Incidental Mutation 'R9186:Hps5'
| ID |
697376 |
| 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 |
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.104)
|
| Stock # |
R9186 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
7 |
| Chromosomal Location |
46409890-46445488 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 46438370 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Cysteine
at position 89
(Y89C)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000014562
(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: Y89C
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000014562
Gene: ENSMUSG00000014418
AA Change: Y89C
| 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: Y89C
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000103280
Gene: ENSMUSG00000014418
AA Change: Y89C
| 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: Y89C
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000103281
Gene: ENSMUSG00000014418
AA Change: Y89C
| 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: ENSMUST00000123725
AA Change: Y89C
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000116770
Gene: ENSMUSG00000014418
AA Change: Y89C
| 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: Y89C
PolyPhen 2
Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000122887
Gene: ENSMUSG00000014418
AA Change: Y89C
| 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 |
probably damaging
Transcript: ENSMUST00000152759
AA Change: Y89C
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| SMART Domains |
Protein: ENSMUSP00000115786
Gene: ENSMUSG00000014418
AA Change: Y89C
| 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 damaging
Transcript: ENSMUST00000211347
AA Change: Y89C
PolyPhen 2
Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
|
| Predicted Effect |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.3%
|
| 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: 59 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700017B05Rik |
C |
A |
9: 57,164,472 (GRCm39) |
R634L |
probably damaging |
Het |
| Ankhd1 |
T |
C |
18: 36,767,383 (GRCm39) |
I210T |
possibly damaging |
Het |
| Ankle2 |
G |
A |
5: 110,400,610 (GRCm39) |
V649M |
possibly damaging |
Het |
| Arid3b |
A |
T |
9: 57,702,217 (GRCm39) |
|
probably null |
Het |
| Arl10 |
A |
G |
13: 54,726,620 (GRCm39) |
N133D |
probably damaging |
Het |
| Bag6 |
C |
T |
17: 35,363,667 (GRCm39) |
R784W |
probably damaging |
Het |
| Ccnl1 |
T |
C |
3: 65,865,426 (GRCm39) |
T42A |
unknown |
Het |
| Cd164 |
C |
A |
10: 41,404,695 (GRCm39) |
P151Q |
probably damaging |
Het |
| Cdh23 |
G |
A |
10: 60,143,306 (GRCm39) |
A3005V |
possibly damaging |
Het |
| Ceacam2 |
T |
A |
7: 25,227,213 (GRCm39) |
N218I |
probably damaging |
Het |
| Cfap97 |
C |
T |
8: 46,644,665 (GRCm39) |
R466C |
possibly damaging |
Het |
| Colgalt2 |
C |
A |
1: 152,384,403 (GRCm39) |
T581K |
probably damaging |
Het |
| Dnah11 |
T |
A |
12: 118,154,632 (GRCm39) |
D216V |
probably benign |
Het |
| Dusp13b |
A |
T |
14: 21,798,563 (GRCm39) |
S34T |
probably damaging |
Het |
| Esf1 |
T |
A |
2: 139,990,792 (GRCm39) |
K564I |
possibly damaging |
Het |
| F5 |
A |
G |
1: 164,021,470 (GRCm39) |
N1315S |
probably benign |
Het |
| Fubp1 |
A |
T |
3: 151,926,153 (GRCm39) |
M292L |
probably damaging |
Het |
| Gabrb2 |
A |
T |
11: 42,378,200 (GRCm39) |
M139L |
possibly damaging |
Het |
| Gk5 |
T |
A |
9: 96,015,469 (GRCm39) |
