Incidental Mutation 'R4894:Vps39'
ID |
377471 |
Institutional Source |
Beutler Lab
|
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 # |
R4894 (G1)
|
Quality Score |
126 |
Status
|
Not validated
|
Chromosome |
2 |
Chromosomal Location |
120146942-120183618 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 120183440 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Isoleucine to Asparagine
at position 10
(I10N)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000099559
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028752]
[ENSMUST00000090042]
[ENSMUST00000090046]
[ENSMUST00000102501]
|
AlphaFold |
Q8R5L3 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000028752
AA Change: I10N
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000028752 Gene: ENSMUSG00000027291 AA Change: I10N
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: ENSMUST00000090042
|
SMART Domains |
Protein: ENSMUSP00000087496 Gene: ENSMUSG00000033808
Domain | Start | End | E-Value | Type |
Pfam:Lung_7-TM_R
|
184 |
471 |
1.1e-87 |
PFAM |
low complexity region
|
480 |
486 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000090046
|
SMART Domains |
Protein: ENSMUSP00000087500 Gene: ENSMUSG00000033808
Domain | Start | End | E-Value | Type |
Pfam:Lung_7-TM_R
|
185 |
472 |
1.5e-85 |
PFAM |
low complexity region
|
481 |
487 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000102501
AA Change: I10N
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000099559 Gene: ENSMUSG00000027291 AA Change: I10N
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: ENSMUST00000124806
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000126526
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000129857
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000156296
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147085
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000136410
|
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.0%
- 20x: 94.4%
|
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: 66 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adgrf1 |
C |
A |
17: 43,609,975 (GRCm39) |
Y176* |
probably null |
Het |
Akap13 |
T |
A |
7: 75,375,068 (GRCm39) |
M1900K |
possibly damaging |
Het |
Ankrd36 |
A |
G |
11: 5,585,332 (GRCm39) |
E381G |
probably damaging |
Het |
Ap3s1 |
T |
C |
18: 46,891,183 (GRCm39) |
|
probably null |
Het |
Cacna1e |
G |
T |
1: 154,364,551 (GRCm39) |
S341* |
probably null |
Het |
Camk1d |
G |
A |
2: 5,359,539 (GRCm39) |
S161L |
probably damaging |
Het |
Cdh23 |
G |
T |
10: 60,173,630 (GRCm39) |
H1619Q |
probably benign |
Het |
Chd7 |
T |
A |
4: 8,838,629 (GRCm39) |
I1276N |
probably damaging |
Het |
Clca3a1 |
A |
G |
3: 144,719,662 (GRCm39) |
V436A |
probably damaging |
Het |
Ctcfl |
G |
A |
2: 172,959,196 (GRCm39) |
P177S |
probably benign |
Het |
Dab2ip |
A |
G |
2: 35,620,539 (GRCm39) |
|
probably benign |
Het |
Dnah8 |
G |
A |
17: 30,967,542 (GRCm39) |
D2585N |
probably benign |
Het |
Epc1 |
A |
T |
18: 6,449,011 (GRCm39) |
S495R |
probably benign |
Het |
Espl1 |
A |
G |
15: 102,230,758 (GRCm39) |
|
probably null |
Het |
Eya4 |
T |
C |
10: 22,985,753 (GRCm39) |
E583G |
possibly damaging |
Het |
Fam111a |
C |
G |
19: 12,565,913 (GRCm39) |
T554R |
probably benign |
Het |
Fbh1 |
A |
T |
2: 11,767,771 (GRCm39) |
I359N |
probably damaging |
Het |
Fer1l6 |
T |
C |
15: 58,490,751 (GRCm39) |
C1023R |
probably damaging |
Het |
Helz2 |
G |
C |
2: 180,877,940 (GRCm39) |
P953A |
probably benign |
Het |
Ifi204 |
G |
T |
1: 173,587,808 (GRCm39) |
S117Y |
probably damaging |
Het |
Ift70a1 |
T |
C |
2: 75,810,088 (GRCm39) |
*665W |
