Incidental Mutation 'R5886:Vps39'
| ID |
456076 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps39
|
| Ensembl Gene |
ENSMUSG00000027291 |
| Gene Name |
VPS39 HOPS complex subunit |
| Synonyms |
Vam6, Vam6P, A230065P22Rik, mVam6 |
| MMRRC Submission |
044088-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.950)
|
| Stock # |
R5886 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
120146942-120183618 bp(-) (GRCm39) |
| Type of Mutation |
intron |
| DNA Base Change (assembly) |
A to G
at 120152053 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 |
|
| 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: 99.8%
- 3x: 99.4%
- 10x: 97.2%
- 20x: 91.0%
|
| Validation Efficiency |
96% (78/81) |
| 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: 71 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acap1 |
A |
G |
11: 69,775,162 (GRCm39) |
V367A |
probably benign |
Het |
| Adam26b |
T |
C |
8: 43,973,310 (GRCm39) |
E564G |
possibly damaging |
Het |
| Akap1 |
A |
G |
11: 88,725,486 (GRCm39) |
|
probably null |
Het |
| Akap5 |
T |
A |
12: 76,374,619 (GRCm39) |
V10E |
possibly damaging |
Het |
| Atad2 |
A |
T |
15: 57,961,910 (GRCm39) |
L887* |
probably null |
Het |
| Brd10 |
T |
C |
19: 29,696,677 (GRCm39) |
I939V |
probably benign |
Het |
| C1qbp |
A |
G |
11: 70,873,008 (GRCm39) |
V122A |
probably benign |
Het |
| C1qtnf7 |
G |
A |
5: 43,772,998 (GRCm39) |
G92D |
probably damaging |
Het |
| Cacna1a |
T |
C |
8: 85,249,651 (GRCm39) |
I219T |
probably damaging |
Het |
| Capn12 |
A |
G |
7: 28,587,030 (GRCm39) |
N333S |
probably benign |
Het |
| Ccdc154 |
C |
T |
17: 25,390,792 (GRCm39) |
T644I |
probably benign |
Het |
| Cd200r1 |
T |
C |
16: 44,610,566 (GRCm39) |
S225P |
possibly damaging |
Het |
| Cntnap5a |
T |
C |
1: 116,499,402 (GRCm39) |
|
probably null |
Het |
| Coq4 |
A |
T |
2: 29,680,626 (GRCm39) |
|
probably benign |
Het |
| Cubn |
A |
T |
2: 13,324,834 (GRCm39) |
|
probably benign |
Het |
| Cyp4f17 |
A |
T |
17: 32,743,013 (GRCm39) |
S229C |
possibly damaging |
Het |
| Cysltr2 |
T |
C |
14: 73,266,931 (GRCm39) |
K260E |
probably benign |
Het |
| D930007J09Rik |
C |
A |
13: 32,986,819 (GRCm39) |
A200E |
probably benign |
Het |
| Dnah8 |
C |
T |
17: 31,013,691 (GRCm39) |
P3811S |
probably damaging |
Het |
| Duoxa1 |
A |
T |
2: 122,134,291 (GRCm39) |
S276T |
possibly damaging |
Het |
| Efcab15 |
A |
G |
11: 103,098,947 (GRCm39) |
|
probably null |
Het |
| Efhb |
T |
C |
17: 53,758,582 (GRCm39) |
I351M |
probably benign |
Het |
| Fat1 |
G |
A |
8: 45,480,718 (GRCm39) |
|
probably null |
Het |
| Fat1 |
A |
T |
8: 45,486,432 (GRCm39) |
T3329S |
probably damaging |
Het |
| Gad1-ps |
G |
A |
10: 99,281,009 (GRCm39) |
|
noncoding transcript |
Het |
| Gm973 |
T |
A |
1: 59,597,409 (GRCm39) |
|
probably benign |
Het |
| Gpr156 |
T |
A |
16: 37,799,375 (GRCm39) |
L124Q |
probably damaging |
Het |
| Hars2 |
T |
A |
18: 36,923,150 (GRCm39) |
|
probably benign |
Het |
| Hcrt |
G |
A |
11: 100,652,759 (GRCm39) |
A85V |
probably damaging |
Het |
| Hivep1 |
A |
G |
13: 42,310,088 (GRCm39) |
D776G |
probably damaging |
Het |
| Hmgcr |
A |
T |
13: 96,796,691 (GRCm39) |
S200T |
probably damaging |
Het |
| Krt40 |
C |
T |
11: 99,430,907 (GRCm39) |
A201T |
probably benign |
