Incidental Mutation 'R6054:Hps1'
ID |
484343 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Hps1
|
Ensembl Gene |
ENSMUSG00000025188 |
Gene Name |
HPS1, biogenesis of lysosomal organelles complex 3 subunit 1 |
Synonyms |
6030422N11Rik, Hermansky-Pudlak syndrome 1 |
MMRRC Submission |
044222-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.214)
|
Stock # |
R6054 (G1)
|
Quality Score |
225.009 |
Status
|
Not validated
|
Chromosome |
19 |
Chromosomal Location |
42743544-42768417 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 42759217 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Glutamic Acid
at position 125
(V125E)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000071069
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000026194]
[ENSMUST00000069298]
[ENSMUST00000160455]
[ENSMUST00000162004]
[ENSMUST00000162061]
|
AlphaFold |
no structure available at present |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000026194
AA Change: V125E
PolyPhen 2
Score 0.887 (Sensitivity: 0.82; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000026194 Gene: ENSMUSG00000025188 AA Change: V125E
Domain | Start | End | E-Value | Type |
coiled coil region
|
20 |
47 |
N/A |
INTRINSIC |
low complexity region
|
229 |
246 |
N/A |
INTRINSIC |
|
Predicted Effect |
probably damaging
Transcript: ENSMUST00000069298
AA Change: V125E
PolyPhen 2
Score 0.963 (Sensitivity: 0.78; Specificity: 0.95)
|
SMART Domains |
Protein: ENSMUSP00000071069 Gene: ENSMUSG00000025188 AA Change: V125E
Domain | Start | End | E-Value | Type |
coiled coil region
|
20 |
47 |
N/A |
INTRINSIC |
low complexity region
|
229 |
246 |
N/A |
INTRINSIC |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000159974
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000160455
AA Change: V125E
PolyPhen 2
Score 0.499 (Sensitivity: 0.88; Specificity: 0.90)
|
SMART Domains |
Protein: ENSMUSP00000125662 Gene: ENSMUSG00000025188 AA Change: V125E
Domain | Start | End | E-Value | Type |
coiled coil region
|
20 |
47 |
N/A |
INTRINSIC |
low complexity region
|
229 |
246 |
N/A |
INTRINSIC |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000161761
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000162004
AA Change: V125E
PolyPhen 2
Score 0.887 (Sensitivity: 0.82; Specificity: 0.94)
|
SMART Domains |
Protein: ENSMUSP00000125226 Gene: ENSMUSG00000025188 AA Change: V125E
Domain | Start | End | E-Value | Type |
coiled coil region
|
20 |
47 |
N/A |
INTRINSIC |
low complexity region
|
229 |
246 |
N/A |
INTRINSIC |
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000162061
AA Change: V125E
PolyPhen 2
Score 0.767 (Sensitivity: 0.85; Specificity: 0.92)
|
SMART Domains |
Protein: ENSMUSP00000124209 Gene: ENSMUSG00000025188 AA Change: V125E
Domain | Start | End | E-Value | Type |
coiled coil region
|
20 |
47 |
N/A |
INTRINSIC |
