Incidental Mutation 'R3914:Hps5'
ID |
309557 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Hps5
|
Ensembl Gene |
ENSMUSG00000014418 |
Gene Name |
HPS5, biogenesis of lysosomal organelles complex 2 subunit 2 |
Synonyms |
Hermansky-Pudlak syndrome 5, ru-2, ru2, ruby eye 2 |
MMRRC Submission |
040912-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.104)
|
Stock # |
R3914 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
7 |
Chromosomal Location |
46409890-46445488 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 46432950 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Threonine to Alanine
at position 257
(T257A)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000122887
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000014562]
[ENSMUST00000107653]
[ENSMUST00000107654]
[ENSMUST00000123725]
[ENSMUST00000142663]
[ENSMUST00000152759]
[ENSMUST00000211347]
|
AlphaFold |
P59438 |
Predicted Effect |
probably damaging
Transcript: ENSMUST00000014562
AA Change: T257A
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000014562 Gene: ENSMUSG00000014418 AA Change: T257A
Domain | Start | End | E-Value | Type |
SCOP:d1jjub_
|
44 |
192 |
3e-8 |
SMART |
Blast:WD40
|
63 |
103 |
7e-21 |
BLAST |
Blast:WD40
|
111 |
151 |
1e-19 |
BLAST |
low complexity region
|
429 |
449 |
N/A |
INTRINSIC |
low complexity region
|
775 |
786 |
N/A |
INTRINSIC |
low complexity region
|
989 |
998 |
N/A |
INTRINSIC |
low complexity region
|
1021 |
1033 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000107653
AA Change: T257A
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000103280 Gene: ENSMUSG00000014418 AA Change: T257A
Domain | Start | End | E-Value | Type |
SCOP:d1jjub_
|
44 |
192 |
3e-8 |
SMART |
Blast:WD40
|
63 |
103 |
6e-21 |
BLAST |
Blast:WD40
|
111 |
151 |
1e-19 |
BLAST |
low complexity region
|
396 |
416 |
N/A |
INTRINSIC |
low complexity region
|
742 |
753 |
N/A |
INTRINSIC |
low complexity region
|
956 |
965 |
N/A |
INTRINSIC |
low complexity region
|
988 |
1000 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000107654
AA Change: T257A
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000103281 Gene: ENSMUSG00000014418 AA Change: T257A
Domain | Start | End | E-Value | Type |
SCOP:d1jjub_
|
44 |
192 |
3e-8 |
SMART |
Blast:WD40
|
63 |
103 |
7e-21 |
BLAST |
Blast:WD40
|
111 |
151 |
1e-19 |
BLAST |
low complexity region
|
429 |
449 |
N/A |
INTRINSIC |
low complexity region
|
775 |
786 |
N/A |
INTRINSIC |
low complexity region
|
989 |
998 |
N/A |
INTRINSIC |
low complexity region
|
1021 |
1033 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000123725
|
SMART Domains |
Protein: ENSMUSP00000116770 Gene: ENSMUSG00000014418
Domain | Start | End | E-Value | Type |
SCOP:d1tbga_
|
24 |
107 |
5e-4 |
SMART |
Blast:WD40
|
63 |
103 |
1e-22 |
BLAST |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000142663
AA Change: T257A
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000122887 Gene: ENSMUSG00000014418 AA Change: T257A
Domain | Start | End | E-Value | Type |
