Incidental Mutation 'R1625:Vps39'
| ID |
174942 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Vps39
|
| Ensembl Gene |
ENSMUSG00000027291 |
| Gene Name |
VPS39 HOPS complex subunit |
| Synonyms |
Vam6, Vam6P, A230065P22Rik, mVam6 |
| MMRRC Submission |
039662-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably essential
(E-score: 0.953)
|
| Stock # |
R1625 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
2 |
| Chromosomal Location |
120146942-120183618 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to T
at 120154106 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Methionine
at position 630
(V630M)
|
| 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: V619M
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000028752
Gene: ENSMUSG00000027291
AA Change: V619M
| 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: V630M
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000099559
Gene: ENSMUSG00000027291
AA Change: V630M
| 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: 99.0%
- 3x: 98.1%
- 10x: 95.3%
- 20x: 89.1%
|
| 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: 70 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca8b |
T |
A |
11: 109,857,947 (GRCm39) |
M605L |
probably benign |
Het |
| Abcc5 |
A |
T |
16: 20,184,567 (GRCm39) |
S1031T |
probably damaging |
Het |
| Acot7 |
T |
A |
4: 152,270,748 (GRCm39) |
C31S |
probably benign |
Het |
| Acss3 |
A |
T |
10: 106,773,263 (GRCm39) |
|
probably null |
Het |
| Adipor1 |
T |
C |
1: 134,351,802 (GRCm39) |
F83S |
possibly damaging |
Het |
| Agrn |
G |
A |
4: 156,257,317 (GRCm39) |
S1171L |
probably damaging |
Het |
| Aoc1l1 |
T |
A |
6: 48,952,105 (GRCm39) |
L10Q |
probably damaging |
Het |
| Arhgap5 |
T |
A |
12: 52,564,159 (GRCm39) |
C377S |
probably benign |
Het |
| Arid4b |
T |
A |
13: 14,361,699 (GRCm39) |
V721D |
probably damaging |
Het |
| Aspm |
G |
A |
1: 139,408,777 (GRCm39) |
A2555T |
probably benign |
Het |
| Atp6v0a1 |
T |
A |
11: 100,946,380 (GRCm39) |
L791Q |
probably damaging |
Het |
| Car11 |
A |
G |
7: 45,350,731 (GRCm39) |
K76E |
probably benign |
Het |
| Casp8ap2 |
T |
A |
4: 32,648,068 (GRCm39) |
M1925K |
probably benign |
Het |
| Cc2d1a |
A |
T |
8: 84,866,001 (GRCm39) |
L418Q |
probably damaging |
Het |
| Ccl9 |
G |
A |
11: 83,466,736 (GRCm39) |
R64W |
probably damaging |
Het |
| Cfap20dc |
A |
G |
14: 8,431,668 (GRCm38) |
Y655H |
probably damaging |
Het |
| Cfap43 |
T |
A |
19: 47,739,527 (GRCm39) |
K1325N |
probably damaging |
Het |
| Dars2 |
G |
A |
1: 160,881,614 (GRCm39) |
P305L |
possibly damaging |
Het |
| Ddx11 |
C |
T |
17: 66,457,692 (GRCm39) |
T859I |
probably benign |
Het |
| Dock7 |
C |
T |
4: 98,850,433 (GRCm39) |
|
probably null |
Het |
| Efcab6 |
A |
G |
15: 83,831,839 (GRCm39) |
V570A |
probably benign |
Het |
| Fermt1 |
T |
A |
2: 132,764,751 (GRCm39) |
I369F |
probably damaging |
Het |
| Fras1 |
A |
G |
5: 96,861,849 (GRCm39) |
Y2161C |
probably damaging |
Het |
| Fras1 |
C |
A |
5: 96,857,837 (GRCm39) |
P2044T |
possibly damaging |
Het |
| Gucy1a1 |
T |
C |
3: 82,009,362 (GRCm39) |
I549V |
probably benign |
Het |
| Hspg2 |
G |
A |
4: 137,246,282 (GRCm39) |
S1020N |
probably benign |
Het |
| Kif21a |
A |
G |
15: 90,826,378 (GRCm39) |
S1360P |
probably damaging |
Het |
| Lrp3 |
T |
C |
7: 34,903,350 (GRCm39) |
Y332C |
probably damaging |
Het |
| Ltc4s |
C |
A |
11: 50,128,215 (GRCm39) |
A32S |
possibly damaging |
Het |
| Mgrn1 |
T |
C |
