Incidental Mutation 'IGL01629:Vps39'
| ID |
92857 |
| 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 # |
IGL01629
|
| Quality Score |
|
|
Status
|
|
| Chromosome |
2 |
| Chromosomal Location |
120146942-120183618 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to T
at 120154079 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Methionine
at position 628
(L628M)
|
| 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: L628M
PolyPhen 2
Score 0.113 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: L628M
| 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: L639M
PolyPhen 2
Score 0.069 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: L639M
| 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: 37 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adgra2 |
G |
A |
8: 27,608,761 (GRCm39) |
A540T |
possibly damaging |
Het |
| Adm2 |
T |
A |
15: 89,207,605 (GRCm39) |
|
probably null |
Het |
| Alox12 |
G |
A |
11: 70,133,660 (GRCm39) |
P555S |
probably damaging |
Het |
| Alpk2 |
A |
G |
18: 65,433,113 (GRCm39) |
S1798P |
probably damaging |
Het |
| Amfr |
T |
A |
8: 94,714,136 (GRCm39) |
|
probably null |
Het |
| Arhgef18 |
T |
A |
8: 3,431,942 (GRCm39) |
C168S |
possibly damaging |
Het |
| Atxn7l3 |
A |
T |
11: 102,183,320 (GRCm39) |
|
probably benign |
Het |
| Ccdc191 |
A |
G |
16: 43,779,663 (GRCm39) |
K707E |
possibly damaging |
Het |
| Cdc5l |
G |
T |
17: 45,724,116 (GRCm39) |
D391E |
probably benign |
Het |
| Cmtm2b |
T |
C |
8: 105,056,420 (GRCm39) |
S110P |
possibly damaging |
Het |
| Cyp2j8 |
T |
C |
4: 96,387,840 (GRCm39) |
D207G |
probably damaging |
Het |
| Ddhd2 |
A |
G |
8: 26,225,855 (GRCm39) |
F501L |
possibly damaging |
Het |
| Dnaaf6rt |
T |
A |
1: 31,262,014 (GRCm39) |
|
probably null |
Het |
| Dnah1 |
C |
T |
14: 31,014,277 (GRCm39) |
V1823M |
probably damaging |
Het |
| Gjb4 |
T |
C |
4: 127,245,419 (GRCm39) |
D174G |
possibly damaging |
Het |
| Gm45213 |
A |
G |
7: 65,711,962 (GRCm39) |
D58G |
probably damaging |
Het |
| Hes1 |
C |
T |
16: 29,884,976 (GRCm39) |
|
probably benign |
Het |
| Krt33b |
T |
A |
11: 99,920,386 (GRCm39) |
Q89L |
probably benign |
Het |
| Llcfc1 |
C |
A |
6: 41,661,459 (GRCm39) |
S3Y |
possibly damaging |
Het |
| Ltf |
A |
G |
9: 110,864,874 (GRCm39) |
N569S |
probably damaging |
Het |
| Mknk1 |
T |
A |
4: 115,732,731 (GRCm39) |
W320R |
probably damaging |
Het |
| Mrgprx3-ps |
T |
A |
7: 46,959,353 (GRCm39) |
K213* |
probably null |
Het |
| Mslnl |
T |
G |
17: 25,963,749 (GRCm39) |
V388G |
possibly damaging |
Het |
| Nfkb1 |
T |
C |
3: 135,307,228 (GRCm39) |
I566V |
probably benign |
Het |
| Npy1r |
G |
A |
8: 67,156,873 (GRCm39) |
V98I |
probably benign |
Het |
| Phf1 |
G |
T |
17: 27,153,247 (GRCm39) |
A22S |
probably benign |
Het |
| Plcg1 |
T |
G |
2: 160,599,930 (GRCm39) |
F897V |
possibly damaging |
Het |
| Ric1 |
A |
T |
19: 29,581,381 (GRCm39) |
E1367D |
probably benign |
Het |
| Slc24a3 |
T |
C |
2: 145,482,130 (GRCm39) |
|
probably benign |
Het |
| Sorl1 |
A |
G |
9: 41,968,565 (GRCm39) |
|
probably null |
Het |
| Speer4a2 |
C |
T |
5: 26,290,700 (GRCm39) |
S157N |
probably damaging |
Het |
| Spink5 |
T |
C |
18: 44,129,677 (GRCm39) |
|
probably benign |
Het |
| Syne2 |
A |
G |
12: 76,051,377 (GRCm39) |
I4036V |
possibly damaging |
Het |
| Taok1 |
A |
T |
11: 77,429,030 (GRCm39) |
M890K |
possibly damaging |
Het |
| Tenm2 |
A |
T |
11: 36,755,711 (GRCm39) |
Y96N |
probably damaging |
Het |
| Ttll10 |
T |
A |
4: 156,131,351 (GRCm39) |
T233S |
probably benign |
Het |
| Zfp563 |
G |
A |
17: 33,323,600 (GRCm39) |
R105H |
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 |
|
|
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 |
|
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 |
2013-12-09 |
Incidental Mutation