SCOP:d1jjub_
|
44 |
192 |
8e-8 |
SMART |
Blast:WD40
|
63 |
103 |
9e-20 |
BLAST |
Blast:WD40
|
111 |
151 |
2e-19 |
BLAST |
low complexity region
|
429 |
449 |
N/A |
INTRINSIC |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000145776
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000152759
|
SMART Domains |
Protein: ENSMUSP00000115786 Gene: ENSMUSG00000014418
Domain | Start | End | E-Value | Type |
SCOP:d1jjub_
|
44 |
192 |
2e-8 |
SMART |
Blast:WD40
|
63 |
103 |
1e-21 |
BLAST |
Blast:WD40
|
111 |
151 |
2e-20 |
BLAST |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000211347
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000211528
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000211471
|
Meta Mutation Damage Score |
0.8728 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.4%
|
Validation Efficiency |
100% (36/36) |
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 play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. This protein interacts with Hermansky-Pudlak syndrome 6 protein and may interact with the cytoplasmic domain of integrin, alpha-3. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 5. Multiple transcript variants encoding two distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008] PHENOTYPE: Homozygotes have hypopigmented eyes and hair, impaired secretion of lysosomal enzymes by renal proximal tubules and reduced clotting due to a platelet dense granule defect. Homozygotes for one allele are less susceptible to diet-induced atherosclerosis. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 36 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Atp8b2 |
A |
T |
3: 89,861,755 (GRCm39) |
I266N |
probably damaging |
Het |
AU041133 |
G |
A |
10: 81,987,649 (GRCm39) |
R434Q |
probably damaging |
Het |
Ccdc174 |
G |
T |
6: 91,876,338 (GRCm39) |
A392S |
possibly damaging |
Het |
Cdh18 |
T |
C |
15: 23,410,771 (GRCm39) |
Y419H |
probably damaging |
Het |
Col20a1 |
A |
G |
2: 180,640,285 (GRCm39) |
K509R |
probably benign |
Het |
Csmd2 |
A |
T |
4: 128,215,117 (GRCm39) |
D513V |
probably benign |
Het |
Disp1 |
A |
G |
1: 182,870,666 (GRCm39) |
F585L |
probably benign |
Het |
Entpd7 |
G |
A |
19: 43,679,597 (GRCm39) |
R50Q |
probably benign |
Het |
Exoc1 |
G |
A |
5: 76,691,408 (GRCm39) |
S244N |
possibly damaging |
Het |
Fam234b |
A |
G |
6: 135,202,681 (GRCm39) |
D345G |
probably damaging |
Het |
G530012D18Rik |
CAGAGAGA |
CAGAGAGAGA |
1: 85,504,945 (GRCm39) |
|
probably null |
Het |
Gprc6a |
T |
A |
10: 51,504,371 (GRCm39) |
M158L |
probably benign |
Het |
Hdc |
T |
C |
2: 126,444,926 (GRCm39) |
T255A |
probably damaging |
Het |
Ice1 |
A |
G |
13: 70,754,203 (GRCm39) |
C628R |
probably benign |
Het |
Igkv2-137 |
A |
T |
6: 67,532,968 (GRCm39) |
R44W |
probably damaging |
Het |
Islr2 |
A |
T |
9: 58,105,666 (GRCm39) |
Y531* |
probably null |
Het |
Mast4 |
G |
A |
13: 102,875,829 (GRCm39) |
R1112* |
probably null |
Het |
Mrc2 |
T |
C |
11: 105,238,058 (GRCm39) |
|
probably benign |
Het |
Myo19 |
