Incidental Mutation 'R8787:Vps39'
ID |
670684 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Vps39
|
Ensembl Gene |
ENSMUSG00000027291 |
Gene Name |
VPS39 HOPS complex subunit |
Synonyms |
Vam6, Vam6P, A230065P22Rik, mVam6 |
MMRRC Submission |
068633-MU
|
Accession Numbers |
|
Essential gene? |
Probably essential
(E-score: 0.953)
|
Stock # |
R8787 (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 G
at 120172506 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Serine to Proline
at position 176
(S176P)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000099559
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028752]
[ENSMUST00000102501]
|
AlphaFold |
Q8R5L3 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000028752
AA Change: S165P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000028752 Gene: ENSMUSG00000027291 AA Change: S165P
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: S176P
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000099559 Gene: ENSMUSG00000027291 AA Change: S176P
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 |
|
Meta Mutation Damage Score |
0.7653 |
Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.1%
|
Validation Efficiency |
98% (62/63) |
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: 63 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca13 |
C |
T |
11: 9,225,053 (GRCm39) |
H511Y |
possibly damaging |
Het |
Acp5 |
G |
A |
9: 22,038,489 (GRCm39) |
R271* |
probably null |
Het |
Adamts20 |
A |
T |
15: 94,184,294 (GRCm39) |
V1503E |
possibly damaging |
Het |
Adra2b |
A |
T |
2: 127,206,417 (GRCm39) |
E311D |
probably benign |
Het |
Aldh18a1 |
T |
C |
19: 40,546,230 (GRCm39) |
I556V |
possibly damaging |
Het |
Alox12 |
C |
A |
11: 70,144,146 (GRCm39) |
A116S |
probably benign |
Het |
Alox5 |
G |
T |
6: 116,390,102 (GRCm39) |
A552E |
probably damaging |
Het |
Angpt1 |
G |
T |
15: 42,375,780 (GRCm39) |
L159I |
probably damaging |
Het |
Atp2b4 |
CTT |
CTTTTT |
1: 133,629,485 (GRCm39) |
|
probably benign |
Het |
Bub1b |
T |
A |
2: 118,462,305 (GRCm39) |
L726I |
probably damaging |
Het |
Ccdc78 |
A |
T |
17: 26,006,807 (GRCm39) |
T165S |
probably benign |
Het |
Ccdc88b |
T |
C |
19: 6,824,791 (GRCm39) |
D1323G |
probably damaging |
Het |
Chek1 |
A |
T |
9: 36,625,033 (GRCm39) |
C349* |
probably null |
Het |
Clec1a |
A |
T |
6: 129,428,617 (GRCm39) |
L21Q |
possibly damaging |
Het |
Col1a1 |
T |
C |
11: 94,833,634 (GRCm39) |
V445A |
possibly damaging |
Het |
Efcab7 |
A |
G |
4: 99,757,791 (GRCm39) |
T313A |
probably null |
Het |
Fads1 |
T |
A |
19: 10,170,325 (GRCm39) |
Y288* |
probably null |
Het |
Fgb |
T |
A |
3: 82,953,969 (GRCm39) |
T90S |
probably benign |
Het |
Glg1 |
C |
A |
8: 111,888,114 (GRCm39) |
V1026L |
probably damaging |
Het |
Hadh |
T |
A |
3: 131,027,825 (GRCm39) |
Y313F |
probably damaging |
Het |
Htr4 |
A |
G |
18: 62,570,853 (GRCm39) |
I303V |
possibly damaging |
Het |
Kcnn3 |
A |
G |
3: 89,552,757 (GRCm39) |
D487G |
possibly damaging |
Het |
L1td1 |
G |
A |
4: 98,625,814 (GRCm39) |
V604I |
probably benign |
Het |
Lao1 |
A |
G |
4: 118,825,565 (GRCm39) |
T462A |
probably damaging |
Het |
Lefty1 |
C |
A |
1: 180,764,118 (GRCm39) |
