Incidental Mutation 'R3424:Hps1'
| ID |
267865 |
| 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 |
040642-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.294)
|
| Stock # |
R3424 (G1)
|
| Quality Score |
225 |
|
Status
|
Not validated
|
| Chromosome |
19 |
| Chromosomal Location |
42743544-42768417 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 42748952 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Methionine to Lysine
at position 522
(M522K)
|
| 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: M514K
PolyPhen 2
Score 0.615 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000026194
Gene: ENSMUSG00000025188
AA Change: M514K
| 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: ENSMUST00000069298
AA Change: M522K
PolyPhen 2
Score 0.748 (Sensitivity: 0.85; Specificity: 0.92)
|
| SMART Domains |
Protein: ENSMUSP00000071069
Gene: ENSMUSG00000025188
AA Change: M522K
| 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: M522K
PolyPhen 2
Score 0.466 (Sensitivity: 0.89; Specificity: 0.90)
|
| SMART Domains |
Protein: ENSMUSP00000125662
Gene: ENSMUSG00000025188
AA Change: M522K
| 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: ENSMUST00000160621
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000161252
|
| Predicted Effect |
possibly damaging
Transcript: ENSMUST00000162004
AA Change: M514K
PolyPhen 2
Score 0.615 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000125226
Gene: ENSMUSG00000025188
AA Change: M514K
| 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: M514K
PolyPhen 2
Score 0.619 (Sensitivity: 0.87; Specificity: 0.91)
|
| SMART Domains |
Protein: ENSMUSP00000124209
Gene: ENSMUSG00000025188
AA Change: M514K
| 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: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.4%
|
| 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: 28 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 6030469F06Rik |
G |
T |
12: 31,234,632 (GRCm39) |
|
noncoding transcript |
Het |
| Atp8b3 |
T |
C |
10: 80,372,181 (GRCm39) |
E16G |
probably benign |
Het |
| BC016579 |
T |
A |
16: 45,449,846 (GRCm39) |
I191F |
probably damaging |
Het |
| Cdh23 |
T |
G |
10: 60,212,660 (GRCm39) |
I1584L |
possibly damaging |
Het |
| Cep250 |
G |
A |
2: 155,823,381 (GRCm39) |
D1011N |
probably benign |
Het |
| Coro2b |
A |
T |
9: 62,336,590 (GRCm39) |
|
probably null |
Het |
| Csf3r |
A |
G |
4: 125,937,549 (GRCm39) |
D811G |
probably damaging |
Het |
| Dst |
T |
G |
1: 34,237,586 (GRCm39) |
|
probably benign |
Het |
| Gabrr1 |
T |
C |
4: 33,158,058 (GRCm39) |
L227P |
probably damaging |
Het |
| Galnt10 |
T |
C |
11: 57,536,539 (GRCm39) |
V52A |
probably benign |
Het |
| Golga4 |
A |
C |
9: 118,363,715 (GRCm39) |
D229A |
probably benign |
Het |
| Heatr5b |
G |
A |
17: 79,075,833 (GRCm39) |
T1495I |
possibly damaging |
Het |
| Hoxd4 |
A |
G |
2: 74,557,657 (GRCm39) |
Y12C |
probably damaging |
Het |
| Lrrc8e |
A |
T |
8: 4,284,611 (GRCm39) |
I279F |
probably damaging |
Het |
| Mettl24 |
C |
T |
10: 40,559,637 (GRCm39) |
Q96* |
probably null |
Het |
| Muc2 |
A |
G |
7: 141,279,595 (GRCm39) |
N193S |
probably damaging |
Het |
| Mysm1 |
A |
G |
4: 94,853,558 (GRCm39) |
L347P |
probably benign |
Het |
| Or10g9 |
T |
A |
9: 39,911,830 (GRCm39) |
E231V |
probably damaging |
Het |
| Oxtr |
G |
T |
6: 112,454,191 (GRCm39) |
H24Q |
probably benign |
Het |
| Paxip1 |
A |
G |
5: 27,980,671 (GRCm39) |
|
probably benign |
Het |
| Pclo |
C |
T |
5: 14,730,432 (GRCm39) |
|
probably benign |
Het |
| Ros1 |
C |
A |
10: 52,004,512 (GRCm39) |
|
probably null |
Het |
| Slc18b1 |
T |
G |
10: 23,698,874 (GRCm39) |
M348R |
probably damaging |
Het |
| Slco4c1 |
A |
T |
1: 96,768,976 (GRCm39) |
S295R |
probably benign |
Het |
| Tmeff2 |
A |
G |
1: 51,018,776 (GRCm39) |
|
probably benign |
Het |
| Tspan31 |
T |
A |
10: 126,904,371 (GRCm39) |
Q141L |
probably benign |
Het |
| Virma |
G |
T |
4: 11,513,177 (GRCm39) |
E344* |
probably null |
Het |
| Zbtb17 |
G |
T |
4: 141,192,299 (GRCm39) |
G415C |
probably damaging |
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 |
|
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 |
|
|
R6054:Hps1
|
UTSW |
19 |
42,759,217 (GRCm39) |
missense |
probably damaging |
0.96 |
|
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'- ACACACATGTCTAGCCTCTGG -3'
(R):5'- TGCAGTGTGTCAGAGAACAG -3'
Sequencing Primer
(F):5'- GCTAAGCCAGGCAGAGGATATGAC -3'
(R):5'- AGCTGCCTCCCTGTGTG -3'
|
| Posted On |
2015-02-18 |
Incidental Mutation