Mutagenetix > Incidental Mutation

Incidental Mutation 'R8933:Vps39'

680416

Institutional Source

Beutler Lab

Gene Symbol

Vps39

Ensembl Gene

ENSMUSG00000027291

Gene Name

VPS39 HOPS complex subunit

Synonyms

Vam6, Vam6P, A230065P22Rik, mVam6

MMRRC Submission

068709-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.950) question?

Stock #

R8933 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

120146942-120183618 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 120169066 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 292 (S292P)

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: S281P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: S281P

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: S292P

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: S292P

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

Meta Mutation Damage Score

0.1298

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.8%
20x: 99.2%

Validation Efficiency

100% (86/86)

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: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca4	T	A	3: 121,921,786 (GRCm39)	I1114N	probably damaging	Het
Ache	C	A	5: 137,288,449 (GRCm39)	R52S	possibly damaging	Het
AI182371	A	T	2: 34,975,714 (GRCm39)		probably null	Het
Ankrd17	T	C	5: 90,406,325 (GRCm39)	S1453G	probably damaging	Het
Arvcf	A	G	16: 18,218,845 (GRCm39)	N508S	probably damaging	Het
Aurkc	A	C	7: 7,005,796 (GRCm39)	D136A	possibly damaging	Het
Bfsp2	A	G	9: 103,325,848 (GRCm39)	M265T	probably benign	Het
Bmpr1b	T	C	3: 141,562,369 (GRCm39)	T273A	probably damaging	Het
Cacnb1	T	C	11: 97,896,578 (GRCm39)	K406R	probably damaging	Het
Calcoco2	C	T	11: 95,998,252 (GRCm39)		probably benign	Het
Capza1	T	C	3: 104,748,209 (GRCm39)		probably null	Het
Ccdc63	T	A	5: 122,251,265 (GRCm39)	I382F	probably damaging	Het
Cep350	A	T	1: 155,739,161 (GRCm39)	N2227K	probably benign	Het
Chia1	T	A	3: 106,036,333 (GRCm39)	Y304*	probably null	Het
Col5a2	G	A	1: 45,461,123 (GRCm39)	P258L		Het
Cyp21a1	A	G	17: 35,023,285 (GRCm39)	L30P	probably damaging	Het
Dennd4b	T	A	3: 90,186,523 (GRCm39)	H1351Q	probably benign	Het
Dnah9	T	A	11: 65,746,078 (GRCm39)	I4012F	possibly damaging	Het
Drd1	A	G	13: 54,207,290 (GRCm39)	I301T	possibly damaging	Het
Dzip1	T	A	14: 119,144,326 (GRCm39)	H369L	probably damaging	Het
Fgfrl1	T	A	5: 108,851,257 (GRCm39)	M58K	probably damaging	Het
Ftsj3	G	T	11: 106,141,660 (GRCm39)	D529E	probably benign	Het
Fut9	A	T	4: 25,619,861 (GRCm39)	W318R	probably damaging	Het
Gabrg3	A	G	7: 56,634,706 (GRCm39)	I159T	probably damaging	Het
Gabrr1	A	T	4: 33,146,972 (GRCm39)	D53V	probably benign	Het
Ggps1	A	G	13: 14,228,928 (GRCm39)	V85A	probably benign	Het
Gm5141	C	T	13: 62,924,854 (GRCm39)	W18*	probably null	Het
Grik5	T	A	7: 24,722,743 (GRCm39)	T518S	probably benign	Het
Hapln3	A	T	7: 78,767,378 (GRCm39)		probably benign	Het
Hbs1l	C	T	10: 21,243,584 (GRCm39)	Q646*	probably null	Het
Hmox1	T	C	8: 75,823,644 (GRCm39)	I104T	probably benign	Het
Ifit1bl1	T	C	19: 34,571,413 (GRCm39)	Y348C	probably damaging	Het
Igf2r	A	T	17: 12,920,131 (GRCm39)	S1403T	probably damaging	Het
Igf2r	G	A	17: 12,923,524 (GRCm39)	T1186M	probably damaging	Het
Igfbp1	T	C	11: 7,148,333 (GRCm39)		probably null	Het
Ikbip	C	A	10: 90,919,092 (GRCm39)	A35E	probably benign	Het
