Mutagenetix > Incidental Mutation

Incidental Mutation 'R7869:Vps39'

607954

Institutional Source

Beutler Lab

Gene Symbol

Vps39

Ensembl Gene

ENSMUSG00000027291

Gene Name

VPS39 HOPS complex subunit

Synonyms

Vam6, Vam6P, A230065P22Rik, mVam6

MMRRC Submission

045921-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.950) question?

Stock #

R7869 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

120146942-120183618 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 120169875 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 226 (T226A)

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: T215A

PolyPhen 2 Score 0.964 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: T215A

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: T226A

PolyPhen 2 Score 0.895 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: T226A

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

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: 76 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2900026A02Rik	G	A	5: 113,332,001 (GRCm39)	R738C	possibly damaging	Het
Acot12	G	A	13: 91,919,844 (GRCm39)	V260M	probably benign	Het
Alkbh8	A	T	9: 3,359,503 (GRCm39)	H264L	probably damaging	Het
Arfgef2	C	T	2: 166,715,623 (GRCm39)	T1356I	probably damaging	Het
Arhgap27	A	T	11: 103,251,130 (GRCm39)	N199K	probably damaging	Het
Asic2	T	C	11: 81,858,824 (GRCm39)	R63G	probably damaging	Het
Aspa	T	A	11: 73,204,378 (GRCm39)	M197L	probably benign	Het
BC005537	C	T	13: 24,987,382 (GRCm39)	R7W	possibly damaging	Het
Brdt	A	T	5: 107,518,045 (GRCm39)	I723L	probably benign	Het
C2cd3	T	A	7: 100,118,698 (GRCm39)	F2312Y	probably damaging	Het
Cd19	T	C	7: 126,009,698 (GRCm39)	N456S	probably damaging	Het
Ceacam1	G	T	7: 25,175,954 (GRCm39)	A80E	probably damaging	Het
Cep135	T	C	5: 76,788,803 (GRCm39)	V1132A	probably benign	Het
Cep85	A	G	4: 133,859,609 (GRCm39)	C687R	probably damaging	Het
Cln5	A	G	14: 103,313,501 (GRCm39)	Y251C	probably damaging	Het
Crygc	A	G	1: 65,111,014 (GRCm39)	M91T	possibly damaging	Het
Ddt	T	C	10: 75,609,060 (GRCm39)	K33R	probably damaging	Het
Dhfr	G	A	13: 92,494,471 (GRCm39)	W58*	probably null	Het
Dhx40	T	C	11: 86,688,532 (GRCm39)	E297G	probably benign	Het
Dner	T	C	1: 84,361,602 (GRCm39)	Y669C	probably benign	Het
Dpys	G	T	15: 39,656,782 (GRCm39)	F428L	probably damaging	Het
Dspp	A	C	5: 104,323,531 (GRCm39)	T225P	probably damaging	Het
Elac2	A	G	11: 64,890,213 (GRCm39)	K656E	probably damaging	Het
Ern1	T	A	11: 106,349,845 (GRCm39)	R24*	probably null	Het
F2rl2	T	C	13: 95,837,519 (GRCm39)	I188T	probably damaging	Het
Fam83b	C	T	9: 76,399,426 (GRCm39)	C559Y	possibly damaging	Het
Fat1	T	G	8: 45,504,259 (GRCm39)	F4584C	probably benign	Het
Gabra6	G	A	11: 42,207,322 (GRCm39)	T254I	possibly damaging	Het
Garem1	T	C	18: 21,432,757 (GRCm39)	D24G	probably damaging	Het
Gas2l2	A	T	11: 83,312,816 (GRCm39)	L832*	probably null	Het
Gpr68	C	T	12: 100,845,497 (GRCm39)	D16N	probably benign	Het
