Incidental Mutation 'IGL01936:Vps39'
| ID |
180685 |
| Institutional Source |
Australian Phenomics Network
(link to record)
|
| Gene Symbol |
Vps39
|
| Ensembl Gene |
ENSMUSG00000027291 |
| Gene Name |
VPS39 HOPS complex subunit |
| Synonyms |
Vam6, Vam6P, A230065P22Rik, mVam6 |
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.953)
|
| Stock # |
IGL01936
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
2 |
| Chromosomal Location |
120146942-120183618 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 120153609 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glycine to Aspartic acid
at position 655
(G655D)
|
| 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: G644D
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: G644D
| 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: G655D
PolyPhen 2
Score 0.229 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: G655D
| 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: 68 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adamts3 |
T |
A |
5: 90,009,282 (GRCm39) |
H127L |
probably benign |
Het |
| Adamtsl3 |
T |
C |
7: 82,244,579 (GRCm39) |
V419A |
possibly damaging |
Het |
| Arhgap31 |
T |
A |
16: 38,423,287 (GRCm39) |
L926F |
probably damaging |
Het |
| Asgr2 |
A |
T |
11: 69,988,877 (GRCm39) |
|
probably null |
Het |
| C3ar1 |
T |
A |
6: 122,828,194 (GRCm39) |
T8S |
probably benign |
Het |
| Caskin2 |
T |
C |
11: 115,695,543 (GRCm39) |
I273V |
probably damaging |
Het |
| Ccnl2 |
T |
A |
4: 155,904,856 (GRCm39) |
C242S |
probably damaging |
Het |
| Cdkn2a |
A |
T |
4: 89,212,569 (GRCm39) |
|
probably null |
Het |
| Cfap45 |
T |
G |
1: 172,361,616 (GRCm39) |
M231R |
probably damaging |
Het |
| Clcn7 |
A |
C |
17: 25,374,350 (GRCm39) |
N464H |
probably benign |
Het |
| Col20a1 |
T |
A |
2: 180,651,161 (GRCm39) |
|
probably benign |
Het |
| Col7a1 |
T |
A |
9: 108,797,067 (GRCm39) |
|
probably benign |
Het |
| Cops7a |
T |
C |
6: 124,939,379 (GRCm39) |
D90G |
probably benign |
Het |
| Ctcf |
T |
C |
8: 106,396,864 (GRCm39) |
V363A |
probably benign |
Het |
| Cyp2j12 |
A |
G |
4: 96,021,306 (GRCm39) |
V100A |
probably benign |
Het |
| Dcaf1 |
T |
A |
9: 106,736,800 (GRCm39) |
F1085Y |
possibly damaging |
Het |
| Drc7 |
T |
A |
8: 95,800,760 (GRCm39) |
F594Y |
possibly damaging |
Het |
| Ehbp1l1 |
C |
A |
19: 5,768,277 (GRCm39) |
E1009* |
probably null |
Het |
| Epg5 |
C |
A |
18: 78,028,316 (GRCm39) |
R1286S |
probably damaging |
Het |
| Etv1 |
T |
C |
12: 38,885,060 (GRCm39) |
|
probably benign |
Het |
| Exosc7 |
T |
C |
9: 122,964,956 (GRCm39) |
|
probably benign |
Het |
| Fam227a |
T |
C |
15: 79,496,747 (GRCm39) |
D610G |
possibly damaging |
Het |
| Fat4 |
T |
A |
3: 39,033,923 (GRCm39) |
M2525K |
probably benign |
Het |
| Gimap5 |
G |
T |
6: 48,729,999 (GRCm39) |
A190S |
probably damaging |
Het |
| Glcci1 |
T |
A |
6: 8,579,596 (GRCm39) |
S79T |
probably damaging |
Het |
| Gpnmb |
C |
T |
6: 49,024,384 (GRCm39) |
T233I |
probably null |
Het |
| Hdac1-ps |
T |
C |
17: 78,799,558 (GRCm39) |
V183A |
probably damaging |
Het |
| Hyls1 |
T |
C |
9: 35,473,363 (GRCm39) |
I18V |
probably benign |
Het |
| Ighv1-63 |
C |
T |
12: 115,459,274 (GRCm39) |
E108K |
probably damaging |
Het |
