Incidental Mutation 'R9303:Hps5'
ID |
705058 |
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 # |
R9303 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
7 |
Chromosomal Location |
46409890-46445488 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
G to A
at 46438619 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Threonine to Isoleucine
at position 38
(T38I)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000014562
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000014562]
[ENSMUST00000107653]
[ENSMUST00000107654]
[ENSMUST00000123725]
[ENSMUST00000142663]
[ENSMUST00000152759]
[ENSMUST00000211347]
|
AlphaFold |
P59438 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000014562
AA Change: T38I
PolyPhen 2
Score 0.941 (Sensitivity: 0.80; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000014562 Gene: ENSMUSG00000014418 AA Change: T38I
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 |
possibly damaging
Transcript: ENSMUST00000107653
AA Change: T38I
PolyPhen 2
Score 0.914 (Sensitivity: 0.81; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000103280 Gene: ENSMUSG00000014418 AA Change: T38I
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 |
possibly damaging
Transcript: ENSMUST00000107654
AA Change: T38I
PolyPhen 2
Score 0.941 (Sensitivity: 0.80; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000103281 Gene: ENSMUSG00000014418 AA Change: T38I
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 |
possibly damaging
Transcript: ENSMUST00000123725
AA Change: T38I
PolyPhen 2
Score 0.941 (Sensitivity: 0.80; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000116770 Gene: ENSMUSG00000014418 AA Change: T38I
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: T38I
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
SMART Domains |
Protein: ENSMUSP00000122887 Gene: ENSMUSG00000014418 AA Change: T38I
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 |
possibly damaging
Transcript: ENSMUST00000152759
AA Change: T38I
PolyPhen 2
Score 0.941 (Sensitivity: 0.80; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000115786 Gene: ENSMUSG00000014418 AA Change: T38I
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 |
possibly damaging
Transcript: ENSMUST00000211347
AA Change: T38I
PolyPhen 2
Score 0.941 (Sensitivity: 0.80; Specificity: 0.94)
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000211471
|
Coding Region Coverage |
- 1x: 100.0%
- 3x: 99.9%
- 10x: 99.6%
- 20x: 98.8%
|
Validation Efficiency |
100% (57/57) |
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: 56 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca16 |
A |
G |
7: 120,126,989 (GRCm39) |
I1227V |
probably benign |
Het |
Acte1 |
G |
T |
7: 143,434,902 (GRCm39) |
|
probably null |
Het |
Adamts17 |
T |
C |
7: 66,489,645 (GRCm39) |
L21P |
probably damaging |
Het |
Adcy1 |
T |
C |
11: 7,094,766 (GRCm39) |
V564A |
probably damaging |
Het |
Adgre1 |
A |
G |
17: 57,748,275 (GRCm39) |
N492D |
probably benign |
Het |
Aldh1b1 |
G |
A |
4: 45,803,811 (GRCm39) |
V450M |
probably damaging |
Het |
Arv1 |
T |
A |
8: 125,457,685 (GRCm39) |
H196Q |
probably damaging |
Het |
Atp9a |
A |
T |
2: 168,517,163 (GRCm39) |
I390N |
probably benign |
Het |
Bltp1 |
A |
G |
3: 37,098,969 (GRCm39) |
I1277V |
|
Het |
Capn10 |
T |
C |
1: 92,871,665 (GRCm39) |
|
probably null |
Het |
Casq2 |
A |
G |
3: 102,052,700 (GRCm39) |
D404G |
unknown |
Het |
Cenpf |
T |
C |
1: 189,392,271 (GRCm39) |
|
probably null |
Het |
Cep295nl |
G |
A |
11: 118,224,766 (GRCm39) |
P26L |
