Incidental Mutation 'R1483:Vps39'
| ID |
165676 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps39
|
| Ensembl Gene |
ENSMUSG00000027291 |
| Gene Name |
VPS39 HOPS complex subunit |
| Synonyms |
Vam6, Vam6P, A230065P22Rik, mVam6 |
| MMRRC Submission |
039536-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.953)
|
| Stock # |
R1483 (G1)
|
| Quality Score |
155 |
|
Status
|
Not validated
|
| Chromosome |
2 |
| Chromosomal Location |
120146942-120183618 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 120154129 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Glutamine
at position 622
(L622Q)
|
| 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: L611Q
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: L611Q
| 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 damaging
Transcript: ENSMUST00000102501
AA Change: L622Q
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: L622Q
| 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 |
- 1x: 99.0%
- 3x: 98.1%
- 10x: 95.8%
- 20x: 91.0%
|
| 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: 65 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adam12 |
T |
A |
7: 133,531,754 (GRCm39) |
T494S |
probably benign |
Het |
| Akap6 |
C |
T |
12: 52,842,870 (GRCm39) |
P73S |
probably damaging |
Het |
| Amotl2 |
A |
T |
9: 102,608,096 (GRCm39) |
T763S |
probably benign |
Het |
| Brd10 |
G |
A |
19: 29,696,745 (GRCm39) |
P916L |
possibly damaging |
Het |
| Cdc5l |
A |
T |
17: 45,719,290 (GRCm39) |
V541D |
possibly damaging |
Het |
| Chl1 |
A |
G |
6: 103,624,248 (GRCm39) |
Y52C |
probably damaging |
Het |
| D6Wsu163e |
A |
G |
6: 126,931,733 (GRCm39) |
E255G |
probably benign |
Het |
| Ddhd2 |
A |
G |
8: 26,243,155 (GRCm39) |
S126P |
probably benign |
Het |
| Dner |
CGCTGCTGCTGCTGCTGCTGCTGCTGC |
CGCTGCTGCTGCTGCTGCTGCTGC |
1: 84,563,270 (GRCm39) |
|
probably benign |
Het |
| Drc3 |
A |
G |
11: 60,279,715 (GRCm39) |
I427V |
probably benign |
Het |
| Drg2 |
T |
C |
11: 60,350,353 (GRCm39) |
I104T |
probably damaging |
Het |
| Dst |
C |
T |
1: 34,292,079 (GRCm39) |
A932V |
probably damaging |
Het |
| Ecm1 |
G |
A |
3: 95,643,275 (GRCm39) |
R342C |
probably damaging |
Het |
| Eif3a |
A |
T |
19: 60,757,164 (GRCm39) |
D880E |
unknown |
Het |
| Elf1 |
T |
A |
14: 79,818,078 (GRCm39) |
D569E |
probably benign |
Het |
| Esp6 |
T |
A |
17: 40,873,816 (GRCm39) |
M1K |
probably null |
Het |
| Fer1l6 |
T |
C |
15: 58,509,819 (GRCm39) |
V1427A |
possibly damaging |
Het |
| Gsta1 |
A |
T |
9: 78,149,775 (GRCm39) |
K196M |
probably damaging |
Het |
| Gzme |
T |
A |
14: 56,356,169 (GRCm39) |
I110F |
probably damaging |
Het |
| H2-DMa |
T |
A |
17: 34,354,724 (GRCm39) |
V27E |
possibly damaging |
Het |
| H2-T10 |
A |
T |
17: 36,432,038 (GRCm39) |
S2T |
probably benign |
Het |
| Hadhb |
A |
G |
5: 30,374,492 (GRCm39) |
|
probably null |
Het |
| Hoxa11 |
G |
T |
6: 52,220,436 (GRCm39) |
D282E |
probably damaging |
Het |
| Ifit1bl1 |
A |
G |
19: 34,572,041 (GRCm39) |
Y139H |
possibly damaging |
Het |
| Ift27 |
A |
G |
15: 78,049,436 (GRCm39) |
V88A |
possibly damaging |
Het |
| Knop1 |
C |
T |
7: 118,452,273 (GRCm39) |
A149T |
probably damaging |
Het |
| Macf1 |
T |
A |
4: 123,404,770 (GRCm39) |
K597I |
probably damaging |
Het |
| Med16 |