G |
A |
11: 84,785,429 (GRCm39) |
R224H |
probably damaging |
Het |
Nup58 |
A |
G |
14: 60,469,596 (GRCm39) |
M375T |
possibly damaging |
Het |
Phaf1 |
A |
G |
8: 105,966,615 (GRCm39) |
N121D |
probably benign |
Het |
Phldb2 |
T |
C |
16: 45,577,526 (GRCm39) |
E1133G |
probably damaging |
Het |
Rabl6 |
T |
C |
2: 25,478,718 (GRCm39) |
T238A |
possibly damaging |
Het |
Ranbp17 |
G |
A |
11: 33,429,189 (GRCm39) |
A352V |
probably benign |
Het |
Riok3 |
A |
G |
18: 12,281,879 (GRCm39) |
I283V |
probably benign |
Het |
Rrm1 |
A |
G |
7: 102,106,381 (GRCm39) |
Y300C |
probably damaging |
Het |
Shoc1 |
T |
A |
4: 59,094,201 (GRCm39) |
R174S |
possibly damaging |
Het |
Sipa1l3 |
T |
C |
7: 29,099,510 (GRCm39) |
D253G |
probably benign |
Het |
Slc22a8 |
T |
A |
19: 8,585,550 (GRCm39) |
I305N |
probably damaging |
Het |
Slc26a3 |
A |
T |
12: 31,503,905 (GRCm39) |
E303D |
probably benign |
Het |
Slc32a1 |
C |
T |
2: 158,453,152 (GRCm39) |
|
probably benign |
Het |
Tars3 |
C |
A |
7: 65,333,556 (GRCm39) |
Q585K |
probably benign |
Het |
Ttn |
T |
A |
2: 76,585,168 (GRCm39) |
I22042F |
probably damaging |
Het |
Ubqlnl |
A |
G |
7: 103,798,813 (GRCm39) |
V228A |
probably benign |
Het |
Wnt7b |
T |
A |
15: 85,422,059 (GRCm39) |
D201V |
possibly damaging |
Het |
Xpot |
A |
T |
10: 121,440,443 (GRCm39) |
I596N |
possibly damaging |
Het |
|
Other mutations in Hps5 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL00089:Hps5
|
APN |
7 |
46,425,362 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL00543:Hps5
|
APN |
7 |
46,427,497 (GRCm39) |
missense |
probably benign |
0.37 |
IGL01090:Hps5
|
APN |
7 |
46,437,751 (GRCm39) |
missense |
probably benign |
0.02 |
IGL01351:Hps5
|
APN |
7 |
46,410,856 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL01479:Hps5
|
APN |
7 |
46,412,366 (GRCm39) |
critical splice donor site |
probably null |
|
IGL02056:Hps5
|
APN |
7 |
46,437,606 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL02117:Hps5
|
APN |
7 |
46,432,940 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL02210:Hps5
|
APN |
7 |
46,435,994 (GRCm39) |
missense |
probably benign |
0.03 |
IGL02967:Hps5
|
APN |
7 |
46,418,804 (GRCm39) |
missense |
possibly damaging |
0.69 |
IGL03046:Hps5
|
APN |
7 |
46,426,463 (GRCm39) |
splice site |
probably benign |
|
IGL03187:Hps5
|
APN |
7 |
46,422,631 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL03259:Hps5
|
APN |
7 |
46,412,526 (GRCm39) |
missense |
probably damaging |
0.99 |
dorian_gray
|
UTSW |
7 |
46,784,145 (GRCm38) |
unclassified |
probably benign |
|
smoky
|
UTSW |
7 |
46,418,775 (GRCm39) |
nonsense |
probably null |
|
Titan
|
UTSW |
7 |
46,432,893 (GRCm39) |
critical splice donor site |
probably null |
|
toffee
|
UTSW |
7 |
46,777,075 (GRCm38) |
intron |
probably benign |
|
wombat
|
UTSW |
7 |
46,433,058 (GRCm39) |
missense |
probably damaging |
1.00 |
R0068:Hps5
|
UTSW |
7 |
46,426,466 (GRCm39) |
splice site |
probably benign |
|
R0068:Hps5
|
UTSW |
7 |
46,426,466 (GRCm39) |
splice site |
probably benign |
|
R0141:Hps5
