Incidental Mutation 'IGL02892:Vps39'
| ID |
363259 |
| 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 # |
IGL02892
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
2 |
| Chromosomal Location |
120146942-120183618 bp(-) (GRCm39) |
| Type of Mutation |
splice site |
| DNA Base Change (assembly) |
A to G
at 120153652 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000099559
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028752]
[ENSMUST00000102501]
|
| AlphaFold |
Q8R5L3 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000028752
|
| SMART Domains |
Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
| 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
|
| SMART Domains |
Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
| 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: 66 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcd4 |
A |
T |
12: 84,651,771 (GRCm39) |
L493* |
probably null |
Het |
| Adam32 |
T |
A |
8: 25,368,727 (GRCm39) |
|
probably benign |
Het |
| Alpk1 |
T |
C |
3: 127,473,771 (GRCm39) |
D744G |
possibly damaging |
Het |
| Arhgef12 |
A |
G |
9: 42,912,268 (GRCm39) |
V530A |
possibly damaging |
Het |
| Baz2b |
A |
T |
2: 59,731,080 (GRCm39) |
N2095K |
probably damaging |
Het |
| Btnl2 |
A |
T |
17: 34,581,642 (GRCm39) |
Q240L |
possibly damaging |
Het |
| Cd96 |
T |
C |
16: 45,870,160 (GRCm39) |
|
probably null |
Het |
| Cep350 |
G |
A |
1: 155,744,552 (GRCm39) |
T2089I |
possibly damaging |
Het |
| Chd9 |
T |
C |
8: 91,703,543 (GRCm39) |
|
probably benign |
Het |
| Cib4 |
C |
T |
5: 30,702,051 (GRCm39) |
|
probably benign |
Het |
| Cilp2 |
T |
C |
8: 70,336,970 (GRCm39) |
T280A |
probably benign |
Het |
| Coq5 |
T |
A |
5: 115,432,876 (GRCm39) |
|
probably benign |
Het |
| Cyth3 |
A |
G |
5: 143,693,192 (GRCm39) |
I339V |
possibly damaging |
Het |
| Dcaf7 |
T |
C |
11: 105,937,518 (GRCm39) |
V47A |
possibly damaging |
Het |
| Dcdc2c |
A |
G |
12: 28,585,544 (GRCm39) |
I151T |
probably benign |
Het |
| Defb7 |
T |
A |
8: 19,547,678 (GRCm39) |
F61Y |
probably benign |
Het |
| Diaph3 |
T |
A |
14: 87,104,066 (GRCm39) |
K773* |
probably null |
Het |
| Dmxl1 |
A |
G |
18: 49,992,187 (GRCm39) |
N311S |
probably damaging |
Het |
| Dnah7b |
G |
A |
1: 46,158,458 (GRCm39) |
R347H |
possibly damaging |
Het |
| Egflam |
C |
T |
15: 7,319,277 (GRCm39) |
V234I |
probably benign |
Het |
| Emilin3 |
C |
T |
2: 160,751,069 (GRCm39) |
V180M |
possibly damaging |
Het |
| Fam76b |
A |
T |
9: 13,740,117 (GRCm39) |
E50V |
probably null |
Het |
| Fat3 |
A |
T |
9: 16,288,858 (GRCm39) |
Y222N |
probably damaging |
Het |
| Grm7 |
A |
G |
6: 111,230,981 (GRCm39) |
N468S |
probably damaging |
Het |
| Gucy1a2 |
G |
T |
9: 3,634,471 (GRCm39) |
G172C |
probably damaging |
Het |
| Hmcn1 |
A |
C |
1: 150,551,725 (GRCm39) |
|
probably null |
Het |
| Hydin |
G |
A |
8: 111,325,591 (GRCm39) |
V4667M |
possibly damaging |
Het |
| Idh2 |
T |
C |
7: 79,745,418 (GRCm39) |
S408G |
probably benign |
Het |
| Kcng4 |
T |
C |
8: 120,359,821 (GRCm39) |
Q185R |