low complexity region
|
229 |
246 |
N/A |
INTRINSIC |
|
Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.7%
- 10x: 98.2%
- 20x: 94.8%
|
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. The encoded protein is a component of three different protein complexes termed biogenesis of lysosome-related organelles complex (BLOC)-3, BLOC4, and BLOC5. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 1. Alternative splicing results in multiple transcript variants. A pseudogene related to this gene is located on chromosome 22. [provided by RefSeq, Aug 2015] PHENOTYPE: Homozygotes for spontaneous mutations exhibit hypopigmentation and increased bleeding time. Impaired natural killer cell function, reduced secretion of kidney lysosomal enzymes,and abnormal retinofugal neuronal projections characterize some alleles. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 62 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
4930562C15Rik |
T |
C |
16: 4,653,729 (GRCm39) |
S93P |
unknown |
Het |
Adam28 |
T |
A |
14: 68,879,601 (GRCm39) |
N149I |
probably benign |
Het |
Adam4 |
A |
C |
12: 81,466,828 (GRCm39) |
F598V |
probably damaging |
Het |
Adh5 |
A |
G |
3: 138,151,136 (GRCm39) |
H33R |
possibly damaging |
Het |
Apoh |
A |
G |
11: 108,286,801 (GRCm39) |
N75S |
probably damaging |
Het |
Arrdc5 |
T |
C |
17: 56,601,420 (GRCm39) |
E235G |
possibly damaging |
Het |
Atm |
T |
C |
9: 53,371,173 (GRCm39) |
D2225G |
probably damaging |
Het |
Atp6v0a1 |
C |
T |
11: 100,930,715 (GRCm39) |
P514L |
possibly damaging |
Het |
Brd9 |
T |
A |
13: 74,088,860 (GRCm39) |
M195K |
probably damaging |
Het |
Cacna1a |
T |
G |
8: 85,283,414 (GRCm39) |
S755A |
probably damaging |
Het |
Ccdc85c |
T |
A |
12: 108,241,028 (GRCm39) |
H122L |
unknown |
Het |
Ccs |
A |
T |
19: 4,875,893 (GRCm39) |
D192E |
probably benign |
Het |
Cd3e |
G |
A |
9: 44,913,459 (GRCm39) |
T92M |
possibly damaging |
Het |
Celsr2 |
A |
G |
3: 108,314,279 (GRCm39) |
F1249L |
possibly damaging |
Het |
Col16a1 |
G |
A |
4: 129,955,515 (GRCm39) |
|
probably benign |
Het |
Col17a1 |
A |
G |
19: 47,668,859 (GRCm39) |
Y122H |
probably damaging |
Het |
Col28a1 |
G |
A |
6: 8,083,748 (GRCm39) |
P570S |
possibly damaging |
Het |
Dchs2 |
A |
T |
3: 83,253,543 (GRCm39) |
I2318L |
probably benign |
Het |
Dhx35 |
T |
A |
2: 158,660,219 (GRCm39) |
Y184N |
probably benign |
Het |
Dmxl1 |
T |
G |
18: 49,990,453 (GRCm39) |
N297K |
probably benign |
Het |
Dsp |
G |
A |
13: 38,351,585 (GRCm39) |
G135S |
probably benign |
Het |
Efhb |
C |
T |
17: 53,706,027 (GRCm39) |
V837I |
possibly damaging |
Het |
Efs |
C |
T |
14: 55,158,614 (GRCm39) |
D15N |
probably damaging |
Het |
Fbxl19 |
C |
T |
7: 127,351,681 (GRCm39) |
T314I |
probably damaging |
Het |
Gm11595 |
A |
T |
11: 99,663,474 (GRCm39) |
C69S |
unknown |
Het |
Grxcr2 |
A |
G |
18: 42,119,743 (GRCm39) |
V199A |