A86E |
probably damaging |
Het |
Lmx1b |
T |
C |
2: 33,529,522 (GRCm39) |
Y79C |
|
Het |
Lrp2 |
A |
G |
2: 69,382,745 (GRCm39) |
C47R |
probably damaging |
Het |
Mrc2 |
A |
T |
11: 105,238,465 (GRCm39) |
N1204I |
probably benign |
Het |
Ncf1 |
A |
C |
5: 134,254,145 (GRCm39) |
Y209* |
probably null |
Het |
Or14j7 |
T |
A |
17: 38,235,075 (GRCm39) |
M206K |
probably benign |
Het |
Or2ad1 |
A |
T |
13: 21,326,453 (GRCm39) |
M258K |
possibly damaging |
Het |
Or8k33 |
G |
A |
2: 86,384,297 (GRCm39) |
T57M |
probably damaging |
Het |
Oxtr |
T |
G |
6: 112,466,871 (GRCm39) |
|
probably benign |
Het |
Pcdhac1 |
T |
C |
18: 37,224,942 (GRCm39) |
V585A |
probably damaging |
Het |
Pdcd11 |
T |
G |
19: 47,097,019 (GRCm39) |
L755R |
probably damaging |
Het |
Pkhd1 |
A |
G |
1: 20,358,461 (GRCm39) |
V2705A |
probably damaging |
Het |
Plch2 |
C |
A |
4: 155,070,875 (GRCm39) |
G1168V |
probably benign |
Het |
Prpf39 |
T |
C |
12: 65,089,555 (GRCm39) |
Y98H |
possibly damaging |
Het |
R3hdm2 |
T |
G |
10: 127,293,521 (GRCm39) |
S142A |
probably damaging |
Het |
Rassf10 |
T |
A |
7: 112,554,738 (GRCm39) |
D446E |
probably benign |
Het |
Rgs13 |
T |
C |
1: 144,016,482 (GRCm39) |
Y87C |
probably damaging |
Het |
Serpinb9h |
G |
A |
13: 33,588,204 (GRCm39) |
R263H |
probably benign |
Het |
Smpd3 |
G |
A |
8: 106,982,377 (GRCm39) |
R576C |
probably damaging |
Het |
Spata31e1 |
T |
C |
13: 49,938,704 (GRCm39) |
Y1002C |
probably damaging |
Het |
Srsf11 |
A |
T |
3: 157,718,037 (GRCm39) |
D382E |
unknown |
Het |
Stpg1 |
T |
A |
4: 135,261,108 (GRCm39) |
M306K |
probably benign |
Het |
Svil |
C |
T |
18: 5,059,332 (GRCm39) |
Q696* |
probably null |
Het |
Syna |
C |
T |
5: 134,588,723 (GRCm39) |
M75I |
probably benign |
Het |
Synj2 |
T |
C |
17: 6,036,514 (GRCm39) |
F161S |
possibly damaging |
Het |
Tek |
T |
C |
4: 94,738,037 (GRCm39) |
Y696H |
probably damaging |
Het |
Tgfbr1 |
A |
T |
4: 47,405,555 (GRCm39) |
D386V |
possibly damaging |
Het |
Tgm4 |
G |
T |
9: 122,890,910 (GRCm39) |
G503V |
probably damaging |
Het |
Tnni3k |
T |
C |
3: 154,645,691 (GRCm39) |
E461G |
probably damaging |
Het |
Tom1l1 |
A |
T |
11: 90,561,931 (GRCm39) |
H232Q |
probably benign |
Het |
Ubqln5 |
T |
C |
7: 103,778,329 (GRCm39) |
N165S |
probably benign |
Het |
Vmn1r24 |
G |
A |
6: 57,932,958 (GRCm39) |
L187F |
probably benign |
Het |
Vmn2r82 |
C |
T |
10: 79,213,894 (GRCm39) |
T160I |
probably damaging |
Het |
Vmn2r96 |
G |
T |
17: 18,818,250 (GRCm39) |
G801V |
probably damaging |
Het |
Vsig10 |
C |
A |
5: 117,472,981 (GRCm39) |
H191Q |
probably benign |
Het |
Wtap |
G |
A |
17: 13,186,488 (GRCm39) |
S353L |
possibly damaging |
Het |
Zmym4 |
T |
G |
4: 126,816,953 (GRCm39) |
R248S |
probably benign |
Het |
Zscan10 |
A |
G |
17: 23,829,011 (GRCm39) |
S518G |
probably benign |
Het |
Zscan29 |
A |
T |
2: 120,996,876 (GRCm39) |
Y282N |
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 |
|
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 |
|
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'- TGACTTGTGGAAATGCTAAGTGC -3'
(R):5'- AAGAATTGTGCTCAGGTATGGG -3'
Sequencing Primer
(F):5'- TAAGTGCACTCTCGCGC -3'
(R):5'- AGAATTGTGCTCAGGTATGGGTAGAG -3'
|
Posted On |
2021-04-30 |