| Ighv5-12 |
C |
A |
12: 113,665,927 (GRCm39) |
R57L |
probably damaging |
Het |
| Igkv5-37 |
T |
C |
6: 69,940,323 (GRCm39) |
Y107C |
probably damaging |
Het |
| Il20ra |
T |
A |
10: 19,631,591 (GRCm39) |
V264D |
probably damaging |
Het |
| Jph1 |
A |
T |
1: 17,167,608 (GRCm39) |
V74E |
probably damaging |
Het |
| Kcnab1 |
C |
T |
3: 65,265,695 (GRCm39) |
L280F |
probably damaging |
Het |
| Kcnk1 |
T |
C |
8: 126,751,826 (GRCm39) |
F144S |
probably damaging |
Het |
| Kcnq1 |
G |
A |
7: 142,738,241 (GRCm39) |
E294K |
possibly damaging |
Het |
| Kdm4b |
T |
A |
17: 56,704,355 (GRCm39) |
V813E |
probably damaging |
Het |
| Kntc1 |
T |
A |
5: 123,949,439 (GRCm39) |
F1937I |
probably damaging |
Het |
| Ldb2 |
G |
A |
5: 44,637,586 (GRCm39) |
R241W |
probably damaging |
Het |
| Lgr5 |
T |
C |
10: 115,288,319 (GRCm39) |
N703S |
probably damaging |
Het |
| Map4k1 |
A |
T |
7: 28,688,032 (GRCm39) |
M227L |
possibly damaging |
Het |
| Mbnl1 |
T |
A |
3: 60,520,940 (GRCm39) |
M268K |
possibly damaging |
Het |
| Mcm2 |
C |
A |
6: 88,868,708 (GRCm39) |
G350C |
probably damaging |
Het |
| Myh2 |
A |
T |
11: 67,082,599 (GRCm39) |
T1390S |
possibly damaging |
Het |
| Npat |
T |
A |
9: 53,469,526 (GRCm39) |
|
probably benign |
Het |
| Nr2e1 |
T |
A |
10: 42,443,969 (GRCm39) |
D251V |
possibly damaging |
Het |
| Or1x2 |
A |
G |
11: 50,918,162 (GRCm39) |
N111S |
probably benign |
Het |
| Or4d10 |
C |
T |
19: 12,051,421 (GRCm39) |
V192I |
probably benign |
Het |
| Or5b107 |
C |
A |
19: 13,142,767 (GRCm39) |
P130T |
probably damaging |
Het |
| Plekha5 |
T |
A |
6: 140,470,621 (GRCm39) |
H87Q |
probably damaging |
Het |
| Polr3a |
A |
G |
14: 24,529,256 (GRCm39) |
V368A |
probably damaging |
Het |
| Psmb8 |
T |
A |
17: 34,419,168 (GRCm39) |
L154Q |
probably damaging |
Het |
| Rab40c |
A |
C |
17: 26,103,644 (GRCm39) |
C140G |
probably damaging |
Het |
| Ranbp17 |
G |
A |
11: 33,437,689 (GRCm39) |
T183I |
probably benign |
Het |
| Ruvbl2 |
T |
C |
7: 45,078,122 (GRCm39) |
E117G |
probably damaging |
Het |
| Serpinb3b |
T |
A |
1: 107,082,368 (GRCm39) |
M299L |
probably benign |
Het |
| Smpdl3a |
A |
G |
10: 57,678,530 (GRCm39) |
H111R |
probably damaging |
Het |
| Sspo |
C |
A |
6: 48,452,821 (GRCm39) |
P2843H |
probably damaging |
Het |
| Stk39 |
T |
C |
2: 68,144,908 (GRCm39) |
T389A |
probably benign |
Het |
| Synrg |
T |
A |
11: 83,910,531 (GRCm39) |
F1000Y |
probably benign |
Het |
| Thbs2 |
C |
T |
17: 14,908,076 (GRCm39) |
S229N |
probably benign |
Het |
| Thsd1 |
G |
A |
8: 22,742,247 (GRCm39) |
C305Y |
probably damaging |
Het |
| Ticrr |
C |
A |
7: 79,344,297 (GRCm39) |
D1387E |
probably benign |
Het |
| Tmem145 |
G |
T |
7: 25,010,816 (GRCm39) |
A383S |
probably damaging |
Het |
| Tmprss4 |
A |
G |
9: 45,090,718 (GRCm39) |
V187A |
probably damaging |
Het |
| Unc13c |
T |
A |
9: 73,600,524 (GRCm39) |
M1407L |
probably benign |
Het |
| Wwtr1 |
T |
C |
3: 57,482,241 (GRCm39) |
|
probably benign |
Het |
| Xrn1 |
T |
C |
9: 95,930,397 (GRCm39) |
S1535P |
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 |
|
|
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 |
|
|
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 |
|
| Posted On |
2014-05-07 |
Incidental Mutation