16: 4,728,627 (GRCm39) |
L84P |
probably damaging |
Het |
| Muc2 |
C |
G |
7: 141,283,405 (GRCm39) |
C672W |
probably damaging |
Het |
| Mvp |
A |
T |
7: 126,600,845 (GRCm39) |
V52E |
probably damaging |
Het |
| Ndrg2 |
T |
C |
14: 52,144,420 (GRCm39) |
T269A |
probably damaging |
Het |
| Notch2 |
T |
A |
3: 98,018,891 (GRCm39) |
D684E |
probably damaging |
Het |
| Nup205 |
A |
G |
6: 35,168,878 (GRCm39) |
D316G |
probably benign |
Het |
| Or12e7 |
T |
A |
2: 87,288,016 (GRCm39) |
I169K |
probably damaging |
Het |
| Or2v2 |
T |
C |
11: 49,004,071 (GRCm39) |
M161V |
probably benign |
Het |
| Or7d11 |
A |
G |
9: 19,966,678 (GRCm39) |
L27P |
probably damaging |
Het |
| Pcsk1 |
A |
T |
13: 75,274,971 (GRCm39) |
D520V |
probably benign |
Het |
| Pik3cg |
A |
T |
12: 32,244,741 (GRCm39) |
D904E |
probably damaging |
Het |
| Pitpnm2 |
T |
A |
5: 124,271,496 (GRCm39) |
D359V |
probably benign |
Het |
| Ppih |
T |
C |
4: 119,175,779 (GRCm39) |
I69V |
probably damaging |
Het |
| Rab11fip3 |
T |
C |
17: 26,287,865 (GRCm39) |
E96G |
possibly damaging |
Het |
| Retreg3 |
C |
A |
11: 100,992,875 (GRCm39) |
M1I |
probably null |
Het |
| Rfpl4 |
C |
T |
7: 5,118,409 (GRCm39) |
V54I |
possibly damaging |
Het |
| Rif1 |
T |
C |
2: 51,993,652 (GRCm39) |
I855T |
probably benign |
Het |
| Rrm1 |
T |
A |
7: 102,117,554 (GRCm39) |
I748N |
probably damaging |
Het |
| Sap130 |
T |
A |
18: 31,807,517 (GRCm39) |
N441K |
probably damaging |
Het |
| Sf3b1 |
T |
A |
1: 55,058,536 (GRCm39) |
I18F |
probably damaging |
Het |
| Skor2 |
A |
G |
18: 76,946,499 (GRCm39) |
N74D |
unknown |
Het |
| Slc17a6 |
C |
A |
7: 51,311,208 (GRCm39) |
F307L |
probably benign |
Het |
| Slc25a13 |
G |
A |
6: 6,096,675 (GRCm39) |
L410F |
probably damaging |
Het |
| Slc47a1 |
A |
T |
11: 61,262,625 (GRCm39) |
V38E |
probably damaging |
Het |
| Slc8a1 |
T |
A |
17: 81,956,670 (GRCm39) |
T123S |
probably damaging |
Het |
| Slc9a5 |
C |
A |
8: 106,094,755 (GRCm39) |
T782K |
possibly damaging |
Het |
| Spmip7 |
C |
A |
11: 11,438,644 (GRCm39) |
|
probably benign |
Het |
| Sppl2c |
C |
A |
11: 104,077,995 (GRCm39) |
T265K |
probably damaging |
Het |
| Srfbp1 |
A |
G |
18: 52,621,788 (GRCm39) |
K283R |
probably benign |
Het |
| Ssr1 |
C |
T |
13: 38,173,479 (GRCm39) |
|
probably null |
Het |
| Stard3nl |
T |
C |
13: 19,556,754 (GRCm39) |
|
probably null |
Het |
| Timeless |
G |
T |
10: 128,076,493 (GRCm39) |
S134I |
probably damaging |
Het |
| Tll1 |
A |
G |
8: 64,494,476 (GRCm39) |
F760L |
probably damaging |
Het |
| Tspear |
A |
G |
10: 77,706,333 (GRCm39) |
I368V |
probably benign |
Het |
| Txnrd2 |
G |
T |
16: 18,257,116 (GRCm39) |
W144L |
probably damaging |
Het |
| Unc5d |
T |
C |
8: 29,173,234 (GRCm39) |
E668G |
probably damaging |
Het |
| Urb1 |
C |
T |
16: 90,570,936 (GRCm39) |
|
probably null |
Het |
| Uts2r |
A |
G |
11: 121,052,033 (GRCm39) |
Y299C |
probably damaging |
Het |
| Vmn1r66 |
G |
T |
7: 10,008,316 (GRCm39) |
T239K |
probably benign |
Het |
| Wrn |
T |
C |
8: 33,819,158 (GRCm39) |
T22A |
probably benign |
Het |
| Zfp7 |
T |
A |
15: 76,765,374 (GRCm39) |
D22E |
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 |
|
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 |
|
|
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'- GGCCAGCATGTCTCTTAGCAACAC -3'
(R):5'- GTCCCTGACATCACTGGGTTTTAGC -3'
Sequencing Primer
(F):5'- CTTAGCAACACAGATGTCATTCTGC -3'
(R):5'- TTTTGGACGAGCTGCCC -3'
|
| Posted On |
2014-04-24 |
Incidental Mutation