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

mVam6, Vam6P, Vam6, A230065P22Rik

MMRRC Submission

068709-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.964) question?

Stock #

R8933 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

120316461-120353137 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 120338585 bp (GRCm38)

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: 122,128,137	I1114N	probably damaging	Het
Ache	C	A	5: 137,290,187	R52S	possibly damaging	Het
AI182371	A	T	2: 35,085,702		probably null	Het
Ankrd17	T	C	5: 90,258,466	S1453G	probably damaging	Het
Arvcf	A	G	16: 18,400,095	N508S	probably damaging	Het
Aurkc	A	C	7: 7,002,797	D136A	possibly damaging	Het
Bfsp2	A	G	9: 103,448,649	M265T	probably benign	Het
Bmpr1b	T	C	3: 141,856,608	T273A	probably damaging	Het
Cacnb1	T	C	11: 98,005,752	K406R	probably damaging	Het
Calcoco2	C	T	11: 96,107,426		probably benign	Het
Capza1	T	C	3: 104,840,893		probably null	Het
Ccdc63	T	A	5: 122,113,202	I382F	probably damaging	Het
Cep350	A	T	1: 155,863,415	N2227K	probably benign	Het
Chia1	T	A	3: 106,129,017	Y304*	probably null	Het
Col5a2	G	A	1: 45,421,963	P258L		Het
Cyp21a1	A	G	17: 34,804,311	L30P	probably damaging	Het
Dennd4b	T	A	3: 90,279,216	H1351Q	probably benign	Het
Dnah9	T	A	11: 65,855,252	I4012F	possibly damaging	Het
Drd1	A	G	13: 54,053,271	I301T	possibly damaging	Het
Dzip1	T	A	14: 118,906,914	H369L	probably damaging	Het
Fgfrl1	T	A	5: 108,703,391	M58K	probably damaging	Het
Ftsj3	G	T	11: 106,250,834	D529E	probably benign	Het
Fut9	A	T	4: 25,619,861	W318R	probably damaging	Het
Gabrg3	A	G	7: 56,984,958	I159T	probably damaging	Het
Gabrr1	A	T	4: 33,146,972	D53V	probably benign	Het
Ggps1	A	G	13: 14,054,343	V85A	probably benign	Het
Gm5141	C	T	13: 62,777,040	W18*	probably null	Het
Grik5	T	A	7: 25,023,318	T518S	probably benign	Het
Hapln3	A	T	7: 79,117,630		probably benign	Het
Hbs1l	C	T	10: 21,367,685	Q646*	probably null	Het
Hmox1	T	C	8: 75,097,016	I104T	probably benign	Het
Ifit1bl1	T	C	19: 34,594,013	Y348C	probably damaging	Het
Igf2r	A	T	17: 12,701,244	S1403T	probably damaging	Het
Igf2r	G	A	17: 12,704,637	T1186M	probably damaging	Het
Igfbp1	T	C	11: 7,198,333		probably null	Het
Ikbip	C	A	10: 91,083,230	A35E	probably benign	Het
Isca1	C	T	13: 59,769,683	A8T	probably damaging	Het
Itgb2	T	C	10: 77,565,188	L754P	probably damaging	Het
Itgb6	C	T	2: 60,627,903	C502Y	probably damaging	Het
Kdm3a	A	G	6: 71,600,108	V741A	probably benign	Het
Kdsr	T	C	1: 106,753,219	D83G	possibly damaging	Het
Kiz	T	A	2: 146,942,117	N523K		Het
Kmt2a	T	C	9: 44,822,505		probably benign	Het
Krt25	T	C	11: 99,321,238	E191G	probably benign	Het
Lipn	A	G	19: 34,069,480	I61V	probably damaging	Het
Lmbr1l	T	A	15: 98,909,269		probably null	Het
Lrrc4c	A	G	2: 97,629,481	K151E	probably benign	Het
Mab21l3	T	C	3: 101,823,458	Q155R	probably benign	Het
Mtfr2	G	A	10: 20,357,528	R281H	possibly damaging	Het
Muc5ac	A	G	7: 141,789,756	Y35C	possibly damaging	Het
Myadm	C	T	7: 3,296,917	T65I	probably benign	Het
Nap1l1	T	C	10: 111,492,849	V213A	probably benign	Het
Nav2	A	G	7: 49,461,957	D737G	probably damaging	Het
Ndst4	T	A	3: 125,611,506	V470D	probably damaging	Het
Nek5	T	A	8: 22,111,210	Y165F	probably damaging	Het
Nek5	A	T	8: 22,120,843	V48E	probably damaging	Het
Nr6a1	T	C	2: 38,760,388	I77V	probably damaging	Het
Nvl	A	T	1: 181,139,073	D93E	probably benign	Het
Olfr450	A	G	6: 42,818,016	T182A	probably benign	Het
Olfr552	A	T	7: 102,604,430	L25F	probably damaging	Het
Olfr656	A	T	7: 104,617,666	T4S	probably benign	Het
Olfr678	A	G	7: 105,069,392		probably benign	Het
Olfr780	A	T	10: 129,322,390	I256F	probably damaging	Het
Olfr96	C	A	17: 37,225,455	T110K	possibly damaging	Het
Pla2g4c	G	A	7: 13,339,702	V225I	probably benign	Het
Plppr4	T	A	3: 117,323,041	N331I	probably damaging	Het
Ptpn13	A	G	5: 103,579,805	R2051G	probably benign	Het
Rbm45	T	C	2: 76,378,724	S346P	probably damaging	Het
Samd14	A	C	11: 95,021,201	D168A	probably damaging	Het
Slc15a1	C	T	14: 121,486,679	G172R	probably benign	Het
Slco3a1	G	T	7: 74,284,500	Y641*	probably null	Het
Srcap	G	A	7: 127,552,394	R2027H	probably damaging	Het
Stra8	A	T	6: 34,927,689		probably benign	Het
Syt11	T	C	3: 88,747,704	Y430C	probably damaging	Het
Tanc1	T	G	2: 59,785,456	V269G	possibly damaging	Het
Tead1	A	G	7: 112,898,611	N342S	probably benign	Het
Tenm3	C	T	8: 48,279,060	A1254T	possibly damaging	Het
Txlnb	A	T	10: 17,806,798	N156I	probably damaging	Het
Ufl1	A	T	4: 25,262,258	S409R	possibly damaging	Het
Usp17la	A	G	7: 104,861,100	H304R	probably benign	Het
Vmn1r203	T	A	13: 22,524,521	H157Q	possibly damaging	Het
Vmn1r37	C	T	6: 66,732,247	R249*	probably null	Het
Vmn2r96	A	G	17: 18,583,979	Q497R	probably benign	Het
Wnk1	A	G	6: 120,036,998	V212A	probably damaging	Het
Xbp1	T	C	11: 5,524,741	V161A	probably benign	Het
Zfp113	T	C	5: 138,144,830	Q386R	probably 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
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
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
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'- GTGGACTCAAACCCTGCATC -3'
(R):5'- GAGATCCGAACACTGGAACC -3'

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

Posted On

2021-08-31