Incidental Mutation 'IGL02943:Vps39'
| ID |
364584 |
| 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 # |
IGL02943
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
2 |
| Chromosomal Location |
120146942-120183618 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 120169968 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Serine to Proline
at position 195
(S195P)
|
| 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: S184P
PolyPhen 2
Score 0.764 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: S184P
| 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: S195P
PolyPhen 2
Score 0.768 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: S195P
| 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
|
| 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: 62 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Akp3 |
T |
A |
1: 87,054,091 (GRCm39) |
Y236* |
probably null |
Het |
| Ankrd13c |
C |
T |
3: 157,653,564 (GRCm39) |
T134M |
probably damaging |
Het |
| Arhgef18 |
T |
C |
8: 3,498,553 (GRCm39) |
S529P |
probably damaging |
Het |
| Cdkl2 |
T |
A |
5: 92,185,103 (GRCm39) |
N96I |
possibly damaging |
Het |
| Cep57 |
A |
T |
9: 13,730,149 (GRCm39) |
|
probably benign |
Het |
| Chchd7 |
T |
C |
4: 3,942,796 (GRCm39) |
Y44H |
probably damaging |
Het |
| Ciart |
T |
C |
3: 95,786,314 (GRCm39) |
I254V |
possibly damaging |
Het |
| Cyp2a12 |
T |
C |
7: 26,731,967 (GRCm39) |
I236T |
probably benign |
Het |
| Dlgap5 |
A |
G |
14: 47,650,433 (GRCm39) |
|
probably null |
Het |
| Ednra |
T |
A |
8: 78,446,683 (GRCm39) |
I132F |
probably damaging |
Het |
| En2 |
T |
C |
5: 28,371,524 (GRCm39) |
|
probably benign |
Het |
| Fcgbpl1 |
A |
G |
7: 27,846,613 (GRCm39) |
R1102G |
probably damaging |
Het |
| Fsip2 |
C |
A |
2: 82,822,701 (GRCm39) |
Q6145K |
probably benign |
Het |
| Galnt5 |
A |
T |
2: 57,889,780 (GRCm39) |
D460V |
probably damaging |
Het |
| Gm6401 |
C |
T |
14: 41,788,851 (GRCm39) |
E73K |
possibly damaging |
Het |
| Gpr84 |
T |
C |
15: 103,217,316 (GRCm39) |
I254V |
probably benign |
Het |
| Hacd3 |
A |
T |
9: 64,897,718 (GRCm39) |
I298N |
probably damaging |
Het |
| Hyal6 |
T |
A |
6: 24,743,438 (GRCm39) |
V378E |
probably damaging |
Het |
| Il20rb |
G |
T |
9: 100,348,305 (GRCm39) |
H210N |
probably benign |
Het |
| Iqgap2 |
A |
G |
13: 95,798,243 (GRCm39) |
|
probably benign |
Het |
| Itga1 |
C |
T |
13: 115,185,832 (GRCm39) |
E57K |
possibly damaging |
Het |
| Jmjd1c |
T |
A |
10: 67,055,433 (GRCm39) |
D571E |
probably damaging |
Het |
| Kmt2c |
T |
C |
5: 25,495,821 (GRCm39) |
S623G |
probably damaging |
Het |
| L3mbtl2 |
T |
A |
15: 81,570,456 (GRCm39) |
S645T |
possibly damaging |
Het |
| Lrp2 |
A |
G |
2: 69,285,854 (GRCm39) |
V3779A |
possibly damaging |
Het |
| Lrpprc |
T |
C |
17: 85,078,878 (GRCm39) |
R279G |
probably benign |
Het |
| Lurap1l |
A |
G |
