Incidental Mutation 'R0402:Hps5'
| ID |
35620 |
| 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 |
038607-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.104)
|
| Stock # |
R0402 (G1)
|
| Quality Score |
139 |
|
Status
|
Validated
|
| Chromosome |
7 |
| Chromosomal Location |
46409890-46445488 bp(-) (GRCm39) |
| Type of Mutation |
splice site |
| DNA Base Change (assembly) |
A to G
at 46440333 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000014562]
[ENSMUST00000107653]
[ENSMUST00000107654]
[ENSMUST00000123725]
[ENSMUST00000142663]
[ENSMUST00000152759]
[ENSMUST00000211347]
|
| AlphaFold |
P59438 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000014562
|
| SMART Domains |
Protein: ENSMUSP00000014562
Gene: ENSMUSG00000014418
| 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: ENSMUST00000107653
|
| SMART Domains |
Protein: ENSMUSP00000103280
Gene: ENSMUSG00000014418
| 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
|
| SMART Domains |
Protein: ENSMUSP00000103281
Gene: ENSMUSG00000014418
| 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 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 |
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: ENSMUST00000211471
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000211347
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 98.2%
- 3x: 97.0%
- 10x: 94.5%
- 20x: 88.7%
|
| Validation Efficiency |
100% (74/74) |
| 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: 65 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1700017N19Rik |
A |
T |
10: 100,445,115 (GRCm39) |
K165N |
probably damaging |
Het |
| Adam6b |
T |
A |
12: 113,453,615 (GRCm39) |
M144K |
probably damaging |
Het |
| Arhgap44 |
T |
C |
11: 64,922,903 (GRCm39) |
|
probably benign |
Het |
| Arl5c |
T |
A |
11: 97,885,939 (GRCm39) |
I21F |
probably damaging |
Het |
| Bglap2 |
C |
T |
3: 88,285,552 (GRCm39) |
G40D |
probably damaging |
Het |
| Bptf |
T |
C |
11: 106,964,940 (GRCm39) |
E1303G |
probably damaging |
Het |
| Calhm1 |
T |
C |
19: 47,129,896 (GRCm39) |
T209A |
probably damaging |
Het |
| Ccr8 |
A |
G |
9: 119,923,976 (GRCm39) |
|
probably null |
Het |
| Chkb |
C |
T |
15: 89,313,610 (GRCm39) |
R65Q |
probably benign |
Het |
| Col4a1 |
T |
C |
8: 11,249,838 (GRCm39) |
|
probably benign |
Het |
| Cryzl2 |
A |
G |
1: 157,292,014 (GRCm39) |
T98A |
probably benign |
Het |
| D430041D05Rik |
T |
C |
2: 103,998,509 (GRCm39) |
T1080A |
probably damaging |
Het |
| Dhx8 |
C |
A |
11: 101,643,223 (GRCm39) |
T765N |
probably damaging |
Het |
| Dicer1 |
T |
C |
12: 104,697,323 (GRCm39) |
D78G |
probably benign |
Het |
| Drd2 |
A |
G |
9: 49,316,271 (GRCm39) |
I344V |
probably benign |
Het |
| Edil3 |
A |
T |
13: 89,347,570 (GRCm39) |
|
probably benign |
Het |
| Fbxw19 |
C |
T |
9: 109,313,493 (GRCm39) |
G235D |
probably benign |
Het |
| Fzd1 |
T |
C |
5: 4,805,702 (GRCm39) |
K627E |
possibly damaging |
Het |
| Garin1b |
A |
G |
6: 29,323,901 (GRCm39) |
T209A |
probably benign |
Het |
| Garin4 |
T |
C |
1: 190,896,637 (GRCm39) |
D2G |
probably benign |
Het |
| Gm10638 |
A |
G |
8: 87,472,828 (GRCm39) |
|
probably benign |
Het |
| H6pd |
G |
T |
4: 150,080,773 (GRCm39) |
A24E |
probably damaging |
Het |
| Hectd2 |
G |
T |
19: 36,578,929 (GRCm39) |
|
probably null |
Het |
| Irx3 |
T |
C |
8: 92,527,296 (GRCm39) |
N136S |
possibly damaging |
Het |
| Kcmf1 |
T |
C |
6: 72,826,568 (GRCm39) |
M1V |
