Incidental Mutation 'R3771:Vps39'
ID |
273257 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps39
|
Ensembl Gene |
ENSMUSG00000027291 |
Gene Name |
VPS39 HOPS complex subunit |
Synonyms |
Vam6, Vam6P, A230065P22Rik, mVam6 |
MMRRC Submission |
040747-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.953)
|
Stock # |
R3771 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
2 |
Chromosomal Location |
120146942-120183618 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to T
at 120172497 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Isoleucine
at position 179
(V179I)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000099559
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028752]
[ENSMUST00000102501]
|
AlphaFold |
Q8R5L3 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000028752
AA Change: V168I
PolyPhen 2
Score 0.851 (Sensitivity: 0.83; Specificity: 0.93)
|
SMART Domains |
Protein: ENSMUSP00000028752 Gene: ENSMUSG00000027291 AA Change: V168I
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: V179I
PolyPhen 2
Score 0.853 (Sensitivity: 0.83; Specificity: 0.93)
|
SMART Domains |
Protein: ENSMUSP00000099559 Gene: ENSMUSG00000027291 AA Change: V179I
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: ENSMUST00000138854
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147085
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000156296
|
Meta Mutation Damage Score |
0.1795 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 95.3%
|
Validation Efficiency |
99% (69/70) |
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: 65 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Aanat |
G |
T |
11: 116,487,697 (GRCm39) |
G132V |
probably damaging |
Het |
Abcb11 |
T |
A |
2: 69,159,720 (GRCm39) |
|
probably benign |
Het |
Adam26b |
T |
A |
8: 43,973,751 (GRCm39) |
D417V |
probably damaging |
Het |
Ank1 |
T |
C |
8: 23,613,913 (GRCm39) |
S1482P |
probably benign |
Het |
Aoc1l2 |
T |
C |
6: 48,908,130 (GRCm39) |
Y377H |
probably damaging |
Het |
Armc2 |
C |
T |
10: 41,798,223 (GRCm39) |
V768M |
probably damaging |
Het |
Ascc3 |
C |
T |
10: 50,596,814 (GRCm39) |
|
probably benign |
Het |
Birc6 |
T |
A |
17: 74,925,424 (GRCm39) |
|
probably benign |
Het |
Cd109 |
CATTTATTTATTTATTTATTTATTTATTTATTTAT |
CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT |
9: 78,619,782 (GRCm39) |
|
probably benign |
Het |
Cdh12 |
A |
T |
15: 21,578,640 (GRCm39) |
|
probably benign |
Het |
Chd1 |
A |
G |
17: 17,594,913 (GRCm39) |
D16G |
probably damaging |
Het |
Clstn2 |
A |
G |
9: 97,464,615 (GRCm39) |
I180T |
probably damaging |
Het |
Cxcr6 |
A |
G |
9: 123,639,550 (GRCm39) |
I184V |
probably benign |
Het |
Dagla |
G |
A |
19: 10,225,831 (GRCm39) |
P778S |
possibly damaging |
Het |
Ddx19b |
T |
C |
8: 111,747,613 (GRCm39) |
K107R |
probably benign |
Het |
Dpyd |
G |
A |
3: 119,205,927 (GRCm39) |
|
probably null |
Het |
Elf1 |
T |
C |
14: 79,804,650 (GRCm39) |
V105A |
possibly damaging |
Het |
Fam13a |
T |
G |
6: 58,964,171 (GRCm39) |
K87T |
probably benign |
Het |
Fap |
C |
A |
2: 62,363,354 (GRCm39) |
S359I |
probably damaging |
Het |
Fbxo39 |
T |
C |
11: 72,208,041 (GRCm39) |
I131T |
possibly damaging |
Het |
Fmn1 |
T |
G |
2: 113,412,463 (GRCm39) |
S996A |
probably damaging |
Het |
Gm5866 |
T |
C |
5: 52,740,088 (GRCm39) |
|
noncoding transcript |
Het |
Hmcn2 |
C |
T |
2: 31,250,908 (GRCm39) |
T790M |
probably damaging |
Het |
Irf2bp2 |
