Incidental Mutation 'R8131:Hps5'
| ID |
632012 |
| 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 |
067560-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.104)
|
| Stock # |
R8131 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
7 |
| Chromosomal Location |
46409890-46445488 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 46421312 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 717
(D717G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000014562
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000014562]
[ENSMUST00000107653]
[ENSMUST00000107654]
[ENSMUST00000142663]
[ENSMUST00000211347]
|
| AlphaFold |
P59438 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000014562
AA Change: D717G
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000014562
Gene: ENSMUSG00000014418
AA Change: D717G
| 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
AA Change: D684G
PolyPhen 2
Score 0.071 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000103280
Gene: ENSMUSG00000014418
AA Change: D684G
| 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: D717G
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000103281
Gene: ENSMUSG00000014418
AA Change: D717G
| 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 |
|
| SMART Domains |
Protein: ENSMUSP00000114384
Gene: ENSMUSG00000014418
AA Change: D33G
| 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 |
|
| SMART Domains |
Protein: ENSMUSP00000119876
Gene: ENSMUSG00000014418
AA Change: D182G
| 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 |
probably benign
Transcript: ENSMUST00000211347
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000211571
|
| Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.8%
- 10x: 99.0%
- 20x: 96.1%
|
| Validation Efficiency |
100% (50/50) |
| 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: 51 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 4930544D05Rik |
A |
G |
11: 70,506,834 (GRCm39) |
|
probably null |
Het |
| Abcb10 |
C |
T |
8: 124,691,757 (GRCm39) |
A403T |
|
Het |
| Acan |
C |
T |
7: 78,741,086 (GRCm39) |
P484L |
possibly damaging |
Het |
| Amotl2 |
T |
A |
9: 102,597,615 (GRCm39) |
Y125N |
probably damaging |
Het |
| Apaf1 |
C |
A |
10: 90,913,420 (GRCm39) |
V168F |
possibly damaging |
Het |
| Arhgap32 |
C |
T |
9: 32,158,426 (GRCm39) |
H154Y |
probably damaging |
Het |
| B4galnt3 |
A |
G |
6: 120,271,346 (GRCm39) |
|
probably null |
Het |
| Bahcc1 |
C |
T |
11: 120,163,664 (GRCm39) |
A654V |
probably benign |
Het |
| Bcl11b |
T |
A |
12: 107,931,967 (GRCm39) |
M202L |
probably benign |
Het |
| Cdc40 |
C |
A |
10: 40,717,473 (GRCm39) |
R406L |
possibly damaging |
Het |
| Cemip |
C |
A |
7: 83,652,616 (GRCm39) |
|
probably benign |
Het |
| Col26a1 |
T |
C |
5: 136,775,894 (GRCm39) |
D353G |
probably benign |
Het |
| Col6a5 |
T |
A |
9: 105,778,815 (GRCm39) |
Q1682L |
unknown |
Het |
| Cul9 |
C |
T |
17: 46,822,168 (GRCm39) |
G1819D |
probably damaging |
Het |
| Cyp2b10 |
C |
T |
7: 25,614,242 (GRCm39) |
Q239* |
probably null |