probably benign |
Het |
Hadha |
T |
C |
5: 30,328,682 (GRCm39) |
E468G |
probably benign |
Het |
Hax1 |
GTCATCATCATCATCATC |
GTCATCATCATCATCATCATC |
3: 89,905,247 (GRCm39) |
|
probably benign |
Het |
Hrg |
A |
T |
16: 22,772,412 (GRCm39) |
T74S |
probably benign |
Het |
Idh3a |
T |
C |
9: 54,493,829 (GRCm39) |
|
probably null |
Het |
Leng8 |
C |
A |
7: 4,148,522 (GRCm39) |
|
probably null |
Het |
Maml2 |
TCAGCAGCAGCAGCAGCAGC |
TCAGCAGCAGCAGCAGC |
9: 13,532,695 (GRCm39) |
|
probably benign |
Het |
Mctp2 |
T |
C |
7: 71,908,851 (GRCm39) |
H154R |
probably benign |
Het |
Megf6 |
A |
G |
4: 154,347,636 (GRCm39) |
E777G |
probably benign |
Het |
Miip |
A |
G |
4: 147,950,135 (GRCm39) |
S154P |
probably benign |
Het |
Mprip |
T |
C |
11: 59,649,251 (GRCm39) |
V985A |
probably benign |
Het |
Nmrk2 |
G |
A |
10: 81,035,468 (GRCm39) |
R158W |
probably damaging |
Het |
Nsd2 |
T |
C |
5: 34,039,505 (GRCm39) |
S180P |
probably damaging |
Het |
Oga |
A |
G |
19: 45,764,571 (GRCm39) |
S190P |
probably damaging |
Het |
Opa1 |
T |
G |
16: 29,433,952 (GRCm39) |
S596A |
probably damaging |
Het |
Or1ad1 |
G |
A |
11: 50,875,631 (GRCm39) |
M34I |
probably benign |
Het |
Or51b4 |
A |
G |
7: 103,531,033 (GRCm39) |
V139A |
probably damaging |
Het |
Pcdha2 |
A |
G |
18: 37,073,857 (GRCm39) |
E496G |
probably damaging |
Het |
Pcdhb5 |
T |
G |
18: 37,454,133 (GRCm39) |
V171G |
probably damaging |
Het |
Pramel6 |
A |
G |
2: 87,339,003 (GRCm39) |
T68A |
probably benign |
Het |
Ptprq |
T |
C |
10: 107,418,219 (GRCm39) |
Y1719C |
probably damaging |
Het |
Pzp |
T |
C |
6: 128,490,727 (GRCm39) |
N412S |
probably benign |
Het |
Rb1cc1 |
G |
T |
1: 6,320,058 (GRCm39) |
R1159L |
probably benign |
Het |
Rev3l |
T |
A |
10: 39,700,146 (GRCm39) |
S1548T |
probably benign |
Het |
Rora |
A |
G |
9: 69,286,084 (GRCm39) |
I471M |
probably benign |
Het |
Scube1 |
C |
A |
15: 83,535,877 (GRCm39) |
V266L |
probably benign |
Het |
Sema6a |
C |
T |
18: 47,416,470 (GRCm39) |
D386N |
possibly damaging |
Het |
Siglecf |
T |
A |
7: 43,004,430 (GRCm39) |
L253Q |
probably damaging |
Het |
Spata31d1b |
A |
G |
13: 59,863,464 (GRCm39) |
H204R |
probably benign |
Het |
Syt17 |
T |
C |
7: 118,007,356 (GRCm39) |
T313A |
possibly damaging |
Het |
Tbc1d32 |
T |
C |
10: 56,038,304 (GRCm39) |
T578A |
possibly damaging |
Het |
Trpm1 |
A |
G |
7: 63,918,450 (GRCm39) |
S597G |
probably benign |
Het |
Vmn2r9 |
T |
A |
5: 108,996,126 (GRCm39) |
H174L |
probably damaging |
Het |
Vrk2 |
A |
T |
11: 26,436,975 (GRCm39) |
S281T |
probably benign |
Het |
Wdr48 |
A |
G |
9: 119,736,843 (GRCm39) |
D22G |
probably damaging |
Het |
Zfp408 |
C |
A |
2: 91,479,636 (GRCm39) |
V61L |
probably benign |
Het |
Zfp652 |
G |
A |
11: 95,640,689 (GRCm39) |
A205T |
probably benign |
Het |
|
Other mutations in Hps1 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL02116:Hps1
|
APN |
19 |