probably null |
Het |
Igfn1 |
G |
A |
1: 135,882,520 (GRCm39) |
T2775M |
probably damaging |
Het |
Igsf9 |
A |
G |
1: 172,325,634 (GRCm39) |
T1101A |
probably benign |
Het |
Ipo13 |
A |
C |
4: 117,760,638 (GRCm39) |
I614S |
probably damaging |
Het |
Ipo13 |
A |
G |
4: 117,761,687 (GRCm39) |
I476T |
possibly damaging |
Het |
Kdm2b |
C |
A |
5: 123,079,030 (GRCm39) |
E308* |
probably null |
Het |
Klhl20 |
A |
T |
1: 160,937,102 (GRCm39) |
M91K |
possibly damaging |
Het |
Klrb1f |
T |
C |
6: 129,030,151 (GRCm39) |
F64L |
probably benign |
Het |
Ldlrad3 |
C |
T |
2: 101,888,293 (GRCm39) |
C106Y |
probably damaging |
Het |
Lilra6 |
T |
C |
7: 3,915,530 (GRCm39) |
T161A |
probably benign |
Het |
Lrriq1 |
A |
T |
10: 102,997,613 (GRCm39) |
M1334K |
possibly damaging |
Het |
Mepe |
C |
G |
5: 104,473,268 (GRCm39) |
P3R |
probably damaging |
Het |
Mgat4e |
A |
G |
1: 134,468,856 (GRCm39) |
V396A |
probably benign |
Het |
Nfx1 |
T |
G |
4: 40,996,877 (GRCm39) |
S651A |
probably damaging |
Het |
Or10ak13 |
A |
T |
4: 118,639,483 (GRCm39) |
C100S |
probably damaging |
Het |
Or2w6 |
T |
C |
13: 21,843,352 (GRCm39) |
N47S |
probably damaging |
Het |
Or4c109 |
T |
C |
2: 88,817,783 (GRCm39) |
I254M |
possibly damaging |
Het |
Rag2 |
T |
C |
2: 101,460,022 (GRCm39) |
S111P |
probably damaging |
Het |
Rai1 |
T |
A |
11: 60,077,572 (GRCm39) |
D545E |
probably damaging |
Het |
Ralgps1 |
A |
G |
2: 33,033,115 (GRCm39) |
V498A |
possibly damaging |
Het |
Rasal2 |
G |
A |
1: 157,020,374 (GRCm39) |
S205L |
probably damaging |
Het |
Rec8 |
T |
C |
14: 55,862,787 (GRCm39) |
L582P |
probably damaging |
Het |
Retn |
G |
A |
8: 3,707,358 (GRCm39) |
R106H |
probably damaging |
Het |
Rnf112 |
A |
G |
11: 61,343,488 (GRCm39) |
L116P |
probably damaging |
Het |
Rnf213 |
T |
C |
11: 119,372,066 (GRCm39) |
Y4885H |
probably damaging |
Het |
Sacm1l |
A |
G |
9: 123,411,409 (GRCm39) |
I399M |
probably benign |
Het |
Sez6 |
G |
T |
11: 77,866,086 (GRCm39) |
G738V |
probably damaging |
Het |
Spata17 |
A |
G |
1: 186,872,643 (GRCm39) |
V56A |
probably benign |
Het |
Spata31d1a |
A |
T |
13: 59,849,542 (GRCm39) |
V862D |
probably damaging |
Het |
Sptb |
A |
G |
12: 76,671,768 (GRCm39) |
|
probably null |
Het |
Srpk2 |
C |
A |
5: 23,750,527 (GRCm39) |
G59W |
probably damaging |
Het |
Tyro3 |
T |
C |
2: 119,632,779 (GRCm39) |
S96P |
probably damaging |
Het |
Ube2v1 |
A |
G |
2: 167,452,280 (GRCm39) |
S108P |
probably damaging |
Het |
Usp2 |
C |
T |
9: 43,987,125 (GRCm39) |
S141L |
probably benign |
Het |
Vamp5 |
T |
C |
6: 72,347,181 (GRCm39) |
D46G |
possibly damaging |
Het |
Vmn1r23 |
T |
A |
6: 57,903,310 (GRCm39) |
Q156L |
probably benign |
Het |
Vmn2r6 |
C |
T |
3: 64,454,829 (GRCm39) |
S490N |
probably benign |
Het |
Vwf |
C |
T |
6: 125,622,897 (GRCm39) |
Q1755* |
probably null |
Het |
Wdfy4 |
A |
T |
14: 32,877,717 (GRCm39) |
H82Q |
probably benign |
Het |
Wdr24 |
T |
C |
17: 26,045,101 (GRCm39) |
Y279H |
probably damaging |
Het |
Wdr72 |
A |
G |
9: 74,117,843 (GRCm39) |
T852A |
probably benign |
Het |
Zfp1 |
T |
A |
8: 112,396,355 (GRCm39) |
C92* |
probably null |
Het |
Zfp1004 |
T |
A |
2: 150,033,899 (GRCm39) |
C104* |
probably null |
Het |
Zfp426 |
A |
T |
9: 20,386,369 (GRCm39) |
|
probably benign |
Het |
Zfp442 |
C |
T |
2: 150,253,130 (GRCm39) |
|
probably null |
Het |
Zfp74 |
T |
C |
7: 29,635,470 (GRCm39) |
|
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 |
|
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'- CTTAGCAATCACGCAAGCCG -3'
(R):5'- GCAGCTGGTATGGATGTGAACTC -3'
Sequencing Primer
(F):5'- GCCCGGGGTCCAGTCAC -3'
(R):5'- GCTTAAGGCAACAGGAAGTCC -3'
|
Posted On |
2016-03-17 |