Incidental Mutation 'R5949:Vps39'
| ID |
472312 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps39
|
| Ensembl Gene |
ENSMUSG00000027291 |
| Gene Name |
VPS39 HOPS complex subunit |
| Synonyms |
Vam6, Vam6P, A230065P22Rik, mVam6 |
| MMRRC Submission |
044139-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.950)
|
| Stock # |
R5949 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
2 |
| Chromosomal Location |
120146942-120183618 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 120159149 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Histidine
at position 380
(Y380H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000028752
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000028752]
[ENSMUST00000102501]
|
| AlphaFold |
Q8R5L3 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000028752
AA Change: Y380H
PolyPhen 2
Score 0.226 (Sensitivity: 0.91; Specificity: 0.88)
|
| SMART Domains |
Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: Y380H
| 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
AA Change: Y391H
PolyPhen 2
Score 0.142 (Sensitivity: 0.92; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: Y391H
| 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 |
0.0640 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 98.0%
- 20x: 94.1%
|
| Validation Efficiency |
92% (58/63) |
| 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: 50 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| A2m |
A |
G |
6: 121,655,032 (GRCm39) |
Y1452C |
probably damaging |
Het |
| Adcy10 |
A |
T |
1: 165,367,386 (GRCm39) |
H552L |
possibly damaging |
Het |
| Alms1-ps1 |
A |
T |
6: 85,698,943 (GRCm39) |
|
noncoding transcript |
Het |
| Arhgap21 |
A |
G |
2: 20,853,852 (GRCm39) |
S1837P |
probably damaging |
Het |
| Atad5 |
G |
T |
11: 79,986,835 (GRCm39) |
E641* |
probably null |
Het |
| Atp8b4 |
T |
A |
2: 126,247,242 (GRCm39) |
T276S |
probably benign |
Het |
| Bptf |
A |
G |
11: 107,001,915 (GRCm39) |
I399T |
probably damaging |
Het |
| Carf |
A |
C |
1: 60,178,472 (GRCm39) |
K295T |
probably damaging |
Het |
| Cd209d |
T |
A |
8: 3,927,949 (GRCm39) |
N52Y |
possibly damaging |
Het |
| Cdh2 |
T |
A |
18: 16,734,687 (GRCm39) |
I779F |
probably damaging |
Het |
| Cdon |
G |
A |
9: 35,398,247 (GRCm39) |
R988H |
probably benign |
Het |
| Cfhr4 |
A |
T |
1: 139,660,887 (GRCm39) |
H600Q |
probably damaging |
Het |
| Cic |
C |
T |
7: 24,971,730 (GRCm39) |
T487M |
probably damaging |
Het |
| Dcps |
A |
G |
9: 35,036,557 (GRCm39) |
|
probably benign |
Het |
| Ddx41 |
A |
G |
13: 55,679,874 (GRCm39) |
C427R |
probably damaging |
Het |
| Diras2 |
T |
C |
13: 52,661,747 (GRCm39) |
K187E |
possibly damaging |
Het |
| Emb |
A |
G |
13: 117,403,928 (GRCm39) |
I227V |
probably benign |
Het |
| Fam193a |
T |
A |
5: 34,597,816 (GRCm39) |
S538T |
possibly damaging |
Het |
| Fchsd1 |
C |
T |
18: 38,092,926 (GRCm39) |
|
probably benign |
Het |
| Galnt6 |
A |
T |
15: 100,594,431 (GRCm39) |
N533K |
probably damaging |
Het |
| Grip1 |
A |
G |
10: 119,886,147 (GRCm39) |
D499G |
probably benign |
Het |
| Ifih1 |
T |
C |
2: 62,440,904 (GRCm39) |
N421D |
probably benign |
Het |
| Ifng |
G |
C |
10: 118,278,529 (GRCm39) |
M63I |
probably benign |
Het |
| Ighv1-43 |
A |
G |
12: 114,910,002 (GRCm39) |
M1T |
probably null |
Het |
| Kif20a |
G |
A |
18: 34,765,468 (GRCm39) |
A822T |
probably benign |
Het |
| Krt87 |
A |
T |
15: 101,385,476 (GRCm39) |
C299S |
probably damaging |
Het |
| Lrrn1 |
G |
T |
6: 107,544,465 (GRCm39) |
V88L |
probably benign |
Het |
| Mapkapk2 |
A |
G |
1: 130,985,742 (GRCm39) |
V173A |
possibly damaging |
Het |
| Mrap2 |
T |
G |
9: 87,064,658 (GRCm39) |
V133G |
probably benign |
Het |
| Nlrp1a |
T |
A |
11: 70,989,815 (GRCm39) |
D984V |
probably damaging |
Het |
| Or4c125 |
A |
G |
2: 89,170,229 (GRCm39) |
V139A |
probably damaging |
Het |
| Or5p59 |
T |
C |
7: 107,703,404 (GRCm39) |
L296P |
probably damaging |
Het |
| Pcdh17 |
T |
C |
14: 84,684,996 (GRCm39) |
Y488H |
probably damaging |
Het |
| Pih1d2 |
C |
T |
9: 50,536,284 (GRCm39) |
P313L |
probably damaging |
Het |
| Ralgapb |
T |
C |
2: 158,296,179 (GRCm39) |
C839R |
probably damaging |
Het |
| Rdh5 |
C |
A |
10: 128,754,136 (GRCm39) |
R29L |
probably benign |
Het |
| Rfx6 |
A |
G |
10: 51,554,429 (GRCm39) |
D90G |
probably benign |
Het |
| Rnf213 |
A |
G |
11: 119,333,905 (GRCm39) |
Y3038C |
probably damaging |
Het |
| Sec14l2 |
A |
T |
11: 4,058,972 (GRCm39) |
V191D |
probably damaging |
Het |
| Slc3a2 |
T |
C |
19: 8,690,759 (GRCm39) |
Y118C |
probably damaging |
Het |
| Sorbs2 |
T |
C |
8: 46,222,934 (GRCm39) |
|
probably null |
Het |
| Stab2 |
A |
G |
10: 86,805,713 (GRCm39) |
L211P |
possibly damaging |
Het |
| Tbc1d9b |
T |
C |
11: 50,038,876 (GRCm39) |
C289R |
probably benign |
Het |
| Tfpi |
T |
C |
2: 84,275,092 (GRCm39) |
E172G |
probably benign |
Het |
| Tmem106b |
T |
A |
6: 13,083,418 (GRCm39) |
M229K |
probably damaging |
Het |
| Tsfm |
G |
A |
10: 126,864,244 (GRCm39) |
T157M |
probably damaging |
Het |
| Tshr |
G |
A |
12: 91,503,992 (GRCm39) |
R310H |
probably damaging |
Het |
| Ttn |
G |
A |
2: 76,608,244 (GRCm39) |
A17893V |
possibly damaging |
Het |
| Xylt2 |
G |
A |
11: 94,559,309 (GRCm39) |
R383C |
probably damaging |
Het |
| Zfp719 |
C |
T |
7: 43,233,541 (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 |
|
|
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 |
|
|
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'- TTGCTGCCACAGTGAAGCAG -3'
(R):5'- TAGACTCATTTCCTAGGGTGAGAG -3'
Sequencing Primer
(F):5'- GCAGTGCTGGAACTCTGAG -3'
(R):5'- CCAGCCTGGTTTATGTAATAAGGCC -3'
|
| Posted On |
2017-03-31 |
Incidental Mutation