probably null |
Het |
| Klrb1 |
A |
T |
6: 128,687,583 (GRCm39) |
F104I |
probably benign |
Het |
| Lrfn5 |
T |
C |
12: 61,886,803 (GRCm39) |
M197T |
probably benign |
Het |
| Mpdz |
A |
C |
4: 81,279,677 (GRCm39) |
M51R |
possibly damaging |
Het |
| Mtbp |
G |
T |
15: 55,432,466 (GRCm39) |
E258* |
probably null |
Het |
| Mylk3 |
T |
A |
8: 86,079,539 (GRCm39) |
H373L |
probably damaging |
Het |
| Myrfl |
A |
G |
10: 116,664,882 (GRCm39) |
S383P |
probably damaging |
Het |
| Nt5c |
T |
C |
11: 115,381,468 (GRCm39) |
*195W |
probably null |
Het |
| Ocstamp |
A |
G |
2: 165,238,184 (GRCm39) |
V360A |
possibly damaging |
Het |
| Or10ak16 |
A |
T |
4: 118,750,426 (GRCm39) |
I49F |
possibly damaging |
Het |
| Or10al6 |
T |
A |
17: 38,083,284 (GRCm39) |
C247S |
probably damaging |
Het |
| Or4k35 |
A |
G |
2: 111,100,208 (GRCm39) |
F168S |
probably damaging |
Het |
| Or4p19 |
A |
T |
2: 88,242,378 (GRCm39) |
V208D |
probably damaging |
Het |
| Or5an9 |
A |
G |
19: 12,186,953 (GRCm39) |
T8A |
probably damaging |
Het |
| Otop2 |
T |
C |
11: 115,217,234 (GRCm39) |
|
probably benign |
Het |
| Pom121l2 |
A |
T |
13: 22,172,649 (GRCm39) |
|
probably benign |
Het |
| Pon2 |
T |
A |
6: 5,272,410 (GRCm39) |
K137* |
probably null |
Het |
| Ppip5k2 |
T |
A |
1: 97,647,579 (GRCm39) |
Q1049L |
probably benign |
Het |
| Ralgapa2 |
C |
T |
2: 146,276,729 (GRCm39) |
V504M |
probably damaging |
Het |
| Rph3a |
G |
A |
5: 121,080,317 (GRCm39) |
H654Y |
probably damaging |
Het |
| Sh2d1b1 |
T |
C |
1: 170,107,342 (GRCm39) |
|
probably benign |
Het |
| Slc15a2 |
G |
A |
16: 36,595,960 (GRCm39) |
T154I |
probably benign |
Het |
| Slc45a3 |
T |
C |
1: 131,905,265 (GRCm39) |
V96A |
possibly damaging |
Het |
| Slc7a4 |
A |
G |
16: 17,393,497 (GRCm39) |
S101P |
probably damaging |
Het |
| Smco2 |
T |
C |
6: 146,772,633 (GRCm39) |
|
probably benign |
Het |
| Spata2 |
A |
T |
2: 167,325,580 (GRCm39) |
V413E |
probably benign |
Het |
| Specc1l |
A |
G |
10: 75,082,260 (GRCm39) |
E552G |
probably damaging |
Het |
| Sstr5 |
C |
T |
17: 25,711,008 (GRCm39) |
V74M |
probably benign |
Het |
| Timm50 |
G |
A |
7: 28,006,280 (GRCm39) |
R274W |
probably damaging |
Het |
| Tll2 |
A |
G |
19: 41,087,132 (GRCm39) |
V573A |
possibly damaging |
Het |
| Tm7sf3 |
C |
A |
6: 146,507,685 (GRCm39) |
R459M |
possibly damaging |
Het |
| Txk |
A |
G |
5: 72,889,105 (GRCm39) |
|
probably null |
Het |
| Uroc1 |
A |
G |
6: 90,324,284 (GRCm39) |
D436G |
probably damaging |
Het |
| Vmn1r13 |
T |
A |
6: 57,187,083 (GRCm39) |
Y81N |
possibly damaging |
Het |
| Vmn2r19 |
A |
G |
6: 123,313,141 (GRCm39) |
E737G |
probably damaging |
Het |
| Wfs1 |
A |
G |
5: 37,134,324 (GRCm39) |
|
probably benign |
Het |
| Zfp1 |
G |
A |
8: 112,396,875 (GRCm39) |
E285K |
probably damaging |
Het |
| Zfp1005 |
T |
A |
2: 150,111,136 (GRCm39) |
C609S |
possibly damaging |
Het |
| Zfp661 |
G |
A |
2: 127,419,640 (GRCm39) |
Q167* |
probably null |
Het |
| Zswim8 |
T |
C |
14: 20,760,834 (GRCm39) |
F36S |
probably damaging |
Het |
| Zw10 |
A |
G |
9: 48,980,023 (GRCm39) |
T385A |
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 |
|
|
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 |
|
| Predicted Primers |
PCR Primer
(F):5'- GGGTTGTATCAAAATACTCCGCGCA -3'
(R):5'- ACCCCAACTTCCAGAGGTGGTT -3'
Sequencing Primer
(F):5'- TACTCCGCGCAAAGTAACTG -3'
(R):5'- GTTGCCTCTTTTTCTGTTGAATG -3'
|
| Posted On |
2013-05-09 |
Incidental Mutation