Il17b	T	C	18: 61,825,480 (GRCm39)	I172T	probably damaging	Het
Ildr2	T	G	1: 166,136,861 (GRCm39)	S567A	probably benign	Het
Kalrn	A	G	16: 33,809,217 (GRCm39)	V2557A	probably damaging	Het
Kif1b	A	G	4: 149,268,833 (GRCm39)	S1627P	probably benign	Het
Kif5a	G	A	10: 127,079,343 (GRCm39)	T285M	probably damaging	Het
Lrif1	G	A	3: 106,640,459 (GRCm39)		probably null	Het
Lrrn2	C	T	1: 132,867,116 (GRCm39)	T727I	unknown	Het
Lsg1	T	C	16: 30,383,540 (GRCm39)	E560G	probably benign	Het
Map4k4	C	A	1: 40,013,204 (GRCm39)	Q100K	unknown	Het
Mipep	A	T	14: 61,040,385 (GRCm39)	R302W	probably damaging	Het
Morf4l1	G	T	9: 89,975,844 (GRCm39)	T316K	probably damaging	Het
Mov10	A	T	3: 104,711,994 (GRCm39)	V126E	probably damaging	Het
Muc2	T	A	7: 141,303,471 (GRCm39)	C559S		Het
Myh7	A	G	14: 55,226,530 (GRCm39)	Y410H	probably damaging	Het
Nf1	T	A	11: 79,309,414 (GRCm39)	Y433N	probably damaging	Het
Nmd3	T	C	3: 69,633,750 (GRCm39)	L79P	probably damaging	Het
Nol10	G	T	12: 17,408,239 (GRCm39)	S155I	probably null	Het
Or2n1	T	C	17: 38,486,830 (GRCm39)	L285P	possibly damaging	Het
Or4p8	T	C	2: 88,727,408 (GRCm39)	I178V	probably benign	Het
Or52n2c	T	A	7: 104,574,311 (GRCm39)	Y220F	probably damaging	Het
Or5b12	A	G	19: 12,896,911 (GRCm39)	I254T	probably benign	Het
Pde3b	T	C	7: 114,093,922 (GRCm39)	S389P	probably benign	Het
Polr1c	C	T	17: 46,555,817 (GRCm39)	G188D	probably benign	Het
Prpf31	A	G	7: 3,633,859 (GRCm39)	M65V	probably benign	Het
Pum2	A	G	12: 8,763,595 (GRCm39)	T251A	probably benign	Het
Rabgap1	G	A	2: 37,377,142 (GRCm39)	V325I	probably benign	Het
Repin1	G	T	6: 48,574,279 (GRCm39)	E403*	probably null	Het
Rpl15	G	T	14: 18,269,017 (GRCm38)	Y203*	probably null	Het
Sac3d1	G	A	19: 6,168,456 (GRCm39)	P54L	possibly damaging	Het
Serpina3g	A	G	12: 104,206,510 (GRCm39)	I104V	probably benign	Het
Setd2	C	T	9: 110,379,082 (GRCm39)	Q966*	probably null	Het
Simc1	G	T	13: 54,651,713 (GRCm39)	D9Y	unknown	Het
Slc5a8	T	C	10: 88,757,567 (GRCm39)	L519S	probably benign	Het
Srcap	C	A	7: 127,138,366 (GRCm39)	Q1179K	possibly damaging	Het
Srd5a3	T	C	5: 76,295,583 (GRCm39)	L91P	probably damaging	Het
Stab1	T	C	14: 30,876,429 (GRCm39)	T887A	probably benign	Het
Sult2a6	A	G	7: 13,988,737 (GRCm39)	F8L	not run	Het
Thsd7a	A	T	6: 12,471,123 (GRCm39)	C498*	probably null	Het
Timp4	T	C	6: 115,227,355 (GRCm39)	I75V	probably benign	Het
Tspyl4	T	A	10: 34,174,096 (GRCm39)	M196K	probably damaging	Het
Ubr2	T	C	17: 47,301,934 (GRCm39)	E172G	probably benign	Het
Ubr5	G	A	15: 37,980,076 (GRCm39)	A2434V	probably null	Het
Unc13c	T	G	9: 73,602,159 (GRCm39)	L1362F	probably damaging	Het
Vmn2r11	A	G	5: 109,199,986 (GRCm39)	V489A	probably damaging	Het
Zan	C	T	5: 137,471,863 (GRCm39)	E185K	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
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'- AGGCAGAGTCTACCTATCTGC -3'
(R):5'- TCATGTCAAACAAGGACCATTACTG -3'

Sequencing Primer
(F):5'- CCTATCTGCTAGGATCATGATAG -3'
(R):5'- ATGTGGATTTTCCCAGGCTGC -3'

Posted On

2019-12-20