Incidental Mutation 'R9302:Vps39'
| ID |
726297 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps39
|
| Ensembl Gene |
ENSMUSG00000027291 |
| Gene Name |
VPS39 HOPS complex subunit |
| Synonyms |
Vam6, Vam6P, A230065P22Rik, mVam6 |
| MMRRC Submission |
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.950)
|
| Stock # |
R9302 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
120146942-120183618 bp(-) (GRCm39) |
| Type of Mutation |
splice site |
| DNA Base Change (assembly) |
A to T
at 120151525 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.4%
|
| Validation Efficiency |
100% (54/54) |
| 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 |
|---|
| Aar2 |
T |
C |
2: 156,392,956 (GRCm39) |
L115P |
probably damaging |
Het |
| Acsl1 |
T |
A |
8: 46,983,470 (GRCm39) |
D494E |
probably damaging |
Het |
| Adgrl1 |
T |
C |
8: 84,656,426 (GRCm39) |
V243A |
possibly damaging |
Het |
| Ak9 |
A |
T |
10: 41,196,486 (GRCm39) |
I103F |
|
Het |
| Ank3 |
C |
T |
10: 69,761,849 (GRCm39) |
|
probably benign |
Het |
| Ano4 |
T |
A |
10: 88,831,220 (GRCm39) |
I468L |
probably benign |
Het |
| Anxa2r1 |
A |
G |
13: 120,496,626 (GRCm39) |
I81T |
probably benign |
Het |
| Arhgef10l |
G |
A |
4: 140,242,548 (GRCm39) |
S959L |
probably benign |
Het |
| Cdh23 |
G |
A |
10: 60,143,306 (GRCm39) |
A3005V |
possibly damaging |
Het |
| Cfap221 |
T |
C |
1: 119,853,365 (GRCm39) |
I776M |
probably benign |
Het |
| Col3a1 |
C |
T |
1: 45,350,980 (GRCm39) |
Q25* |
probably null |
Het |
| Crabp2 |
C |
A |
3: 87,859,833 (GRCm39) |
L100I |
probably benign |
Het |
| Dnah5 |
A |
G |
15: 28,240,032 (GRCm39) |
D463G |
probably benign |
Het |
| Dst |
T |
C |
1: 34,264,636 (GRCm39) |
L2602P |
probably damaging |
Het |
| Dusp1 |
A |
G |
17: 26,726,148 (GRCm39) |
Y182H |
probably damaging |
Het |
| Fhip1a |
C |
A |
3: 85,579,941 (GRCm39) |
D755Y |
probably damaging |
Het |
| Fras1 |
T |
A |
5: 96,682,751 (GRCm39) |
C83S |
probably damaging |
Het |
| Frrs1 |
G |
T |
3: 116,692,899 (GRCm39) |
|
probably null |
Het |
| Gcnt3 |
A |
G |
9: 69,942,529 (GRCm39) |
L13P |
possibly damaging |
Het |
| Gm8094 |
T |
C |
14: 42,932,834 (GRCm39) |
D88G |
probably benign |
Het |
| Hfe |
C |
T |
13: 23,890,025 (GRCm39) |
M249I |
probably benign |
Het |
| Hipk1 |
T |
C |
3: 103,685,099 (GRCm39) |
E172G |
probably benign |
Het |
| Iws1 |
G |
A |
18: 32,213,213 (GRCm39) |
E214K |
possibly damaging |
Het |
| Ltb4r2 |
A |
T |
14: 55,999,733 (GRCm39) |
Q118L |
probably damaging |
Het |
| Ltbp4 |
A |
T |
7: 27,008,481 (GRCm39) |
C1342S |
possibly damaging |
Het |
| Lyst |
A |
G |
13: 13,904,947 (GRCm39) |
D3208G |
possibly damaging |
Het |
| Mbnl2 |
A |
G |
14: 120,622,950 (GRCm39) |
T163A |
probably benign |
Het |
| Mre11a |
