Incidental Mutation 'R2178:Vps39'
| ID |
236976 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps39
|
| Ensembl Gene |
ENSMUSG00000027291 |
| Gene Name |
VPS39 HOPS complex subunit |
| Synonyms |
Vam6, Vam6P, A230065P22Rik, mVam6 |
| MMRRC Submission |
040180-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.953)
|
| Stock # |
R2178 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
2 |
| Chromosomal Location |
120146942-120183618 bp(-) (GRCm39) |
| Type of Mutation |
nonsense |
| DNA Base Change (assembly) |
C to A
at 120154160 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Glutamic Acid to Stop codon
at position 612
(E612*)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000099559
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028752]
[ENSMUST00000102501]
|
| AlphaFold |
Q8R5L3 |
| Predicted Effect |
probably null
Transcript: ENSMUST00000028752
AA Change: E601*
|
| SMART Domains |
Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: E601*
| 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 null
Transcript: ENSMUST00000102501
AA Change: E612*
|
| SMART Domains |
Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: E612*
| 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 |
- 1x: 99.2%
- 3x: 98.7%
- 10x: 97.6%
- 20x: 95.9%
|
| 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: 40 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Adcy6 |
A |
T |
15: 98,492,236 (GRCm39) |
N1007K |
probably damaging |
Het |
| Apon |
C |
A |
10: 128,090,634 (GRCm39) |
A104E |
probably benign |
Het |
| Cdh15 |
T |
A |
8: 123,591,715 (GRCm39) |
|
probably null |
Het |
| Cep135 |
T |
C |
5: 76,779,297 (GRCm39) |
V769A |
probably benign |
Het |
| Cep152 |
A |
T |
2: 125,421,954 (GRCm39) |
|
probably null |
Het |
| Clca3a1 |
T |
C |
3: 144,711,863 (GRCm39) |
N711D |
probably damaging |
Het |
| Col1a2 |
T |
C |
6: 4,531,143 (GRCm39) |
F731L |
unknown |
Het |
| Cpt1b |
T |
C |
15: 89,303,246 (GRCm39) |
E603G |
probably damaging |
Het |
| Cspp1 |
T |
G |
1: 10,174,471 (GRCm39) |
D641E |
possibly damaging |
Het |
| Ddr2 |
C |
T |
1: 169,822,251 (GRCm39) |
R399Q |
probably benign |
Het |
| Dzip1 |
T |
C |
14: 119,126,816 (GRCm39) |
|
probably null |
Het |
| Greb1 |
A |
G |
12: 16,746,388 (GRCm39) |
V1294A |
probably damaging |
Het |
| Hmgb4 |
A |
G |
4: 128,154,275 (GRCm39) |
S98P |
probably damaging |
Het |
| Kif12 |
G |
A |
4: 63,085,196 (GRCm39) |
P515L |
probably benign |
Het |
| Kmt5b |
A |
C |
19: 3,865,372 (GRCm39) |
E789A |
possibly damaging |
Het |
| Lama1 |
G |
T |
17: 68,076,510 (GRCm39) |
V1095F |
probably benign |
Het |
| Leprot |
T |
C |
4: 101,513,308 (GRCm39) |
V32A |
probably benign |
Het |
| Mcoln1 |
A |
G |
8: 3,558,766 (GRCm39) |
T255A |
probably damaging |
Het |
| Mertk |
G |
A |
2: 128,634,984 (GRCm39) |
E765K |
probably damaging |
Het |
| Muc5b |
A |
G |
7: 141,417,853 (GRCm39) |
T3600A |
possibly damaging |
Het |
| Ncapd3 |
A |
T |
9: 26,999,845 (GRCm39) |
E1395V |
probably benign |
Het |
| Ntrk2 |
T |
C |
13: 58,956,616 (GRCm39) |
F25S |
probably benign |
Het |
| Or2a5 |
A |
G |
6: 42,873,732 (GRCm39) |
M116V |
probably benign |
Het |
| Or6z1 |
G |
T |
7: 6,504,487 (GRCm39) |
A246D |
probably damaging |
Het |
| Or7c70 |
T |
A |
10: 78,683,612 (GRCm39) |
I46F |
probably damaging |
Het |
| Pappa |
C |
A |
4: 65,269,924 (GRCm39) |
H1613N |
probably benign |
Het |
| Polq |
T |
C |
16: 36,883,191 (GRCm39) |
V1785A |
probably damaging |
Het |
| Pramel23 |
A |
T |
4: 143,424,612 (GRCm39) |
I277K |
possibly damaging |
Het |
| Prkar2a |
T |
C |
9: 108,617,737 (GRCm39) |
|
probably null |
Het |
| Qrich2 |
T |
C |
11: 116,334,603 (GRCm39) |
D2194G |
probably damaging |
Het |
| Rnf183 |
T |
C |
4: 62,346,333 (GRCm39) |
N155S |
probably benign |
Het |
| S1pr5 |
T |
C |
9: 21,155,760 (GRCm39) |
N222S |
probably benign |
Het |
| Scnn1a |
C |
T |
6: 125,307,965 (GRCm39) |
R170C |
probably damaging |
Het |
| Slc25a2 |
T |
C |
18: 37,771,311 (GRCm39) |
T73A |
probably benign |
Het |
| Tgfb1 |
A |
G |
7: 25,404,234 (GRCm39) |
N347S |
probably damaging |
Het |
| Ticrr |
T |
C |
7: 79,315,433 (GRCm39) |
V229A |
probably benign |
Het |
| Tjp3 |
T |
C |
10: 81,115,941 (GRCm39) |
E313G |
probably benign |
Het |
| Tnfsf11 |
A |
G |
14: 78,521,682 (GRCm39) |
S176P |
probably benign |
Het |
| Vmn2r68 |
TCC |
TC |
7: 84,870,758 (GRCm39) |
|
probably null |
Het |
| Vwf |
T |
A |
6: 125,619,095 (GRCm39) |
Y1258N |
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 |
|
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 |
|
| Predicted Primers |
PCR Primer
(F):5'- CAGTGTCTCTGACTCCTCTAAAGG -3'
(R):5'- CCTGACATCACTGGGTTTTAGC -3'
Sequencing Primer
(F):5'- GGACTTCCTGTCTACCTGGAGAAC -3'
(R):5'- CATAGTTTTTGGACGAGCTGCCC -3'
|
| Posted On |
2014-10-02 |
Incidental Mutation