4: 80,871,872 (GRCm39) |
K122E |
probably damaging |
Het |
| Met |
T |
C |
6: 17,535,928 (GRCm39) |
Y785H |
possibly damaging |
Het |
| Myh3 |
T |
C |
11: 66,981,891 (GRCm39) |
F796L |
probably benign |
Het |
| Myo16 |
T |
C |
8: 10,450,595 (GRCm39) |
|
probably benign |
Het |
| Nedd4l |
T |
C |
18: 65,294,723 (GRCm39) |
|
probably null |
Het |
| Nlrp4c |
T |
C |
7: 6,068,974 (GRCm39) |
C292R |
probably damaging |
Het |
| Nmnat1 |
A |
G |
4: 149,557,745 (GRCm39) |
L99P |
probably damaging |
Het |
| Or1j12 |
A |
T |
2: 36,343,051 (GRCm39) |
L151F |
probably benign |
Het |
| Or5p64 |
A |
G |
7: 107,854,623 (GRCm39) |
F241L |
possibly damaging |
Het |
| Pclo |
T |
C |
5: 14,719,235 (GRCm39) |
V1124A |
unknown |
Het |
| Phf20l1 |
A |
G |
15: 66,466,733 (GRCm39) |
Y54C |
probably damaging |
Het |
| Postn |
T |
C |
3: 54,285,029 (GRCm39) |
|
probably null |
Het |
| Ppp2r1b |
A |
G |
9: 50,794,885 (GRCm39) |
D570G |
probably damaging |
Het |
| Prdm2 |
A |
C |
4: 142,858,542 (GRCm39) |
S1583A |
probably benign |
Het |
| Proser1 |
T |
C |
3: 53,386,524 (GRCm39) |
V802A |
probably damaging |
Het |
| Ptprc |
A |
T |
1: 138,027,251 (GRCm39) |
N532K |
probably damaging |
Het |
| Ptprk |
A |
G |
10: 28,351,172 (GRCm39) |
H555R |
possibly damaging |
Het |
| Ranbp6 |
T |
C |
19: 29,789,524 (GRCm39) |
D276G |
possibly damaging |
Het |
| Rasgrf2 |
A |
G |
13: 92,131,752 (GRCm39) |
V635A |
probably damaging |
Het |
| Rbm5 |
T |
C |
9: 107,621,542 (GRCm39) |
Y620C |
probably damaging |
Het |
| Sall1 |
C |
T |
8: 89,757,749 (GRCm39) |
R785H |
probably damaging |
Het |
| Slc22a2 |
G |
T |
17: 12,828,948 (GRCm39) |
L351F |
probably damaging |
Het |
| Sorcs3 |
A |
T |
19: 48,748,377 (GRCm39) |
Q782L |
probably benign |
Het |
| Sphkap |
A |
T |
1: 83,254,552 (GRCm39) |
S779T |
probably damaging |
Het |
| Stxbp2 |
A |
T |
8: 3,691,971 (GRCm39) |
I538F |
probably benign |
Het |
| Tas2r107 |
T |
A |
6: 131,636,369 (GRCm39) |
M227L |
probably damaging |
Het |
| Tecpr2 |
C |
T |
12: 110,934,183 (GRCm39) |
T1281I |
probably benign |
Het |
| Topbp1 |
T |
A |
9: 103,205,639 (GRCm39) |
V759E |
probably benign |
Het |
| Trim2 |
T |
C |
3: 84,085,483 (GRCm39) |
T504A |
probably benign |
Het |
| Trpc1 |
A |
G |
9: 95,590,906 (GRCm39) |
|
probably benign |
Het |
| Tssk4 |
T |
A |
14: 55,889,023 (GRCm39) |
V183E |
probably damaging |
Het |
| Vmn1r202 |
T |
C |
13: 22,686,364 (GRCm39) |
T18A |
probably benign |
Het |
| Vmn1r225 |
T |
C |
17: 20,722,567 (GRCm39) |
S3P |
possibly damaging |
Het |
| Vmn2r101 |
T |
A |
17: 19,831,666 (GRCm39) |
V554E |
probably damaging |
Het |
| Vps13a |
T |
C |
19: 16,641,250 (GRCm39) |
I2291V |
probably damaging |
Het |
| Zfand4 |
T |
A |
6: 116,250,837 (GRCm39) |
|
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 |
|
|
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 |
2015-12-18 |
Incidental Mutation