Incidental Mutation 'IGL03259:Hps5'
ID |
414767 |
Institutional Source |
Australian Phenomics Network
(link to record)
|
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 |
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.104)
|
Stock # |
IGL03259
|
Quality Score |
|
Status
|
|
Chromosome |
7 |
Chromosomal Location |
46409890-46445488 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
G to T
at 46412526 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Proline to Glutamine
at position 1021
(P1021Q)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000103280
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000014562]
[ENSMUST00000107653]
[ENSMUST00000107654]
[ENSMUST00000142663]
[ENSMUST00000211347]
|
AlphaFold |
P59438 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000014562
AA Change: P1054Q
PolyPhen 2
Score 0.393 (Sensitivity: 0.90; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000014562 Gene: ENSMUSG00000014418 AA Change: P1054Q
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: P1021Q
PolyPhen 2
Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
|
SMART Domains |
Protein: ENSMUSP00000103280 Gene: ENSMUSG00000014418 AA Change: P1021Q
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 benign
Transcript: ENSMUST00000107654
AA Change: P1054Q
PolyPhen 2
Score 0.393 (Sensitivity: 0.90; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000103281 Gene: ENSMUSG00000014418 AA Change: P1054Q
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: ENSMUST00000130365
|
SMART Domains |
Protein: ENSMUSP00000114384 Gene: ENSMUSG00000014418
Domain | Start | End | E-Value | Type |
low complexity region
|
92 |
103 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000138480
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000142663
|
SMART Domains |
Protein: ENSMUSP00000122887 Gene: ENSMUSG00000014418
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 |
unknown
Transcript: ENSMUST00000153789
AA Change: P481Q
|
SMART Domains |
Protein: ENSMUSP00000119876 Gene: ENSMUSG00000014418 AA Change: P481Q
Domain | Start | End | E-Value | Type |
low complexity region
|
241 |
252 |
N/A |
INTRINSIC |
low complexity region
|
417 |
426 |
N/A |
INTRINSIC |
low complexity region
|
449 |
461 |
N/A |
INTRINSIC |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000143627
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000145776
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000211571
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000211347
|
Coding Region Coverage |
|
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 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: 26 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Atp8a1 |
T |
C |
5: 67,781,349 (GRCm39) |
|
probably null |
Het |
Btbd3 |
T |
C |
2: 138,121,680 (GRCm39) |
M121T |
probably damaging |
Het |
Cep192 |
A |
T |
18: 67,953,483 (GRCm39) |
N500I |
probably damaging |
Het |
Clca4a |
A |
G |
3: 144,663,841 (GRCm39) |
L534P |
probably damaging |
Het |
Cyp2d11 |
C |
T |
15: 82,274,221 (GRCm39) |
V387M |
probably damaging |
Het |
Dlgap3 |
T |
C |
4: 127,094,077 (GRCm39) |
I443T |
probably benign |
Het |
Heatr5b |
T |
A |
17: 79,098,985 (GRCm39) |
D1305V |
probably damaging |
Het |
Iqca1 |
T |
C |
1: 89,980,156 (GRCm39) |
D637G |
probably damaging |
Het |
Kank1 |
A |
G |
19: 25,407,705 (GRCm39) |
D1233G |
probably damaging |
Het |
Lad1 |
A |
T |
1: 135,755,394 (GRCm39) |
R223S |
probably benign |
Het |
Ms4a13 |
A |
G |
19: 11,161,210 (GRCm39) |
S110P |
probably damaging |
Het |
Nmd3 |
T |
A |
3: 69,652,576 (GRCm39) |
D387E |
possibly damaging |
Het |
Or1m1 |
A |
G |
9: 18,666,811 (GRCm39) |
V40A |
probably benign |
Het |
Or7a41 |
C |
A |
10: 78,871,234 (GRCm39) |
Y201* |
probably null |
Het |
Or8k3b |
G |
T |
2: 86,520,894 (GRCm39) |
Q142K |
probably benign |
Het |
Pcgf5 |
T |
A |
19: 36,433,059 (GRCm39) |
D234E |
probably benign |
Het |
Pcnx2 |
T |
A |
8: 126,480,388 (GRCm39) |
H1973L |
probably benign |
Het |
Peak1 |
A |
G |
9: 56,167,251 (GRCm39) |
F226L |
probably damaging |
Het |
Pgp |
A |
G |
17: 24,690,022 (GRCm39) |
K180R |
probably damaging |
Het |
Sdk1 |
A |
T |
5: 141,938,788 (GRCm39) |
K404* |
probably null |
Het |
Serinc5 |
T |
A |
13: 92,827,500 (GRCm39) |
V272D |
probably damaging |
Het |
Slc4a5 |
A |
G |
6: 83,247,979 (GRCm39) |
H395R |
probably damaging |
Het |
Spice1 |
T |
A |
16: 44,176,530 (GRCm39) |
V40D |
probably damaging |
Het |
Syne2 |
A |
G |
12: 76,035,853 (GRCm39) |
I3713M |
probably benign |
Het |
Vmn1r58 |
A |
T |
7: 5,414,086 (GRCm39) |
L48* |
probably null |
Het |
Vwa7 |
A |
G |
17: 35,239,002 (GRCm39) |
|
probably null |
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 |
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 |
R3914:Hps5
|
UTSW |
7 |
46,432,950 (GRCm39) |
missense |
probably damaging |
1.00 |
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 |
|
Posted On |
2016-08-02 |