Isca1	C	T	13: 59,917,497 (GRCm39)	A8T	probably damaging	Het
Itgb2	T	C	10: 77,401,022 (GRCm39)	L754P	probably damaging	Het
Itgb6	C	T	2: 60,458,247 (GRCm39)	C502Y	probably damaging	Het
Kdm3a	A	G	6: 71,577,092 (GRCm39)	V741A	probably benign	Het
Kdsr	T	C	1: 106,680,949 (GRCm39)	D83G	possibly damaging	Het
Kiz	T	A	2: 146,784,037 (GRCm39)	N523K		Het
Kmt2a	T	C	9: 44,733,802 (GRCm39)		probably benign	Het
Krt25	T	C	11: 99,212,064 (GRCm39)	E191G	probably benign	Het
Lipn	A	G	19: 34,046,880 (GRCm39)	I61V	probably damaging	Het
Lmbr1l	T	A	15: 98,807,150 (GRCm39)		probably null	Het
Lrrc4c	A	G	2: 97,459,826 (GRCm39)	K151E	probably benign	Het
Mab21l3	T	C	3: 101,730,774 (GRCm39)	Q155R	probably benign	Het
Mtfr2	G	A	10: 20,233,274 (GRCm39)	R281H	possibly damaging	Het
Muc5ac	A	G	7: 141,343,493 (GRCm39)	Y35C	possibly damaging	Het
Myadm	C	T	7: 3,345,433 (GRCm39)	T65I	probably benign	Het
Nap1l1	T	C	10: 111,328,710 (GRCm39)	V213A	probably benign	Het
Nav2	A	G	7: 49,111,705 (GRCm39)	D737G	probably damaging	Het
Ndst4	T	A	3: 125,405,155 (GRCm39)	V470D	probably damaging	Het
Nek5	T	A	8: 22,601,226 (GRCm39)	Y165F	probably damaging	Het
Nek5	A	T	8: 22,610,859 (GRCm39)	V48E	probably damaging	Het
Nr6a1	T	C	2: 38,650,400 (GRCm39)	I77V	probably damaging	Het
Nvl	A	T	1: 180,966,638 (GRCm39)	D93E	probably benign	Het
Or11a4	C	A	17: 37,536,346 (GRCm39)	T110K	possibly damaging	Het
Or2q1	A	G	6: 42,794,950 (GRCm39)	T182A	probably benign	Het
Or52e5	A	G	7: 104,718,599 (GRCm39)		probably benign	Het
Or52k2	A	T	7: 102,253,637 (GRCm39)	L25F	probably damaging	Het
Or52p1	A	T	7: 104,266,873 (GRCm39)	T4S	probably benign	Het
Or6c68	A	T	10: 129,158,259 (GRCm39)	I256F	probably damaging	Het
Pla2g4c	G	A	7: 13,073,627 (GRCm39)	V225I	probably benign	Het
Plppr4	T	A	3: 117,116,690 (GRCm39)	N331I	probably damaging	Het
Ptpn13	A	G	5: 103,727,671 (GRCm39)	R2051G	probably benign	Het
Rbm45	T	C	2: 76,209,068 (GRCm39)	S346P	probably damaging	Het
Samd14	A	C	11: 94,912,027 (GRCm39)	D168A	probably damaging	Het
Slc15a1	C	T	14: 121,724,091 (GRCm39)	G172R	probably benign	Het
Slco3a1	G	T	7: 73,934,248 (GRCm39)	Y641*	probably null	Het
Srcap	G	A	7: 127,151,566 (GRCm39)	R2027H	probably damaging	Het
Stra8	A	T	6: 34,904,624 (GRCm39)		probably benign	Het
Syt11	T	C	3: 88,655,011 (GRCm39)	Y430C	probably damaging	Het
Tanc1	T	G	2: 59,615,800 (GRCm39)	V269G	possibly damaging	Het
Tead1	A	G	7: 112,497,818 (GRCm39)	N342S	probably benign	Het
Tenm3	C	T	8: 48,732,095 (GRCm39)	A1254T	possibly damaging	Het
Txlnb	A	T	10: 17,682,546 (GRCm39)	N156I	probably damaging	Het
Ufl1	A	T	4: 25,262,258 (GRCm39)	S409R	possibly damaging	Het
Usp17la	A	G	7: 104,510,307 (GRCm39)	H304R	probably benign	Het
Vmn1r203	T	A	13: 22,708,691 (GRCm39)	H157Q	possibly damaging	Het
Vmn1r37	C	T	6: 66,709,231 (GRCm39)	R249*	probably null	Het
Vmn2r96	A	G	17: 18,804,241 (GRCm39)	Q497R	probably benign	Het
Wnk1	A	G	6: 120,013,959 (GRCm39)	V212A	probably damaging	Het
Xbp1	T	C	11: 5,474,741 (GRCm39)	V161A	probably benign	Het
Zfp113	T	C	5: 138,143,092 (GRCm39)	Q386R	probably 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
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
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'- GTGGACTCAAACCCTGCATC -3'
(R):5'- GAGATCCGAACACTGGAACC -3'

Sequencing Primer
(F):5'- ACCAATCTCTATGTGAGTTTAGCTGC -3'
(R):5'- CAAGGCTTCTGGTCCAAAGCATTG -3'

Posted On

2021-08-31