T |
A |
9: 14,696,826 (GRCm39) |
|
probably null |
Het |
| Myo15b |
A |
G |
11: 115,776,238 (GRCm39) |
N610D |
possibly damaging |
Het |
| Nt5c1b |
T |
C |
12: 10,430,882 (GRCm39) |
S390P |
probably damaging |
Het |
| Or10ag53 |
T |
A |
2: 87,082,906 (GRCm39) |
F208L |
probably benign |
Het |
| Pde3b |
A |
G |
7: 114,122,621 (GRCm39) |
T730A |
probably damaging |
Het |
| Pdzd2 |
G |
T |
15: 12,374,342 (GRCm39) |
T1931N |
possibly damaging |
Het |
| Pla2g15 |
C |
T |
8: 106,877,201 (GRCm39) |
A28V |
probably benign |
Het |
| Pmfbp1 |
A |
T |
8: 110,268,474 (GRCm39) |
D1007V |
probably damaging |
Het |
| Polr1a |
T |
A |
6: 71,901,683 (GRCm39) |
|
probably null |
Het |
| Ppp1r3a |
T |
C |
6: 14,721,891 (GRCm39) |
K312E |
probably benign |
Het |
| Prmt5 |
G |
A |
14: 54,749,583 (GRCm39) |
T269I |
probably benign |
Het |
| Pwp2 |
A |
G |
10: 78,009,540 (GRCm39) |
S793P |
probably benign |
Het |
| Rbm12b1 |
C |
A |
4: 12,146,181 (GRCm39) |
H718N |
probably benign |
Het |
| Rfx1 |
T |
A |
8: 84,817,662 (GRCm39) |
M512K |
possibly damaging |
Het |
| Rp1 |
T |
C |
1: 4,416,789 (GRCm39) |
E1441G |
probably damaging |
Het |
| Slc16a6 |
C |
T |
11: 109,350,634 (GRCm39) |
V207I |
probably benign |
Het |
| Slc6a9 |
G |
A |
4: 117,706,596 (GRCm39) |
R7H |
possibly damaging |
Het |
| Sptlc1 |
A |
T |
13: 53,528,047 (GRCm39) |
V39D |
probably benign |
Het |
| Strc |
A |
T |
2: 121,211,336 (GRCm39) |
L3Q |
unknown |
Het |
| Svep1 |
C |
T |
4: 58,120,565 (GRCm39) |
E823K |
possibly damaging |
Het |
| Tat |
A |
G |
8: 110,725,031 (GRCm39) |
|
probably benign |
Het |
| Thoc1 |
T |
A |
18: 9,968,800 (GRCm39) |
N190K |
possibly damaging |
Het |
| Tomt |
T |
C |
7: 101,549,826 (GRCm39) |
E154G |
probably damaging |
Het |
| Topaz1 |
T |
A |
9: 122,617,887 (GRCm39) |
V1228E |
possibly damaging |
Het |
| Trim55 |
G |
A |
3: 19,727,153 (GRCm39) |
V407M |
probably benign |
Het |
| Ttll5 |
T |
A |
12: 85,873,338 (GRCm39) |
M5K |
possibly damaging |
Het |
| Ugt2a2 |
A |
C |
5: 87,609,940 (GRCm39) |
Y380* |
probably null |
Het |
| Usp46 |
A |
G |
5: 74,163,922 (GRCm39) |
Y272H |
probably benign |
Het |
| Zfp12 |
T |
A |
5: 143,230,421 (GRCm39) |
H281Q |
probably damaging |
Het |
| Zfp142 |
C |
A |
1: 74,606,302 (GRCm39) |
R1756L |
probably damaging |
Het |
| Zmynd10 |
T |
A |
9: 107,426,516 (GRCm39) |
I183K |
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 |
|
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 |
|
|
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 |
|
| Predicted Primers |
PCR Primer
(F):5'- AAGAAAGCTCTTGCCTGCCC -3'
(R):5'- AGAAAGAGCAGTATTGGTGTCC -3'
Sequencing Primer
(F):5'- GCCAGCCCTGTCCCCTC -3'
(R):5'- GGCTGCTTGATTTTGCCAAAAAG -3'
|
| Posted On |
2022-09-26 |
Incidental Mutation