Incidental Mutation 'IGL02379:Vps39'
| ID |
291265 |
| 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: 0.950)
|
| Stock # |
IGL02379
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
2 |
| Chromosomal Location |
120146942-120183618 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to A
at 120154089 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Lysine to Asparagine
at position 624
(K624N)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000028752
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028752]
[ENSMUST00000102501]
|
| AlphaFold |
Q8R5L3 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000028752
AA Change: K624N
PolyPhen 2
Score 0.165 (Sensitivity: 0.92; Specificity: 0.87)
|
| SMART Domains |
Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: K624N
| 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: K635N
PolyPhen 2
Score 0.050 (Sensitivity: 0.94; Specificity: 0.83)
|
| SMART Domains |
Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: K635N
| 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: 58 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acad10 |
T |
A |
5: 121,760,106 (GRCm39) |
I996F |
probably damaging |
Het |
| Adamts9 |
T |
A |
6: 92,774,014 (GRCm39) |
D1133V |
probably damaging |
Het |
| Adi1 |
T |
A |
12: 28,729,466 (GRCm39) |
D106E |
probably damaging |
Het |
| Agl |
A |
G |
3: 116,572,740 (GRCm39) |
F837S |
probably damaging |
Het |
| Alb |
T |
A |
5: 90,613,738 (GRCm39) |
D207E |
probably benign |
Het |
| Alms1 |
T |
G |
6: 85,606,615 (GRCm39) |
V2286G |
probably damaging |
Het |
| Alpl |
G |
A |
4: 137,469,869 (GRCm39) |
A485V |
probably damaging |
Het |
| Antxrl |
C |
A |
14: 33,778,492 (GRCm39) |
|
probably null |
Het |
| Apc |
C |
T |
18: 34,431,798 (GRCm39) |
T417I |
probably benign |
Het |
| Ash2l |
T |
C |
8: 26,312,799 (GRCm39) |
D390G |
probably damaging |
Het |
| Asph |
G |
A |
4: 9,474,980 (GRCm39) |
P582S |
probably damaging |
Het |
| Bcr |
T |
A |
10: 74,992,980 (GRCm39) |
L825Q |
probably benign |
Het |
| Bhlha15 |
T |
A |
5: 144,128,159 (GRCm39) |
N90K |
probably damaging |
Het |
| Cgnl1 |
T |
A |
9: 71,552,835 (GRCm39) |
Y1043F |
possibly damaging |
Het |
| Chek1 |
T |
C |
9: 36,635,242 (GRCm39) |
D47G |
probably benign |
Het |
| Clca4b |
T |
A |
3: 144,627,619 (GRCm39) |
M451L |
probably benign |
Het |
| Csnk1g3 |
T |
C |
18: 54,066,564 (GRCm39) |
S346P |
probably benign |
Het |
| Cspg4 |
G |
T |
9: 56,799,893 (GRCm39) |
|
probably benign |
Het |
| Ctr9 |
A |
G |
7: 110,650,726 (GRCm39) |
K884E |
probably damaging |
Het |
| Cyld |
T |
A |
8: 89,471,556 (GRCm39) |
C813* |
probably null |
Het |
| Fn3k |
A |
T |
11: 121,325,950 (GRCm39) |
T46S |
probably benign |
Het |
| Foxred1 |
T |
C |
9: 35,121,282 (GRCm39) |
R89G |
probably benign |
Het |
| Gpr174 |
T |
C |
X: 106,337,084 (GRCm39) |