|
UTSW |
7 |
46,438,605 (GRCm39) |
missense |
probably damaging |
1.00 |
R0383:Hps5
|
UTSW |
7 |
46,418,712 (GRCm39) |
splice site |
probably null |
|
R0402:Hps5
|
UTSW |
7 |
46,440,333 (GRCm39) |
splice site |
probably benign |
|
R0684:Hps5
|
UTSW |
7 |
46,432,893 (GRCm39) |
critical splice donor site |
probably null |
|
R1159:Hps5
|
UTSW |
7 |
46,421,978 (GRCm39) |
splice site |
probably null |
|
R1938:Hps5
|
UTSW |
7 |
46,422,691 (GRCm39) |
missense |
probably damaging |
1.00 |
R2058:Hps5
|
UTSW |
7 |
46,417,475 (GRCm39) |
missense |
probably damaging |
1.00 |
R3613:Hps5
|
UTSW |
7 |
46,426,298 (GRCm39) |
critical splice donor site |
probably null |
|
R3881:Hps5
|
UTSW |
7 |
46,421,420 (GRCm39) |
missense |
possibly damaging |
0.54 |
R3882:Hps5
|
UTSW |
7 |
46,421,420 (GRCm39) |
missense |
possibly damaging |
0.54 |
R4095:Hps5
|
UTSW |
7 |
46,425,218 (GRCm39) |
missense |
probably benign |
0.01 |
R4457:Hps5
|
UTSW |
7 |
46,433,037 (GRCm39) |
missense |
probably benign |
0.00 |
R4739:Hps5
|
UTSW |
7 |
46,436,013 (GRCm39) |
missense |
probably benign |
|
R4838:Hps5
|
UTSW |
7 |
46,437,778 (GRCm39) |
missense |
probably damaging |
1.00 |
R4934:Hps5
|
UTSW |
7 |
46,418,775 (GRCm39) |
nonsense |
probably null |
|
R5876:Hps5
|
UTSW |
7 |
46,438,620 (GRCm39) |
missense |
probably damaging |
1.00 |
R6056:Hps5
|
UTSW |
7 |
46,416,521 (GRCm39) |
missense |
probably benign |
0.00 |
R6129:Hps5
|
UTSW |
7 |
46,421,198 (GRCm39) |
missense |
probably benign |
|
R6878:Hps5
|
UTSW |
7 |
46,433,058 (GRCm39) |
missense |
probably damaging |
1.00 |
R7912:Hps5
|
UTSW |
7 |
46,418,826 (GRCm39) |
missense |
probably benign |
0.15 |
R7977:Hps5
|
UTSW |
7 |
46,418,475 (GRCm39) |
missense |
probably benign |
0.03 |
R7987:Hps5
|
UTSW |
7 |
46,418,475 (GRCm39) |
missense |
probably benign |
0.03 |
R8131:Hps5
|
UTSW |
7 |
46,421,312 (GRCm39) |
missense |
probably benign |
0.00 |
R8243:Hps5
|
UTSW |
7 |
46,436,066 (GRCm39) |
missense |
probably damaging |
1.00 |
R8245:Hps5
|
UTSW |
7 |
46,418,485 (GRCm39) |
nonsense |
probably null |
|
R8878:Hps5
|
UTSW |
7 |
46,421,345 (GRCm39) |
missense |
probably benign |
0.07 |
R9050:Hps5
|
UTSW |
7 |
46,422,607 (GRCm39) |
missense |
probably benign |
0.00 |
R9186:Hps5
|
UTSW |
7 |
46,438,370 (GRCm39) |
missense |
probably damaging |
1.00 |
R9278:Hps5
|
UTSW |
7 |
46,440,397 (GRCm39) |
missense |
probably benign |
0.00 |
R9290:Hps5
|
UTSW |
7 |
46,424,331 (GRCm39) |
missense |
probably damaging |
0.97 |
R9303:Hps5
|
UTSW |
7 |
46,438,619 (GRCm39) |
missense |
possibly damaging |
0.94 |
R9305:Hps5
|
UTSW |
7 |
46,438,619 (GRCm39) |
missense |
possibly damaging |
0.94 |
R9650:Hps5
|
UTSW |
7 |
46,425,354 (GRCm39) |
missense |
probably damaging |
1.00 |
X0021:Hps5
|
UTSW |
7 |
46,412,517 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Predicted Primers |
PCR Primer
(F):5'- GACAGTTGCTTAAGGACTCTCC -3'
(R):5'- GCCATGTTGAATGTGAGTGC -3'
Sequencing Primer
(F):5'- GGACTCTCCTGGTTTCTCTGAATC -3'
(R):5'- CCATGTTGAATGTGAGTGCTTTGAC -3'
|
Posted On |
2015-04-17 |