A |
T |
10: 79,738,934 (GRCm39) |
I284N |
possibly damaging |
Het |
| Melk |
T |
A |
4: 44,308,937 (GRCm39) |
I98K |
probably damaging |
Het |
| Mst1 |
G |
T |
9: 107,958,849 (GRCm39) |
G127V |
probably benign |
Het |
| Nacad |
A |
G |
11: 6,552,217 (GRCm39) |
S325P |
probably damaging |
Het |
| Nbea |
G |
A |
3: 55,910,211 (GRCm39) |
P1328L |
probably benign |
Het |
| Nek5 |
C |
T |
8: 22,586,806 (GRCm39) |
S335N |
probably benign |
Het |
| Nif3l1 |
C |
A |
1: 58,486,885 (GRCm39) |
R24S |
probably benign |
Het |
| Nlrp14 |
T |
G |
7: 106,789,329 (GRCm39) |
N39K |
possibly damaging |
Het |
| Nup50 |
T |
A |
15: 84,823,928 (GRCm39) |
V427D |
probably damaging |
Het |
| Nwd1 |
C |
T |
8: 73,383,714 (GRCm39) |
P78L |
probably damaging |
Het |
| Or5an9 |
T |
A |
19: 12,187,114 (GRCm39) |
Y61* |
probably null |
Het |
| Pate8 |
G |
A |
9: 36,492,620 (GRCm39) |
S95L |
probably benign |
Het |
| Pnkd |
A |
G |
1: 74,388,550 (GRCm39) |
Y242C |
probably benign |
Het |
| Ppm1g |
T |
C |
5: 31,360,465 (GRCm39) |
D423G |
probably benign |
Het |
| Pramel32 |
T |
A |
4: 88,547,071 (GRCm39) |
Q116L |
probably damaging |
Het |
| Prkci |
A |
T |
3: 31,097,941 (GRCm39) |
N464Y |
probably damaging |
Het |
| Ptprf |
C |
T |
4: 118,093,161 (GRCm39) |
V494M |
possibly damaging |
Het |
| Rapgef4 |
T |
G |
2: 71,885,370 (GRCm39) |
|
probably null |
Het |
| Rbak |
T |
C |
5: 143,160,099 (GRCm39) |
E318G |
probably damaging |
Het |
| Rora |
A |
G |
9: 69,271,667 (GRCm39) |
D215G |
probably benign |
Het |
| Rp1l1 |
C |
T |
14: 64,266,496 (GRCm39) |
T694I |
possibly damaging |
Het |
| Scrib |
A |
G |
15: 75,929,771 (GRCm39) |
L1032P |
probably damaging |
Het |
| Sectm1b |
G |
A |
11: 120,946,652 (GRCm39) |
T81M |
probably benign |
Het |
| Sgk3 |
T |
C |
1: 9,942,518 (GRCm39) |
F97L |
possibly damaging |
Het |
| Socs3 |
A |
T |
11: 117,858,394 (GRCm39) |
Y221* |
probably null |
Het |
| Spata31d1e |
A |
T |
13: 59,890,717 (GRCm39) |
S368T |
probably damaging |
Het |
| Tdrd6 |
T |
A |
17: 43,938,498 (GRCm39) |
H850L |
probably benign |
Het |
| Tex44 |
G |
T |
1: 86,354,908 (GRCm39) |
Q272H |
probably damaging |
Het |
| Tgfbr2 |
A |
C |
9: 115,938,625 (GRCm39) |
S426A |
probably benign |
Het |
| Tmem39b |
T |
C |
4: 129,570,456 (GRCm39) |
Y461C |
probably damaging |
Het |
| Ttn |
T |
A |
2: 76,555,337 (GRCm39) |
D30556V |
probably damaging |
Het |
| Tubgcp5 |
T |
A |
7: 55,475,455 (GRCm39) |
|
probably null |
Het |
| Vmn2r70 |
T |
C |
7: 85,208,375 (GRCm39) |
I701V |
probably benign |
Het |
| Wdfy4 |
T |
A |
14: 32,822,923 (GRCm39) |
H1347L |
probably benign |
Het |
| Xpo1 |
A |
G |
11: 23,234,863 (GRCm39) |
I540V |
probably benign |
Het |
| Xylt2 |
A |
C |
11: 94,560,393 (GRCm39) |
M294R |
probably benign |
Het |
| Zfp788 |
T |
G |
7: 41,298,499 (GRCm39) |
Y326* |
probably null |
Het |
| Zim1 |
A |
G |
7: 6,685,124 (GRCm39) |
F109L |
probably benign |
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 |
|
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 |
|
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'- GGCCAGCATGTCTCTTAGCAACAC -3'
(R):5'- GTCCCTGACATCACTGGGTTTTAGC -3'
Sequencing Primer
(F):5'- AAAGGACTTCCTGTCTACCTGG -3'
(R):5'- CATAGTTTTTGGACGAGCTGCC -3'
|
| Posted On |
2014-03-28 |
Incidental Mutation