Het |
| Lca5 |
G |
A |
9: 83,281,734 (GRCm39) |
A350V |
probably benign |
Het |
| Lrig2 |
T |
A |
3: 104,370,014 (GRCm39) |
M515L |
probably benign |
Het |
| Mbd5 |
A |
G |
2: 49,162,464 (GRCm39) |
D90G |
probably damaging |
Het |
| Mfsd4a |
C |
T |
1: 131,995,465 (GRCm39) |
V56I |
probably damaging |
Het |
| Mpi |
A |
G |
9: 57,455,745 (GRCm39) |
|
probably benign |
Het |
| Mroh4 |
G |
T |
15: 74,478,296 (GRCm39) |
D935E |
possibly damaging |
Het |
| Mtg1 |
G |
T |
7: 139,729,778 (GRCm39) |
|
probably null |
Het |
| Nanos1 |
T |
A |
19: 60,745,268 (GRCm39) |
C189S |
probably damaging |
Het |
| Naprt |
A |
C |
15: 75,763,324 (GRCm39) |
|
probably null |
Het |
| Nubpl |
T |
A |
12: 52,228,092 (GRCm39) |
|
probably null |
Het |
| Or10ad1b |
T |
C |
15: 98,124,672 (GRCm39) |
T285A |
possibly damaging |
Het |
| Or10d4 |
G |
T |
9: 39,581,252 (GRCm39) |
V300L |
probably benign |
Het |
| Or8g23 |
T |
A |
9: 38,971,678 (GRCm39) |
T95S |
probably benign |
Het |
| Or9g20 |
A |
G |
2: 85,630,147 (GRCm39) |
S156P |
probably damaging |
Het |
| Otud4 |
T |
A |
8: 80,399,436 (GRCm39) |
Y717N |
probably damaging |
Het |
| Pakap |
T |
A |
4: 57,856,295 (GRCm39) |
D582E |
probably damaging |
Het |
| Pnpla1 |
T |
C |
17: 29,095,837 (GRCm39) |
F86S |
possibly damaging |
Het |
| Prlhr |
C |
T |
19: 60,456,014 (GRCm39) |
W184* |
probably null |
Het |
| Rtp3 |
A |
G |
9: 110,816,204 (GRCm39) |
S116P |
probably damaging |
Het |
| Sema3c |
T |
C |
5: 17,886,984 (GRCm39) |
I345T |
possibly damaging |
Het |
| Skor2 |
T |
C |
18: 76,947,124 (GRCm39) |
L282P |
unknown |
Het |
| Slc24a4 |
T |
C |
12: 102,226,674 (GRCm39) |
V468A |
probably damaging |
Het |
| Slfn8 |
C |
T |
11: 82,894,160 (GRCm39) |
M826I |
probably benign |
Het |
| Tacc2 |
A |
G |
7: 130,330,850 (GRCm39) |
D378G |
probably benign |
Het |
| Thbs3 |
C |
A |
3: 89,127,470 (GRCm39) |
D370E |
probably damaging |
Het |
| Tk1 |
CC |
GA |
11: 117,707,948 (GRCm39) |
|
probably benign |
Het |
| Tm7sf2 |
A |
G |
19: 6,116,572 (GRCm39) |
|
probably benign |
Het |
| Trappc8 |
T |
C |
18: 21,007,737 (GRCm39) |
Y126C |
probably damaging |
Het |
| Trim35 |
C |
G |
14: 66,541,502 (GRCm39) |
L209V |
possibly damaging |
Het |
| Trim35 |
T |
C |
14: 66,541,503 (GRCm39) |
L209P |
probably damaging |
Het |
| Trip12 |
C |
T |
1: 84,708,179 (GRCm39) |
|
probably benign |
Het |
| Trp53bp1 |
A |
G |
2: 121,035,502 (GRCm39) |
V1583A |
probably damaging |
Het |
| Tuba5-ps |
A |
G |
1: 134,447,937 (GRCm39) |
|
noncoding transcript |
Het |
| Tubgcp6 |
A |
T |
15: 88,987,450 (GRCm39) |
N1166K |
possibly damaging |
Het |
| Usp54 |
C |
T |
14: 20,611,910 (GRCm39) |
D969N |
probably benign |
Het |
| Vldlr |
C |
A |
19: 27,221,171 (GRCm39) |
S612R |
probably benign |
Het |
| Vps13a |
T |
C |
19: 16,641,926 (GRCm39) |
T2234A |
probably benign |
Het |
| Zdhhc3 |
A |
T |
9: 122,920,146 (GRCm39) |
C120S |
probably benign |
Het |
| Zfp37 |
A |
G |
4: 62,109,471 (GRCm39) |
F531S |
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 |
|
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'- ATCACCTCATCCTAGGGACAGG -3'
(R):5'- CTCACAGAGATGAGCAGCCATG -3'
Sequencing Primer
(F):5'- TCATCCTAGGGACAGGGTGGG -3'
(R):5'- AGAGGGCATTTCACCTCCC -3'
|
| Posted On |
2017-02-15 |
Incidental Mutation