Het |
| Dthd1 |
T |
A |
5: 63,000,259 (GRCm39) |
I527N |
probably damaging |
Het |
| Dzip3 |
C |
T |
16: 48,754,156 (GRCm39) |
|
probably null |
Het |
| Ecm2 |
A |
G |
13: 49,671,940 (GRCm39) |
E147G |
probably benign |
Het |
| Ercc6l2 |
C |
T |
13: 63,982,561 (GRCm39) |
T132M |
probably damaging |
Het |
| Esf1 |
G |
A |
2: 139,990,751 (GRCm39) |
Q578* |
probably null |
Het |
| Gria4 |
C |
T |
9: 4,502,429 (GRCm39) |
R368H |
probably benign |
Het |
| Hrh1 |
A |
T |
6: 114,457,253 (GRCm39) |
D178V |
probably benign |
Het |
| Inppl1 |
T |
C |
7: 101,479,268 (GRCm39) |
N537S |
possibly damaging |
Het |
| Itih1 |
T |
C |
14: 30,663,521 (GRCm39) |
Y165C |
probably damaging |
Het |
| Krt71 |
T |
A |
15: 101,643,141 (GRCm39) |
I456F |
possibly damaging |
Het |
| Larp4 |
T |
C |
15: 99,892,570 (GRCm39) |
V255A |
probably damaging |
Het |
| Lrriq1 |
T |
G |
10: 103,051,572 (GRCm39) |
R393S |
possibly damaging |
Het |
| Mep1a |
T |
A |
17: 43,813,558 (GRCm39) |
I31L |
probably benign |
Het |
| Muc5b |
C |
T |
7: 141,396,146 (GRCm39) |
T134I |
unknown |
Het |
| Neurl4 |
T |
C |
11: 69,800,067 (GRCm39) |
Y1052H |
probably benign |
Het |
| Nlrc5 |
C |
G |
8: 95,208,420 (GRCm39) |
N755K |
probably damaging |
Het |
| Nrde2 |
T |
C |
12: 100,108,502 (GRCm39) |
K363R |
probably benign |
Het |
| Pcdhb12 |
T |
C |
18: 37,570,335 (GRCm39) |
S494P |
possibly damaging |
Het |
| Pcnx1 |
C |
A |
12: 81,965,292 (GRCm39) |
S486R |
possibly damaging |
Het |
| Pira13 |
T |
A |
7: 3,825,161 (GRCm39) |
R494* |
probably null |
Het |
| Plrg1 |
T |
A |
3: 82,977,081 (GRCm39) |
V374E |
probably damaging |
Het |
| Plxnb2 |
A |
G |
15: 89,042,916 (GRCm39) |
I1491T |
probably damaging |
Het |
| Repin1 |
G |
T |
6: 48,574,279 (GRCm39) |
E403* |
probably null |
Het |
| Scn4a |
T |
C |
11: 106,232,367 (GRCm39) |
E490G |
probably benign |
Het |
| Sec16a |
A |
G |
2: 26,300,958 (GRCm39) |
V887A |
|
Het |
| Serpina3a |
T |
C |
12: 104,082,467 (GRCm39) |
I80T |
probably damaging |
Het |
| Setd1b |
A |
T |
5: 123,281,443 (GRCm39) |
I66F |
unknown |
Het |
| Slirp |
T |
A |
12: 87,494,428 (GRCm39) |
|
probably null |
Het |
| Socs6 |
A |
C |
18: 88,888,169 (GRCm39) |
S249A |
probably benign |
Het |
| Thoc2l |
A |
G |
5: 104,669,027 (GRCm39) |
E1183G |
possibly damaging |
Het |
| Ttn |
A |
T |
2: 76,616,077 (GRCm39) |
I16622N |
probably damaging |
Het |
| Uox |
A |
T |
3: 146,331,589 (GRCm39) |
T237S |
probably damaging |
Het |
| Vmn2r43 |
T |
A |
7: 8,258,326 (GRCm39) |
I296L |
probably benign |
Het |
| Vmn2r74 |
T |
A |
7: 85,601,943 (GRCm39) |
D565V |
probably benign |
Het |
| Vps13b |
T |
C |
15: 35,372,255 (GRCm39) |
|
probably null |
Het |
| Vps13d |
A |
G |
4: 144,882,707 (GRCm39) |
V962A |
|
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 |
|
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'- CCTTTGCTCTTTTCAAGTCCAGAAG -3'
(R):5'- CCGGCATTTCCAATACCAGC -3'
Sequencing Primer
(F):5'- GTACTTCTTTAGGAAACGACAAGCC -3'
(R):5'- GGCATTTCCAATACCAGCAGTCC -3'
|
| Posted On |
2020-06-30 |
Incidental Mutation