F299L |
probably damaging |
Het |
| Hdac7 |
T |
C |
15: 97,706,266 (GRCm39) |
D312G |
probably damaging |
Het |
| Il36b |
A |
G |
2: 24,044,650 (GRCm39) |
S17G |
probably benign |
Het |
| Kcna5 |
G |
T |
6: 126,511,472 (GRCm39) |
P219T |
probably damaging |
Het |
| Kcnh2 |
A |
C |
5: 24,531,636 (GRCm39) |
V425G |
probably damaging |
Het |
| Klk1b5 |
A |
G |
7: 43,500,246 (GRCm39) |
N278S |
probably damaging |
Het |
| Mars2 |
T |
A |
1: 55,277,212 (GRCm39) |
W272R |
probably damaging |
Het |
| Msl3l2 |
C |
A |
10: 55,992,017 (GRCm39) |
S247R |
possibly damaging |
Het |
| Myh7 |
T |
C |
14: 55,216,925 (GRCm39) |
E1144G |
probably damaging |
Het |
| Nefm |
T |
C |
14: 68,357,688 (GRCm39) |
|
probably benign |
Het |
| Nwd2 |
A |
G |
5: 63,962,644 (GRCm39) |
K743E |
probably damaging |
Het |
| Nyap2 |
C |
T |
1: 81,065,147 (GRCm39) |
T53I |
probably damaging |
Het |
| Odad4 |
A |
T |
11: 100,457,809 (GRCm39) |
N471Y |
possibly damaging |
Het |
| Or10ag58 |
T |
C |
2: 87,265,668 (GRCm39) |
V279A |
probably benign |
Het |
| Or52z12 |
T |
C |
7: 103,234,099 (GRCm39) |
V290A |
possibly damaging |
Het |
| Peli2 |
A |
G |
14: 48,405,755 (GRCm39) |
H60R |
probably damaging |
Het |
| Pias2 |
T |
A |
18: 77,232,844 (GRCm39) |
|
probably benign |
Het |
| Pik3c2b |
A |
G |
1: 133,022,529 (GRCm39) |
D1157G |
probably damaging |
Het |
| Pip4k2a |
C |
T |
2: 18,870,922 (GRCm39) |
|
probably null |
Het |
| Raf1 |
A |
T |
6: 115,621,509 (GRCm39) |
D23E |
probably benign |
Het |
| Rhox10 |
G |
A |
X: 37,155,733 (GRCm39) |
R87H |
probably benign |
Het |
| Rpgrip1 |
A |
G |
14: 52,376,345 (GRCm39) |
T449A |
possibly damaging |
Het |
| Serpina3a |
T |
A |
12: 104,084,919 (GRCm39) |
S105T |
probably benign |
Het |
| Slc12a9 |
T |
G |
5: 137,319,691 (GRCm39) |
Q608P |
probably damaging |
Het |
| Smg6 |
C |
A |
11: 74,944,751 (GRCm39) |
P167T |
probably damaging |
Het |
| Spata7 |
C |
T |
12: 98,600,519 (GRCm39) |
T44I |
probably damaging |
Het |
| Spink12 |
C |
T |
18: 44,239,575 (GRCm39) |
|
probably benign |
Het |
| Srrm1 |
G |
A |
4: 135,052,415 (GRCm39) |
P658L |
unknown |
Het |
| Stag2 |
C |
T |
X: 41,339,474 (GRCm39) |
T754I |
probably benign |
Het |
| Supt6 |
C |
T |
11: 78,116,195 (GRCm39) |
V723M |
possibly damaging |
Het |
| Ubr3 |
A |
G |
2: 69,778,832 (GRCm39) |
D614G |
possibly damaging |
Het |
| Vwa5b1 |
A |
T |
4: 138,340,170 (GRCm39) |
L29Q |
probably damaging |
Het |
| Wtap |
G |
A |
17: 13,188,336 (GRCm39) |
A188V |
probably benign |
Het |
| Zc3hc1 |
A |
G |
6: 30,390,974 (GRCm39) |
F5L |
probably benign |
Het |
| Zfp655 |
C |
T |
5: 145,180,765 (GRCm39) |
P208S |
probably benign |
Het |
| Zswim3 |
A |
T |
2: 164,662,602 (GRCm39) |
|
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 |
|
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 |
2015-04-16 |
Incidental Mutation