Incidental Mutation 'R7504:Hps1'
| ID |
581697 |
| 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 |
045577-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.214)
|
| Stock # |
R7504 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Validated
|
| Chromosome |
19 |
| Chromosomal Location |
42743544-42768417 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 42755159 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Aspartic acid to Glycine
at position 261
(D261G)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000125662
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000026194]
[ENSMUST00000069298]
[ENSMUST00000160455]
[ENSMUST00000162004]
[ENSMUST00000162061]
|
| AlphaFold |
no structure available at present |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000026194
AA Change: D261G
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000026194
Gene: ENSMUSG00000025188
AA Change: D261G
| 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 benign
Transcript: ENSMUST00000069298
AA Change: D261G
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000071069
Gene: ENSMUSG00000025188
AA Change: D261G
| 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 benign
Transcript: ENSMUST00000160455
AA Change: D261G
PolyPhen 2
Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
|
| SMART Domains |
Protein: ENSMUSP00000125662
Gene: ENSMUSG00000025188
AA Change: D261G
| 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 benign
Transcript: ENSMUST00000162004
AA Change: D261G
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000125226
Gene: ENSMUSG00000025188
AA Change: D261G
| 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 benign
Transcript: ENSMUST00000162061
AA Change: D261G
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000124209
Gene: ENSMUSG00000025188
AA Change: D261G
| Domain | Start | End | E-Value | Type |
|---|
|
coiled coil region
|
20 |
47 |
N/A |
INTRINSIC |
|
low complexity region
|
229 |
246 |
N/A |
INTRINSIC |
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.2%
|
| Validation Efficiency |
100% (43/43) |
| 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: 45 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1600012H06Rik |
C |
G |
17: 15,163,915 (GRCm39) |
A14G |
probably damaging |
Het |
| Btn1a1 |
A |
T |
13: 23,645,886 (GRCm39) |
M161K |
probably benign |
Het |
| Camkk2 |
G |
A |
5: 122,884,371 (GRCm39) |
T350I |
probably damaging |
Het |
| Cdc42bpg |
C |
A |
19: 6,356,814 (GRCm39) |
D23E |
possibly damaging |
Het |
| Cdkn1a |
T |
C |
17: 29,317,488 (GRCm39) |
L36P |
probably damaging |
Het |
| Dek |
A |
G |
13: 47,241,511 (GRCm39) |
I351T |
probably damaging |
Het |
| Dst |
T |
C |
1: 34,240,098 (GRCm39) |
Y1816H |
probably damaging |
Het |
| Efl1 |
T |
A |
7: 82,332,257 (GRCm39) |
N300K |
probably damaging |
Het |
| Ephx2 |
A |
G |
14: 66,339,066 (GRCm39) |
Y294H |
probably damaging |
Het |
| Fancd2 |
T |
A |
6: 113,521,999 (GRCm39) |
I198N |
probably damaging |
Het |
| Grid1 |
G |
T |
14: 35,284,470 (GRCm39) |
A738S |
probably damaging |
Het |
| Gsx2 |
G |
A |
5: 75,237,060 (GRCm39) |
|
probably null |
Het |
| Hc |
G |
A |
2: 34,951,331 (GRCm39) |
T22I |
not run |
Het |
| Ift80 |
T |
C |
3: 68,825,338 (GRCm39) |
Y539C |
probably damaging |
Het |
| Insc |
G |
T |
7: 114,390,533 (GRCm39) |
|
probably null |
Het |
| Isg15 |
T |
C |
4: 156,284,502 (GRCm39) |
M9V |
probably damaging |
Het |
| Kalrn |
A |
G |
16: 34,076,603 (GRCm39) |
L695P |
unknown |
Het |
| Nars1 |
A |
C |
18: 64,645,093 (GRCm39) |
F52V |
probably benign |
Het |
| Nmt1 |
T |
G |
11: 102,947,285 (GRCm39) |
F225V |
probably damaging |
Het |
| Or10q12 |
T |
A |
19: 13,746,096 (GRCm39) |
I130N |
probably damaging |
Het |
| Or7a36 |
A |
G |
10: 78,820,494 (GRCm39) |
Y290C |
possibly damaging |
Het |
| Or8c8 |
A |
T |
9: 38,165,539 (GRCm39) |
K272N |
possibly damaging |
Het |
| Pbx3 |
T |
C |
2: 34,065,936 (GRCm39) |
T385A |
probably damaging |
Het |
| Pcdhb11 |
A |
T |
18: 37,554,852 (GRCm39) |
T61S |
probably benign |
Het |
| Pramel40 |
G |
T |
5: 94,464,906 (GRCm39) |
V431L |
probably benign |
Het |
| Rab11fip1 |
T |
C |
8: 27,642,981 (GRCm39) |
E606G |
possibly damaging |
Het |
| Rnf216 |
A |
G |
5: 143,061,514 (GRCm39) |
Y589H |
probably benign |
Het |
| Scara3 |
A |
G |
14: 66,168,780 (GRCm39) |
I279T |
possibly damaging |
Het |
| Sdk2 |
T |
A |
11: 113,758,793 (GRCm39) |
Y477F |
possibly damaging |
Het |
| Secisbp2l |
T |
C |
2: 125,600,091 (GRCm39) |
K415E |
probably benign |
Het |
| Stag1 |
C |
T |
9: 100,770,381 (GRCm39) |
T639I |
probably benign |
Het |
| Sv2b |
A |
T |
7: 74,786,131 (GRCm39) |
F430I |
probably benign |
Het |
| Tenm2 |
C |
T |
11: 36,030,570 (GRCm39) |
C743Y |
probably damaging |
Het |
| Tet2 |
C |
A |
3: 133,193,100 (GRCm39) |
V445L |
probably benign |
Het |
| Tmem132c |
T |
C |
5: 127,631,696 (GRCm39) |
S652P |
probably damaging |
Het |
| Togaram1 |
A |
G |
12: 65,039,391 (GRCm39) |
D1155G |
possibly damaging |
Het |
| Traip |
T |
C |
9: 107,838,743 (GRCm39) |
I169T |
probably benign |
Het |
| Trmt9b |
A |
C |
8: 36,979,309 (GRCm39) |
N304T |
probably benign |
Het |
| Usp45 |
T |
G |
4: 21,816,892 (GRCm39) |
M374R |
possibly damaging |
Het |
| Vmn2r81 |
A |
T |
10: 79,104,166 (GRCm39) |
H263L |
probably benign |
Het |
| Wdr95 |
T |
C |
5: 149,505,311 (GRCm39) |
V364A |
probably damaging |
Het |
| Zfp128 |
G |
A |
7: 12,624,405 (GRCm39) |
D258N |
probably damaging |
Het |
| Zfp335 |
G |
A |
2: 164,751,338 (GRCm39) |
T76I |
probably benign |
Het |
| Zfp688 |
C |
A |
7: 127,018,483 (GRCm39) |
C214F |
probably damaging |
Het |
| Zfp760 |
T |
C |
17: 21,941,655 (GRCm39) |
S277P |
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 |
|
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 |
|
|
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 |
|
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'- CTATGATCCGCATGAGTGACCC -3'
(R):5'- AACCTGTATATCTCCAGCAAGG -3'
Sequencing Primer
(F):5'- CCCCTGAGATGGCAAGTGAGTG -3'
(R):5'- CAAGGTTTTAGTTGCATGCTCACAG -3'
|
| Posted On |
2019-10-17 |
Incidental Mutation