possibly damaging |
Het |
Chmp4c |
T |
G |
3: 10,454,974 (GRCm39) |
S214A |
probably benign |
Het |
Chrna5 |
T |
C |
9: 54,912,156 (GRCm39) |
F319L |
probably benign |
Het |
Csmd1 |
G |
T |
8: 16,011,532 (GRCm39) |
T2507K |
probably benign |
Het |
Ctnnd2 |
T |
C |
15: 30,967,037 (GRCm39) |
M996T |
probably damaging |
Het |
Dbf4 |
T |
C |
5: 8,448,102 (GRCm39) |
T328A |
unknown |
Het |
Ddc |
C |
T |
11: 11,779,132 (GRCm39) |
V331I |
probably benign |
Het |
Fads2b |
A |
T |
2: 85,330,649 (GRCm39) |
C219* |
probably null |
Het |
Fat1 |
T |
A |
8: 45,463,498 (GRCm39) |
W1347R |
probably damaging |
Het |
Fbxw21 |
A |
G |
9: 108,986,727 (GRCm39) |
F51L |
probably benign |
Het |
Gng2 |
G |
T |
14: 19,925,961 (GRCm39) |
H44N |
probably damaging |
Het |
Igf2 |
G |
A |
7: 142,208,153 (GRCm39) |
R64C |
probably damaging |
Het |
Inpp4b |
C |
T |
8: 82,759,758 (GRCm39) |
A601V |
probably damaging |
Het |
Kdm2a |
A |
G |
19: 4,395,606 (GRCm39) |
Y342H |
probably benign |
Het |
Kidins220 |
C |
A |
12: 25,107,110 (GRCm39) |
T1430K |
probably benign |
Het |
Knl1 |
T |
C |
2: 118,898,829 (GRCm39) |
C177R |
possibly damaging |
Het |
Krt32 |
T |
C |
11: 99,972,029 (GRCm39) |
T440A |
probably benign |
Het |
Kynu |
T |
A |
2: 43,569,768 (GRCm39) |
F350Y |
probably damaging |
Het |
Lama4 |
T |
C |
10: 38,973,137 (GRCm39) |
L1568P |
probably damaging |
Het |
Lrp1b |
A |
T |
2: 41,618,574 (GRCm39) |
S281T |
|
Het |
Or2y3 |
A |
T |
17: 38,393,629 (GRCm39) |
V80D |
probably damaging |
Het |
Or5h23 |
A |
G |
16: 58,906,802 (GRCm39) |
S15P |
probably benign |
Het |
Or8c19-ps1 |
C |
T |
9: 38,220,463 (GRCm39) |
T124M |
probably benign |
Het |
Orc3 |
G |
A |
4: 34,607,181 (GRCm39) |
R50* |
probably null |
Het |
Osbpl6 |
T |
A |
2: 76,378,716 (GRCm39) |
D124E |
probably damaging |
Het |
Parp4 |
TG |
T |
14: 56,832,790 (GRCm39) |
|
probably null |
Het |
Parp4 |
T |
C |
14: 56,852,224 (GRCm39) |
|
probably null |
Het |
Pcdhb18 |
A |
C |
18: 37,625,004 (GRCm39) |
H778P |
probably benign |
Het |
Polg |
A |
T |
7: 79,105,860 (GRCm39) |
Y710N |
probably benign |
Het |
Ppp2r2b |
C |
A |
18: 42,779,025 (GRCm39) |
R370L |
possibly damaging |
Het |
Raet1e |
C |
T |
10: 22,057,872 (GRCm39) |
T213I |
possibly damaging |
Het |
Reln |
T |
A |
5: 22,193,705 (GRCm39) |
S1418C |
possibly damaging |
Het |
Reln |
T |
C |
5: 22,285,689 (GRCm39) |
S427G |
probably benign |
Het |
Rhobtb2 |
G |
A |
14: 70,025,376 (GRCm39) |
H633Y |
probably damaging |
Het |
Serpina3i |
T |
C |
12: 104,234,881 (GRCm39) |
V404A |
probably damaging |
Het |
Serpinb8 |
T |
C |
1: 107,526,769 (GRCm39) |
|
probably null |
Het |
Sorl1 |
G |
T |
9: 41,900,739 (GRCm39) |
Q1658K |
probably damaging |
Het |
Tmem26 |
G |
A |
10: 68,559,816 (GRCm39) |
W29* |
probably null |
Het |
Togaram2 |
A |
G |
17: 71,996,408 (GRCm39) |
E137G |
probably damaging |
Het |
Ttc39b |
A |
G |
4: 83,151,023 (GRCm39) |
L524S |
probably damaging |
Het |
Usp43 |
T |
C |
11: 67,767,345 (GRCm39) |
N675S |
probably damaging |
Het |
Vmn2r104 |
A |
G |
17: 20,268,439 (GRCm39) |
L10P |
possibly damaging |
Het |
Zbtb1 |
G |
A |
12: 76,432,773 (GRCm39) |
R253Q |
probably damaging |
Het |
Zfp354b |
T |
A |
11: 50,820,256 (GRCm39) |
R36S |
probably 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 |
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 |
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'- TTGCCCCTTCCTAGAACATCAG -3'
(R):5'- TTACATTGTGTCCCGGGCAG -3'
Sequencing Primer
(F):5'- CTAGAACATCAGACAAGAATAGTTCG -3'
(R):5'- CCGGGCAGGGGAGAGAAG -3'
|
Posted On |
2022-03-25 |