42,759,568 (GRCm39) |
nonsense |
probably null |
|
IGL02327:Hps1
|
APN |
19 |
42,744,784 (GRCm39) |
unclassified |
probably benign |
|
IGL02488:Hps1
|
APN |
19 |
42,746,227 (GRCm39) |
unclassified |
probably benign |
|
IGL03161:Hps1
|
APN |
19 |
42,755,710 (GRCm39) |
missense |
probably damaging |
1.00 |
R0127:Hps1
|
UTSW |
19 |
42,759,550 (GRCm39) |
splice site |
probably benign |
|
R0134:Hps1
|
UTSW |
19 |
42,754,619 (GRCm39) |
missense |
probably damaging |
0.98 |
R0234:Hps1
|
UTSW |
19 |
42,750,992 (GRCm39) |
missense |
probably damaging |
1.00 |
R0234:Hps1
|
UTSW |
19 |
42,750,992 (GRCm39) |
missense |
probably damaging |
1.00 |
R0394:Hps1
|
UTSW |
19 |
42,759,338 (GRCm39) |
splice site |
probably null |
|
R1435:Hps1
|
UTSW |
19 |
42,750,714 (GRCm39) |
missense |
probably benign |
0.04 |
R1537:Hps1
|
UTSW |
19 |
42,748,143 (GRCm39) |
critical splice donor site |
probably null |
|
R1616:Hps1
|
UTSW |
19 |
42,755,624 (GRCm39) |
missense |
probably damaging |
1.00 |
R1860:Hps1
|
UTSW |
19 |
42,750,888 (GRCm39) |
missense |
probably damaging |
1.00 |
R2014:Hps1
|
UTSW |
19 |
42,750,951 (GRCm39) |
missense |
probably benign |
0.00 |
R3424:Hps1
|
UTSW |
19 |
42,748,952 (GRCm39) |
missense |
possibly damaging |
0.75 |
R4472:Hps1
|
UTSW |
19 |
42,750,935 (GRCm39) |
missense |
probably damaging |
1.00 |
R5476:Hps1
|
UTSW |
19 |
42,758,041 (GRCm39) |
splice site |
probably null |
|
R6275:Hps1
|
UTSW |
19 |
42,758,046 (GRCm39) |
missense |
probably null |
1.00 |
R6807:Hps1
|
UTSW |
19 |
42,759,217 (GRCm39) |
missense |
possibly damaging |
0.60 |
R6916:Hps1
|
UTSW |
19 |
42,755,164 (GRCm39) |
|
|
|
R7332:Hps1
|
UTSW |
19 |
42,766,351 (GRCm39) |
splice site |
probably null |
|
R7487:Hps1
|
UTSW |
19 |
42,744,700 (GRCm39) |
missense |
probably damaging |
1.00 |
R7504:Hps1
|
UTSW |
19 |
42,755,159 (GRCm39) |
missense |
probably benign |
0.00 |
R7823:Hps1
|
UTSW |
19 |
42,744,146 (GRCm39) |
missense |
possibly damaging |
0.58 |
R7955:Hps1
|
UTSW |
19 |
42,759,221 (GRCm39) |
missense |
probably damaging |
0.99 |
R8198:Hps1
|
UTSW |
19 |
42,755,659 (GRCm39) |
missense |
probably benign |
0.05 |
R8819:Hps1
|
UTSW |
19 |
42,759,648 (GRCm39) |
missense |
probably benign |
0.06 |
R9688:Hps1
|
UTSW |
19 |
42,755,147 (GRCm39) |
missense |
probably benign |
|
Z1176:Hps1
|
UTSW |
19 |
42,755,125 (GRCm39) |
missense |
probably null |
0.00 |
Z1177:Hps1
|
UTSW |
19 |
42,754,657 (GRCm39) |
critical splice acceptor site |
probably null |
|
Z1177:Hps1
|
UTSW |
19 |
42,748,270 (GRCm39) |
missense |
probably damaging |
1.00 |
Z1177:Hps1
|
UTSW |
19 |
42,744,135 (GRCm39) |
missense |
probably benign |
0.00 |
|
Predicted Primers |
PCR Primer
(F):5'- TACACAGCTGGGTGCACTAG -3'
(R):5'- CAGAAACTGCAGTGTATCAGAGTCC -3'
Sequencing Primer
(F):5'- CACTAGGGAGGGTGCCTAAGTTC -3'
(R):5'- CTTACTCTCTGAGACCTGGAAGG -3'
|
Posted On |
2017-07-14 |