330	A	T	11: 58,529,373	Y204*	probably null	Het
Pcdh1	T	C	18: 38,199,485	D155G	possibly damaging	Het
Pex12	A	T	11: 83,297,822	S116T	probably damaging	Het
Plekhh1	C	T	12: 79,078,957		probably benign	Het
Plekhh3	A	G	11: 101,163,600		probably benign	Het
Pnpt1	T	C	11: 29,154,342	M572T	possibly damaging	Het
Ppp1r12b	T	C	1: 134,837,981	R667G	probably benign	Het
Rbpms2	ACTGCTGCTGCTGCTGC	ACTGCTGCTGCTGCTGCTGC	9: 65,651,666		probably benign	Het
Rgs14	T	C	13: 55,382,838		probably benign	Het
Rhbdf2	A	T	11: 116,600,191	V645E	possibly damaging	Het
Robo3	A	G	9: 37,422,327	V696A	probably benign	Het
Sall1	A	G	8: 89,028,716	F1212L	possibly damaging	Het
Sdc4	T	C	2: 164,429,012	E109G	probably benign	Het
Serpind1	G	T	16: 17,342,992	R462L	probably damaging	Het
Smad9	CTTT	CTT	3: 54,789,179		probably benign	Het
Sstr4	C	A	2: 148,395,533	N21K	probably benign	Het
Tap1	C	T	17: 34,188,109	A77V	possibly damaging	Het
Thap4	T	C	1: 93,750,287	E259G	probably benign	Het
Thra	A	G	11: 98,756,143	N30S	probably benign	Het
Tmem207	A	T	16: 26,524,821	V27E	possibly damaging	Het
Top3a	A	G	11: 60,753,888	V305A	probably damaging	Het
Trim59	A	T	3: 69,037,638	I123K	probably damaging	Het
Ttn	T	C	2: 76,861,495		probably benign	Het
Ubac1	T	A	2: 26,007,738	E290V	possibly damaging	Het
Unc13b	T	C	4: 43,258,308		probably benign	Het
Uri1	A	T	7: 37,967,389	D206E	probably benign	Het
Utp4	A	G	8: 106,913,454	H465R	probably benign	Het
Uvssa	T	C	5: 33,389,752	S221P	probably benign	Het
Vmn1r39	T	C	6: 66,805,233		probably null	Het
Vps72	G	A	3: 95,119,218	R158Q	possibly damaging	Het
Wdr59	T	C	8: 111,485,340	D366G	probably benign	Het
Zfp366	C	A	13: 99,228,492	Q54K	probably damaging	Het
Zfp523	T	A	17: 28,194,993	I34N	probably damaging	Het
Zfp974	G	A	7: 27,910,356	P648L	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
Jigsaw	UTSW	2	120333416	missense	probably damaging	0.98
matryoshka	UTSW	2	120324695	missense	probably damaging	1.00
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
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
R5447:Vps39	UTSW	2	120352932	missense	probably benign	0.43
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
R7869:Vps39	UTSW	2	120339394	missense	possibly damaging	0.89
R8061:Vps39	UTSW	2	120344211	missense	probably benign	0.00
R8770:Vps39	UTSW	2	120323067	missense	probably benign
R8787:Vps39	UTSW	2	120342025	missense	probably damaging	1.00
R8933:Vps39	UTSW	2	120338585	missense	probably benign	0.00
R8962:Vps39	UTSW	2	120344206	nonsense	probably null
R9302:Vps39	UTSW	2	120321044	splice site	probably benign
R9573:Vps39	UTSW	2	120324698	missense	possibly damaging	0.89
R9610:Vps39	UTSW	2	120342004	missense	probably damaging	0.99
R9611:Vps39	UTSW	2	120342004	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- CTTACCTAAATGCTGCAGATACTG -3'
(R):5'- AAATGAAGGGTGGGGTTCCC -3'

Sequencing Primer
(F):5'- AGATACTGCACCGTCCTCTCG -3'
(R):5'- TTCCCAGGAAGGAGCTTCTG -3'

Posted On

2014-06-23