Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02892:Vps39'

363259

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Vps39

Ensembl Gene

ENSMUSG00000027291

Gene Name

VPS39 HOPS complex subunit

Synonyms

mVam6, Vam6P, Vam6, A230065P22Rik

Accession Numbers

Is this an essential gene?

Probably essential (E-score: 0.959) question?

Stock #

IGL02892

Quality Score

Status

Chromosome

Chromosomal Location

120316461-120353137 bp(-) (GRCm38)

Type of Mutation

splice site

DNA Base Change (assembly)

A to G at 120323171 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000099559 (fasta)

Gene Model

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

AlphaFold

Q8R5L3

Predicted Effect

probably benign
Transcript: ENSMUST00000028752

SMART Domains

Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291

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

SMART Domains

Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291

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: ENSMUST00000133260

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145193

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147085

Coding Region Coverage

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcd4	A	T	12: 84,604,997	L493*	probably null	Het
Adam32	T	A	8: 24,878,711		probably benign	Het
Alpk1	T	C	3: 127,680,122	D744G	possibly damaging	Het
Arhgef12	A	G	9: 43,000,972	V530A	possibly damaging	Het
Baz2b	A	T	2: 59,900,736	N2095K	probably damaging	Het
Btnl2	A	T	17: 34,362,668	Q240L	possibly damaging	Het
Cd96	T	C	16: 46,049,797		probably null	Het
Cep350	G	A	1: 155,868,806	T2089I	possibly damaging	Het
Chd9	T	C	8: 90,976,915		probably benign	Het
Cib4	C	T	5: 30,544,707		probably benign	Het
Cilp2	T	C	8: 69,884,320	T280A	probably benign	Het
Coq5	T	A	5: 115,294,817		probably benign	Het
Cyth3	A	G	5: 143,707,437	I339V	possibly damaging	Het
Dcaf7	T	C	11: 106,046,692	V47A	possibly damaging	Het
Dcdc2c	A	G	12: 28,535,545	I151T	probably benign	Het
Defb7	T	A	8: 19,497,662	F61Y	probably benign	Het
Diaph3	T	A	14: 86,866,630	K773*	probably null	Het
Dmxl1	A	G	18: 49,859,120	N311S	probably damaging	Het
Dnah7b	G	A	1: 46,119,298	R347H	possibly damaging	Het
Egflam	C	T	15: 7,289,796	V234I	probably benign	Het
Emilin3	C	T	2: 160,909,149	V180M	possibly damaging	Het
Fam76b	A	T	9: 13,828,821	E50V	probably null	Het
Fat3	A	T	9: 16,377,562	Y222N	probably damaging	Het
Grm7	A	G	6: 111,254,020	N468S	probably damaging	Het
Gucy1a2	G	T	9: 3,634,471	G172C	probably damaging	Het
Hmcn1	A	C	1: 150,675,974		probably null	Het
Hydin	G	A	8: 110,598,959	V4667M	possibly damaging	Het
Idh2	T	C	7: 80,095,670	S408G	probably benign	Het
Kcng4	T	C	8: 119,633,082	Q185R	probably benign	Het
Lamp3	A	G	16: 19,676,052	V301A	probably damaging	Het
Lrrc23	T	C	6: 124,774,436	N220S	probably benign	Het
Lrrc41	T	A	4: 116,088,835	M249K	possibly damaging	Het
Ltbp4	T	A	7: 27,310,649	D1162V	probably damaging	Het
Mlh1	T	C	9: 111,252,969	I229V	probably benign	Het
Olfr108	T	C	17: 37,446,034	L160P	probably damaging	Het
Plekhg2	T	A	7: 28,362,917	D525V	probably damaging	Het
Plin4	T	C	17: 56,105,108	K641R	probably damaging	Het
Plxnb2	A	G	15: 89,161,222		probably null	Het
Polr1a	T	C	6: 71,931,696	S502P	possibly damaging	Het
Prss16	A	G	13: 22,003,050	V450A	probably benign	Het
Prss42	G	A	9: 110,799,390	V201M	probably damaging	Het
Pus7	A	T	5: 23,754,556	N322K	probably damaging	Het
Riok1	G	T	13: 38,040,065		probably benign	Het
Rmdn3	T	A	2: 119,154,080	T64S	probably benign	Het
Rmnd5a	T	A	6: 71,414,814	M131L	probably benign	Het
Rtbdn	C	T	8: 84,955,089	R170C	probably damaging	Het
Sesn3	T	C	9: 14,314,734		probably null	Het
Slc2a6	A	G	2: 27,024,293	Y271H	probably benign	Het
Slc5a5	T	G	8: 70,892,517	T49P	probably damaging	Het
Slc7a10	T	C	7: 35,195,168	V84A	possibly damaging	Het
Slc9a4	A	G	1: 40,584,044	T148A	possibly damaging	Het
Smg1	T	A	7: 118,167,955		probably benign	Het
Snx19	T	A	9: 30,428,364	V266E	probably damaging	Het
Synm	T	A	7: 67,735,056	I511F	probably damaging	Het
Tango6	T	A	8: 106,742,010		probably benign	Het
Tie1	T	A	4: 118,486,282	D128V	probably damaging	Het
Timeless	T	C	10: 128,244,251	L423P	probably damaging	Het
Tln1	A	G	4: 43,555,679	L145P	probably damaging	Het
Tmem8	A	G	17: 26,119,120	Y466C	probably damaging	Het
Trp53i13	A	T	11: 77,508,295	D376E	probably damaging	Het
Ubr4	A	T	4: 139,417,331	I1484F	probably damaging	Het
Unc13a	C	T	8: 71,649,910	V943M	probably damaging	Het
Usp50	T	C	2: 126,769,902	K301R	probably damaging	Het
Vmn1r62	G	T	7: 5,676,203	M294I	probably benign	Het
Vwa8	T	A	14: 79,103,700		probably benign	Het
Wdr27	A	T	17: 14,876,176	W748R	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
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
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

Posted On

2015-12-18