T |
C |
8: 127,318,550 (GRCm39) |
K339E |
probably damaging |
Het |
Kat6b |
A |
G |
14: 21,567,166 (GRCm39) |
D75G |
probably damaging |
Het |
Kcnab3 |
A |
G |
11: 69,219,389 (GRCm39) |
T127A |
probably damaging |
Het |
Kdm5b |
G |
T |
1: 134,541,083 (GRCm39) |
C725F |
probably damaging |
Het |
Lrp5 |
G |
A |
19: 3,662,330 (GRCm39) |
R173C |
probably damaging |
Het |
Lrrn3 |
T |
A |
12: 41,502,869 (GRCm39) |
I483L |
probably damaging |
Het |
Man2c1 |
C |
A |
9: 57,047,661 (GRCm39) |
|
probably benign |
Het |
Med23 |
G |
T |
10: 24,778,099 (GRCm39) |
G810C |
probably damaging |
Het |
Nhlrc4 |
T |
A |
17: 26,162,367 (GRCm39) |
K127* |
probably null |
Het |
Numb |
T |
C |
12: 83,846,350 (GRCm39) |
D344G |
probably damaging |
Het |
Nup210l |
T |
G |
3: 90,027,201 (GRCm39) |
Y194* |
probably null |
Het |
Ogg1 |
T |
C |
6: 113,310,804 (GRCm39) |
V317A |
possibly damaging |
Het |
Or1o2 |
T |
A |
17: 37,542,356 (GRCm39) |
I302F |
possibly damaging |
Het |
Or6c69c |
A |
G |
10: 129,911,143 (GRCm39) |
Y288C |
probably damaging |
Het |
Pclo |
A |
T |
5: 14,589,422 (GRCm39) |
|
probably null |
Het |
Pnpt1 |
T |
C |
11: 29,088,174 (GRCm39) |
M195T |
probably benign |
Het |
Polr3c |
T |
A |
3: 96,633,170 (GRCm39) |
T43S |
probably damaging |
Het |
Ptprs |
T |
C |
17: 56,735,978 (GRCm39) |
T152A |
possibly damaging |
Het |
Rasl10b |
A |
T |
11: 83,309,349 (GRCm39) |
T134S |
probably benign |
Het |
Rin2 |
C |
T |
2: 145,702,366 (GRCm39) |
T354I |
probably benign |
Het |
Rnf39 |
T |
C |
17: 37,258,121 (GRCm39) |
W96R |
probably damaging |
Het |
Ros1 |
G |
T |
10: 52,005,087 (GRCm39) |
A949E |
probably damaging |
Het |
Rwdd2a |
A |
C |
9: 86,456,214 (GRCm39) |
N130T |
possibly damaging |
Het |
Scn9a |
T |
C |
2: 66,313,992 (GRCm39) |
N1909D |
probably benign |
Het |
Shisal1 |
A |
T |
15: 84,290,886 (GRCm39) |
Y120* |
probably null |
Het |
Ska3 |
C |
T |
14: 58,047,534 (GRCm39) |
V334I |
probably benign |
Het |
Srebf2 |
A |
G |
15: 82,066,309 (GRCm39) |
K579R |
probably benign |
Het |
Sun1 |
A |
G |
5: 139,224,575 (GRCm39) |
|
probably benign |
Het |
Tc2n |
T |
A |
12: 101,660,833 (GRCm39) |
Q133L |
possibly damaging |
Het |
Tecta |
T |
C |
9: 42,242,292 (GRCm39) |
T2094A |
probably damaging |
Het |
Tex2 |
T |
C |
11: 106,437,720 (GRCm39) |
D650G |
unknown |
Het |
Trio |
A |
G |
15: 27,748,177 (GRCm39) |
S2492P |
probably damaging |
Het |
Ttn |
T |
C |
2: 76,601,711 (GRCm39) |
T16872A |
probably benign |
Het |
Ugcg |
T |
C |
4: 59,189,690 (GRCm39) |
F16S |
probably benign |
Het |
Usp16 |
T |
C |
16: 87,255,571 (GRCm39) |
M1T |
probably null |
Het |
Vmn1r60 |
C |
A |
7: 5,547,710 (GRCm39) |
C130F |
possibly damaging |
Het |
Vmn2r101 |
A |
G |
17: 19,809,919 (GRCm39) |
D235G |
probably benign |
Het |
Vpreb3 |
A |
T |
10: 75,775,800 (GRCm39) |
V26E |
probably benign |
Het |
Xrn2 |
T |
C |
2: 146,903,207 (GRCm39) |
V765A |
probably benign |
Het |
Zfp251 |
A |
G |
15: 76,737,836 (GRCm39) |
I414T |
possibly damaging |
Het |
Zfp426 |
A |
T |
9: 20,384,413 (GRCm39) |
|
probably null |
Het |
Zfp61 |
T |
C |
7: 23,995,406 (GRCm39) |
M1V |
probably null |
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 |
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 |
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'- ACTTGTGGAAATGCTAAGTGC -3'
(R):5'- AAGAATTGTGCTCAGGTATGGG -3'
Sequencing Primer
(F):5'- TAAGTGCACTCTCGCGC -3'
(R):5'- AGAATTGTGCTCAGGTATGGGTAGAG -3'
|
Posted On |
2015-03-25 |