Incidental Mutation 'R6208:Vps39'
ID |
503245 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps39
|
Ensembl Gene |
ENSMUSG00000027291 |
Gene Name |
VPS39 HOPS complex subunit |
Synonyms |
Vam6, Vam6P, A230065P22Rik, mVam6 |
MMRRC Submission |
044342-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.953)
|
Stock # |
R6208 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
2 |
Chromosomal Location |
120146942-120183618 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 120163897 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Methionine to Lysine
at position 355
(M355K)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000028752
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028752]
[ENSMUST00000102501]
|
AlphaFold |
Q8R5L3 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000028752
AA Change: M355K
PolyPhen 2
Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000028752 Gene: ENSMUSG00000027291 AA Change: M355K
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 damaging
Transcript: ENSMUST00000102501
AA Change: M366K
PolyPhen 2
Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000099559 Gene: ENSMUSG00000027291 AA Change: M366K
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: ENSMUST00000147085
|
Meta Mutation Damage Score |
0.5943 |
Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.7%
|
Validation Efficiency |
98% (57/58) |
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: 60 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Actl6a |
A |
T |
3: 32,766,043 (GRCm39) |
I18F |
probably benign |
Het |
Apol11a |
C |
T |
15: 77,401,241 (GRCm39) |
R243C |
probably damaging |
Het |
Asap3 |
A |
G |
4: 135,968,508 (GRCm39) |
M687V |
probably benign |
Het |
Axdnd1 |
C |
T |
1: 156,220,426 (GRCm39) |
|
probably benign |
Het |
Baz2b |
A |
G |
2: 59,755,150 (GRCm39) |
F1026S |
probably damaging |
Het |
Bsg |
T |
C |
10: 79,544,672 (GRCm39) |
L70P |
probably damaging |
Het |
Col10a1 |
A |
G |
10: 34,270,582 (GRCm39) |
N185D |
possibly damaging |
Het |
Col6a2 |
T |
A |
10: 76,450,891 (GRCm39) |
N50I |
possibly damaging |
Het |
Cux2 |
G |
A |
5: 121,998,885 (GRCm39) |
P1352S |
possibly damaging |
Het |
Defa25 |
A |
G |
8: 21,575,197 (GRCm39) |
|
probably null |
Het |
Emc1 |
G |
T |
4: 139,081,582 (GRCm39) |
R70L |
probably damaging |
Het |
Fat1 |
T |
C |
8: 45,480,650 (GRCm39) |
F3028S |
probably damaging |
Het |
Fhit |
T |
C |
14: 9,573,435 (GRCm38) |
E205G |
probably benign |
Het |
Gaa |
C |
A |
11: 119,171,997 (GRCm39) |
A700D |
probably benign |
Het |
Gm20830 |
T |
G |
Y: 6,916,792 (GRCm39) |
E109A |
probably benign |
Homo |
Grm1 |
A |
T |
10: 10,595,690 (GRCm39) |
F646Y |
probably damaging |
Het |
Hp1bp3 |
A |
G |
4: 137,944,481 (GRCm39) |
|
probably benign |
Het |
Lce1d |
G |
A |
3: 92,593,312 (GRCm39) |
P34S |
unknown |
Het |
Lpar1 |
G |
A |
4: 58,504,630 (GRCm39) |
Q13* |
probably null |
Het |
Lrrc61 |
C |
T |
6: 48,545,839 (GRCm39) |
R221* |
probably null |
Het |
Map2 |
A |
G |
1: 66,470,749 (GRCm39) |
N328D |
probably damaging |
Het |
Mndal |
T |
A |
1: 173,684,988 (GRCm39) |
D527V |
possibly damaging |
Het |
Mycbp2 |