V95D |
probably benign |
Het |
| Glcci1 |
C |
A |
6: 8,537,826 (GRCm39) |
P148Q |
possibly damaging |
Het |
| Gm19410 |
A |
T |
8: 36,282,629 (GRCm39) |
S1952C |
possibly damaging |
Het |
| Gstm4 |
T |
C |
3: 107,952,049 (GRCm39) |
|
probably benign |
Het |
| Heatr1 |
T |
A |
13: 12,436,227 (GRCm39) |
L1211Q |
probably damaging |
Het |
| Helz2 |
A |
G |
2: 180,876,457 (GRCm39) |
S1346P |
possibly damaging |
Het |
| Hexb |
A |
C |
13: 97,325,836 (GRCm39) |
V158G |
probably damaging |
Het |
| Hipk3 |
T |
C |
2: 104,301,439 (GRCm39) |
E251G |
probably damaging |
Het |
| Iqub |
A |
T |
6: 24,450,766 (GRCm39) |
V611D |
possibly damaging |
Het |
| Itgbl1 |
G |
A |
14: 124,094,970 (GRCm39) |
D332N |
probably benign |
Het |
| Krtap26-1 |
C |
A |
16: 88,444,609 (GRCm39) |
R4L |
unknown |
Het |
| Lgi3 |
A |
G |
14: 70,772,193 (GRCm39) |
Y246C |
probably damaging |
Het |
| Mug2 |
T |
A |
6: 122,052,248 (GRCm39) |
I1002N |
probably damaging |
Het |
| Myo18a |
C |
T |
11: 77,749,847 (GRCm39) |
T66M |
|
Het |
| Naip6 |
T |
C |
13: 100,436,390 (GRCm39) |
D711G |
possibly damaging |
Het |
| Or4f59 |
C |
A |
2: 111,873,095 (GRCm39) |
C94F |
probably damaging |
Het |
| Orc5 |
T |
A |
5: 22,752,944 (GRCm39) |
Q48L |
probably benign |
Het |
| Oxct2a |
C |
A |
4: 123,216,461 (GRCm39) |
A307S |
probably damaging |
Het |
| Pgls |
T |
C |
8: 72,048,833 (GRCm39) |
*258Q |
probably null |
Het |
| Plekha6 |
C |
T |
1: 133,220,171 (GRCm39) |
R955W |
probably damaging |
Het |
| Polr1c |
G |
T |
17: 46,556,633 (GRCm39) |
N97K |
probably damaging |
Het |
| Prr27 |
C |
A |
5: 87,990,994 (GRCm39) |
P202Q |
probably benign |
Het |
| Prtg |
T |
C |
9: 72,764,159 (GRCm39) |
V544A |
probably benign |
Het |
| Rbl2 |
G |
A |
8: 91,828,006 (GRCm39) |
G574S |
probably damaging |
Het |
| Scamp1 |
T |
A |
13: 94,344,682 (GRCm39) |
T272S |
possibly damaging |
Het |
| Sun2 |
T |
A |
15: 79,611,737 (GRCm39) |
D562V |
probably damaging |
Het |
| Szt2 |
A |
G |
4: 118,242,288 (GRCm39) |
F1565S |
probably damaging |
Het |
| Tatdn2 |
C |
T |
6: 113,687,125 (GRCm39) |
R779C |
probably benign |
Het |
| Tbc1d30 |
T |
C |
10: 121,111,639 (GRCm39) |
I430V |
probably benign |
Het |
| Tmem86b |
T |
C |
7: 4,632,725 (GRCm39) |
D43G |
probably damaging |
Het |
| Tnrc18 |
T |
C |
5: 142,773,488 (GRCm39) |
N447S |
|
Het |
| Trmt2a |
T |
C |
16: 18,069,033 (GRCm39) |
S292P |
probably benign |
Het |
| Trpc2 |
T |
C |
7: 101,737,492 (GRCm39) |
V428A |
probably damaging |
Het |
| Tsc2 |
T |
C |
17: 24,823,862 (GRCm39) |
E981G |
probably damaging |
Het |
| Ucp1 |
G |
T |
8: 84,017,272 (GRCm39) |
G21* |
probably null |
Het |
| Utrn |
T |
C |
10: 12,490,318 (GRCm39) |
T21A |
probably benign |
Het |
| Vapa |
A |
T |
17: 65,900,507 (GRCm39) |
N88K |
probably damaging |
Het |
| Wasl |
T |
C |
6: 24,664,615 (GRCm39) |
R10G |
probably damaging |
Het |
| Zan |
C |
A |
5: 137,391,810 (GRCm39) |
V4662F |
unknown |
Het |
| Zap70 |
G |
A |
1: 36,818,832 (GRCm39) |
M382I |
possibly damaging |
Het |
| Zdhhc17 |
T |
C |
10: 110,780,281 (GRCm39) |
I624M |
probably benign |
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 |
|
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 |
|
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'- ATGTTGTTGCCTCAAATCAGC -3'
(R):5'- TCATTCAGAAAGATGGCTGGAAGC -3'
Sequencing Primer
(F):5'- GCATTTTCCACAAACACCAGGG -3'
(R):5'- GCAAAGGCTGTTTCTCTCTCAC -3'
|
| Posted On |
2022-02-07 |
Incidental Mutation