probably benign |
Het |
| Lamp3 |
A |
G |
16: 19,494,802 (GRCm39) |
V301A |
probably damaging |
Het |
| Lrrc23 |
T |
C |
6: 124,751,399 (GRCm39) |
N220S |
probably benign |
Het |
| Lrrc41 |
T |
A |
4: 115,946,032 (GRCm39) |
M249K |
possibly damaging |
Het |
| Ltbp4 |
T |
A |
7: 27,010,074 (GRCm39) |
D1162V |
probably damaging |
Het |
| Mlh1 |
T |
C |
9: 111,082,037 (GRCm39) |
I229V |
probably benign |
Het |
| Or1o11 |
T |
C |
17: 37,756,925 (GRCm39) |
L160P |
probably damaging |
Het |
| Pgap6 |
A |
G |
17: 26,338,094 (GRCm39) |
Y466C |
probably damaging |
Het |
| Plekhg2 |
T |
A |
7: 28,062,342 (GRCm39) |
D525V |
probably damaging |
Het |
| Plin4 |
T |
C |
17: 56,412,108 (GRCm39) |
K641R |
probably damaging |
Het |
| Plxnb2 |
A |
G |
15: 89,045,425 (GRCm39) |
|
probably null |
Het |
| Polr1a |
T |
C |
6: 71,908,680 (GRCm39) |
S502P |
possibly damaging |
Het |
| Prss16 |
A |
G |
13: 22,187,220 (GRCm39) |
V450A |
probably benign |
Het |
| Prss42 |
G |
A |
9: 110,628,458 (GRCm39) |
V201M |
probably damaging |
Het |
| Pus7 |
A |
T |
5: 23,959,554 (GRCm39) |
N322K |
probably damaging |
Het |
| Riok1 |
G |
T |
13: 38,224,041 (GRCm39) |
|
probably benign |
Het |
| Rmdn3 |
T |
A |
2: 118,984,561 (GRCm39) |
T64S |
probably benign |
Het |
| Rmnd5a |
T |
A |
6: 71,391,798 (GRCm39) |
M131L |
probably benign |
Het |
| Rtbdn |
C |
T |
8: 85,681,718 (GRCm39) |
R170C |
probably damaging |
Het |
| Sesn3 |
T |
C |
9: 14,226,030 (GRCm39) |
|
probably null |
Het |
| Slc2a6 |
A |
G |
2: 26,914,305 (GRCm39) |
Y271H |
probably benign |
Het |
| Slc5a5 |
T |
G |
8: 71,345,161 (GRCm39) |
T49P |
probably damaging |
Het |
| Slc7a10 |
T |
C |
7: 34,894,593 (GRCm39) |
V84A |
possibly damaging |
Het |
| Slc9a4 |
A |
G |
1: 40,623,204 (GRCm39) |
T148A |
possibly damaging |
Het |
| Smg1 |
T |
A |
7: 117,767,178 (GRCm39) |
|
probably benign |
Het |
| Snx19 |
T |
A |
9: 30,339,660 (GRCm39) |
V266E |
probably damaging |
Het |
| Synm |
T |
A |
7: 67,384,804 (GRCm39) |
I511F |
probably damaging |
Het |
| Tango6 |
T |
A |
8: 107,468,642 (GRCm39) |
|
probably benign |
Het |
| Tie1 |
T |
A |
4: 118,343,479 (GRCm39) |
D128V |
probably damaging |
Het |
| Timeless |
T |
C |
10: 128,080,120 (GRCm39) |
L423P |
probably damaging |
Het |
| Tln1 |
A |
G |
4: 43,555,679 (GRCm39) |
L145P |
probably damaging |
Het |
| Trp53i13 |
A |
T |
11: 77,399,121 (GRCm39) |
D376E |
probably damaging |
Het |
| Ubr4 |
A |
T |
4: 139,144,642 (GRCm39) |
I1484F |
probably damaging |
Het |
| Unc13a |
C |
T |
8: 72,102,554 (GRCm39) |
V943M |
probably damaging |
Het |
| Usp50 |
T |
C |
2: 126,611,822 (GRCm39) |
K301R |
probably damaging |
Het |
| Vmn1r62 |
G |
T |
7: 5,679,202 (GRCm39) |
M294I |
probably benign |
Het |
| Vwa8 |
T |
A |
14: 79,341,140 (GRCm39) |
|
probably benign |
Het |
| Wdr27 |
A |
T |
17: 15,096,438 (GRCm39) |
W748R |
possibly 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 |
|
|
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 |
|
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 |
2015-12-18 |
Incidental Mutation