T |
G |
14: 103,532,664 (GRCm39) |
N430T |
probably benign |
Het |
Myo1e |
A |
G |
9: 70,283,887 (GRCm39) |
Y861C |
probably damaging |
Het |
Nav2 |
A |
G |
7: 49,213,851 (GRCm39) |
T1622A |
probably damaging |
Het |
Nom1 |
A |
T |
5: 29,654,617 (GRCm39) |
H773L |
possibly damaging |
Het |
Npc2 |
G |
T |
12: 84,803,919 (GRCm39) |
P144Q |
probably damaging |
Het |
Npnt |
A |
G |
3: 132,655,774 (GRCm39) |
|
probably benign |
Het |
Nxpe4 |
A |
T |
9: 48,304,678 (GRCm39) |
Y255F |
probably benign |
Het |
Obscn |
G |
A |
11: 58,958,474 (GRCm39) |
A3769V |
possibly damaging |
Het |
Optc |
T |
C |
1: 133,832,737 (GRCm39) |
D121G |
probably damaging |
Het |
Pard6a |
T |
C |
8: 106,428,866 (GRCm39) |
F26L |
probably damaging |
Het |
Pcdhga4 |
T |
A |
18: 37,819,762 (GRCm39) |
I437N |
probably damaging |
Het |
Phf12 |
G |
T |
11: 77,914,417 (GRCm39) |
V71F |
probably damaging |
Het |
Phf21b |
T |
A |
15: 84,679,317 (GRCm39) |
S282C |
probably damaging |
Het |
Pou5f1 |
T |
C |
17: 35,821,357 (GRCm39) |
F323S |
possibly damaging |
Het |
Psmd5 |
A |
T |
2: 34,757,023 (GRCm39) |
I67N |
probably damaging |
Het |
Pyroxd1 |
A |
G |
6: 142,303,182 (GRCm39) |
K273R |
probably benign |
Het |
Rnd2 |
C |
T |
11: 101,359,825 (GRCm39) |
L57F |
probably damaging |
Het |
Rpusd1 |
A |
T |
17: 25,949,352 (GRCm39) |
H174L |
probably damaging |
Het |
Ryr2 |
T |
C |
13: 11,910,106 (GRCm39) |
K94R |
probably benign |
Het |
Scn2b |
A |
G |
9: 45,029,328 (GRCm39) |
R3G |
probably benign |
Het |
Sf3b2 |
A |
T |
19: 5,325,126 (GRCm39) |
M782K |
possibly damaging |
Het |
Skint7 |
A |
G |
4: 111,842,073 (GRCm39) |
|
probably null |
Het |
Slc43a1 |
A |
G |
2: 84,687,184 (GRCm39) |
I319V |
possibly damaging |
Het |
Snupn |
T |
A |
9: 56,890,247 (GRCm39) |
M356K |
probably damaging |
Het |
Spata31d1a |
C |
A |
13: 59,848,378 (GRCm39) |
R1250M |
probably damaging |
Het |
Sprr2h |
T |
C |
3: 92,294,216 (GRCm39) |
V21A |
unknown |
Het |
Srpra |
A |
G |
9: 35,127,291 (GRCm39) |
T614A |
possibly damaging |
Het |
Stk36 |
A |
T |
1: 74,650,591 (GRCm39) |
Q327L |
probably benign |
Het |
Syne3 |
A |
G |
12: 104,909,622 (GRCm39) |
I738T |
probably benign |
Het |
Tcea3 |
A |
T |
4: 135,975,360 (GRCm39) |
M1L |
probably damaging |
Het |
Tead2 |
G |
T |
7: 44,867,526 (GRCm39) |
R85L |
probably damaging |
Het |
Thap7 |
T |
C |
16: 17,346,300 (GRCm39) |
N228D |
possibly damaging |
Het |
Trip11 |
T |
A |
12: 101,865,154 (GRCm39) |
E173V |
probably damaging |
Het |
Ttc38 |
T |
A |
15: 85,725,698 (GRCm39) |
M187K |
possibly damaging |
Het |
Vmn1r193 |
T |
A |
13: 22,403,138 (GRCm39) |
T285S |
possibly damaging |
Het |
Vmn2r106 |
T |
C |
17: 20,488,591 (GRCm39) |
T603A |
probably damaging |
Het |
Wnt5b |
G |
T |
6: 119,423,473 (GRCm39) |
L51I |
probably damaging |
Het |
Xxylt1 |
A |
G |
16: 30,826,626 (GRCm39) |
Y230H |
probably benign |
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 |
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'- GTGACCCTCCTAATGCCATC -3'
(R):5'- TTACCACTAAGAATGGGCAAAGC -3'
Sequencing Primer
(F):5'- TCCTAATGCCATCACATAACCAAGG -3'
(R):5'- TTTAATCCCAGCACTCGGGAG -3'
|
Posted On |
2018-02-27 |