Incidental Mutation 'R5954:Vps39'
| ID |
471033 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps39
|
| Ensembl Gene |
ENSMUSG00000027291 |
| Gene Name |
VPS39 HOPS complex subunit |
| Synonyms |
Vam6, Vam6P, A230065P22Rik, mVam6 |
| MMRRC Submission |
044143-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.953)
|
| Stock # |
R5954 (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 120155143 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Alanine
at position 550
(V550A)
|
| 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: V550A
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: V550A
| 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: V561A
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: V561A
| 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: ENSMUST00000145193
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000147085
|
| Meta Mutation Damage Score |
0.8140 |
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.6%
- 10x: 97.9%
- 20x: 93.5%
|
| Validation Efficiency |
100% (62/62) |
| 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: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca3 |
T |
C |
17: 24,616,390 (GRCm39) |
I944T |
probably benign |
Het |
| Ank2 |
T |
C |
3: 126,791,510 (GRCm39) |
T823A |
probably benign |
Het |
| Ankrd42 |
C |
G |
7: 92,273,175 (GRCm39) |
|
probably null |
Het |
| Anks4b |
T |
A |
7: 119,781,396 (GRCm39) |
N142K |
possibly damaging |
Het |
| Armc5 |
A |
G |
7: 127,841,444 (GRCm39) |
E484G |
probably benign |
Het |
| B4galnt3 |
A |
G |
6: 120,202,149 (GRCm39) |
F118L |
possibly damaging |
Het |
| Bbs12 |
C |
T |
3: 37,374,151 (GRCm39) |
L200F |
possibly damaging |
Het |
| Cacna1h |
A |
G |
17: 25,602,175 (GRCm39) |
F1555S |
probably damaging |
Het |
| Cds2 |
A |
G |
2: 132,139,191 (GRCm39) |
T145A |
probably benign |
Het |
| Cenps |
C |
A |
4: 149,214,658 (GRCm39) |
|
probably benign |
Het |
| Chd6 |
A |
C |
2: 160,807,747 (GRCm39) |
H1822Q |
probably benign |
Het |
| Chdh |
C |
T |
14: 29,753,138 (GRCm39) |
R16C |
possibly damaging |
Het |
| Cnga1 |
T |
C |
5: 72,762,221 (GRCm39) |
D431G |
probably damaging |
Het |
| Dock8 |
G |
A |
19: 25,148,983 (GRCm39) |
R1487Q |
probably damaging |
Het |
| Farp1 |
T |
A |
14: 121,460,079 (GRCm39) |
V116D |
probably damaging |
Het |
| Fbxo24 |
T |
A |
5: 137,617,943 (GRCm39) |
T274S |
probably damaging |
Het |
| Fmnl3 |
G |
A |
15: 99,223,791 (GRCm39) |
R302W |
probably damaging |
Het |
| Gatad2b |
T |
C |
3: 90,258,748 (GRCm39) |
L257P |
probably damaging |
Het |
| Gm20402 |
C |
T |
3: 52,176,311 (GRCm39) |
P30L |
probably damaging |
Het |
| Gm7932 |
C |
T |
6: 48,839,793 (GRCm39) |
|
noncoding transcript |
Het |
| Gpatch8 |
A |
T |
11: 102,371,767 (GRCm39) |
D590E |
unknown |
Het |
| Herc1 |
T |
G |
9: 66,358,774 (GRCm39) |
|
probably benign |
Het |
| Hsd3b2 |
T |
A |
3: 98,618,875 (GRCm39) |
I357F |
probably benign |
Het |
| Ipo5 |
A |
G |
14: 121,157,396 (GRCm39) |
Y78C |
probably damaging |
Het |
| Itga8 |
C |
A |
2: 12,137,297 (GRCm39) |
A23S |
probably damaging |
Het |
| Itgb4 |
C |
T |
11: 115,874,983 (GRCm39) |
R447W |
probably benign |
Het |
| Kat2a |
A |
G |
11: 100,599,724 (GRCm39) |
V451A |
possibly damaging |
Het |
| Knstrn |
A |
G |
2: 118,661,436 (GRCm39) |
|
probably benign |
Het |
| Med23 |
A |
G |
10: 24,746,381 (GRCm39) |
|
probably benign |
Het |
| Mefv |
A |
G |
16: 3,533,579 (GRCm39) |
Y231H |
probably benign |
Het |
| Or4d10 |
A |
T |
19: 12,051,447 (GRCm39) |
I183N |
possibly damaging |
Het |
| Or4e5 |
T |
A |
14: 52,727,624 (GRCm39) |
I266F |
probably benign |
Het |
| Or5p69 |
T |
A |
7: 107,966,808 (GRCm39) |
I37N |
probably damaging |
Het |
| Or8g21 |
A |
G |
9: 38,906,711 (GRCm39) |
S7P |
probably damaging |
Het |
| Pak5 |
G |
T |
2: 135,958,383 (GRCm39) |
T235K |
probably benign |
Het |
| Plppr3 |
G |
T |
10: 79,701,960 (GRCm39) |
P294Q |
probably benign |
Het |
| Prepl |
A |
G |
17: 85,372,077 (GRCm39) |
F725L |
probably benign |
Het |
| Ptchd3 |
A |
T |
11: 121,727,413 (GRCm39) |
|
probably benign |
Het |
| Rprd2 |
T |
C |
3: 95,672,175 (GRCm39) |
E1076G |
probably damaging |
Het |
| Sarm1 |
C |
A |
11: 78,381,428 (GRCm39) |
E352* |
probably null |
Het |
| Sccpdh |
T |
A |
1: 179,508,153 (GRCm39) |
H14Q |
probably benign |
Het |
| Senp7 |
A |
G |
16: 55,990,234 (GRCm39) |
I661V |
probably benign |
Het |
| Septin3 |
T |
C |
15: 82,174,628 (GRCm39) |
F140L |
probably damaging |
Het |
| Spag6 |
G |
T |
2: 18,715,417 (GRCm39) |
Q65H |
probably damaging |
Het |
| Tnni3 |
C |
T |
7: 4,522,539 (GRCm39) |
R137H |
probably damaging |
Het |
| Trank1 |
A |
G |
9: 111,194,201 (GRCm39) |
S742G |
probably benign |
Het |
| Ucn3 |
T |
C |
13: 3,991,413 (GRCm39) |
I80V |
probably benign |
Het |
| Ulk2 |
A |
T |
11: 61,694,622 (GRCm39) |
|
probably benign |
Het |
| Uncx |
C |
T |
5: 139,533,384 (GRCm39) |
S483L |
probably benign |
Het |
| Zfp697 |
C |
A |
3: 98,335,909 (GRCm39) |
T558K |
probably damaging |
Het |
| Zfp790 |
G |
T |
7: 29,528,929 (GRCm39) |
G538V |
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 |
|
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'- TGCCCACTTTAGCCTGTGAC -3'
(R):5'- CCATGGTTGAACAGTGAAATCC -3'
Sequencing Primer
(F):5'- ACTTTAGCCTGTGACTCCAGAG -3'
(R):5'- AGCAGATCTGAGGCTGGTGC -3'
|
| Posted On |
2017-03-31 |
Incidental Mutation