Incidental Mutation 'R8819:Hps1'
| ID |
672953 |
| 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 |
068652-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.214)
|
| Stock # |
R8819 (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 42759648 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Valine
at position 55
(I55V)
|
| 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: I55V
PolyPhen 2
Score 0.061 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000026194
Gene: ENSMUSG00000025188
AA Change: I55V
| 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: I55V
PolyPhen 2
Score 0.107 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000071069
Gene: ENSMUSG00000025188
AA Change: I55V
| 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: I55V
PolyPhen 2
Score 0.061 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000125662
Gene: ENSMUSG00000025188
AA Change: I55V
| 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: I55V
PolyPhen 2
Score 0.061 (Sensitivity: 0.94; Specificity: 0.84)
|
| SMART Domains |
Protein: ENSMUSP00000125226
Gene: ENSMUSG00000025188
AA Change: I55V
| 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: I55V
PolyPhen 2
Score 0.107 (Sensitivity: 0.93; Specificity: 0.86)
|
| SMART Domains |
Protein: ENSMUSP00000124209
Gene: ENSMUSG00000025188
AA Change: I55V
| 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 |
0.1564 |
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.3%
|
| Validation Efficiency |
100% (52/52) |
| 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: 53 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abca17 |
A |
G |
17: 24,547,576 (GRCm39) |
L266P |
probably damaging |
Het |
| Als2cl |
T |
C |
9: 110,714,855 (GRCm39) |
F125L |
probably benign |
Het |
| Arhgap33 |
T |
C |
7: 30,228,165 (GRCm39) |
I406V |
probably benign |
Het |
| Bag5 |
T |
C |
12: 111,677,709 (GRCm39) |
N38S |
probably benign |
Het |
| Clk2 |
T |
A |
3: 89,082,730 (GRCm39) |
M392K |
probably damaging |
Het |
| Cngb1 |
C |
T |
8: 95,980,037 (GRCm39) |
|
probably null |
Het |
| Cps1 |
T |
A |
1: 67,267,439 (GRCm39) |
N1402K |
possibly damaging |
Het |
| Cracd |
CTGAGGCAGCGCGAGGCCGAGAGGCAGGAGGAGGAAG |
C |
5: 77,004,793 (GRCm39) |
|
probably benign |
Het |
| Cyp2u1 |
T |
C |
3: 131,092,016 (GRCm39) |
H168R |
probably damaging |
Het |
| Dapl1 |
T |
C |
2: 59,335,056 (GRCm39) |
L70P |
probably damaging |
Het |
| Ddr2 |
T |
A |
1: 169,805,483 (GRCm39) |
K836* |
probably null |
Het |
| Dnmbp |
C |
T |
19: 43,889,854 (GRCm39) |
V638M |
probably benign |
Het |
| Dsel |
A |
G |
1: 111,787,994 (GRCm39) |
L847P |
probably benign |
Het |
| Eef1b2 |
T |
C |
1: 63,217,268 (GRCm39) |
|
probably benign |
Het |
| Eif1ad8 |
C |
T |
12: 87,563,910 (GRCm39) |
R82* |
probably null |
Het |
| Fbll1 |
T |
C |
11: 35,688,802 (GRCm39) |
K154E |
probably benign |
Het |
| Fbxw17 |
A |
T |
13: 50,587,351 (GRCm39) |
K437M |
possibly damaging |
Het |
| Fktn |
T |
C |
4: 53,735,001 (GRCm39) |
V174A |
possibly damaging |
Het |
| Frem1 |
C |
A |
4: 82,821,754 (GRCm39) |
S2118I |
probably damaging |
Het |
| Gabrb3 |
T |
C |
7: 57,442,329 (GRCm39) |
S212P |
probably damaging |
Het |
| Gimap9 |
A |
G |
6: 48,654,821 (GRCm39) |
D136G |
probably benign |
Het |
| Huwe1 |
A |
G |
X: 150,669,993 (GRCm39) |
K1482R |
probably benign |
Het |
| Ift46 |
C |
T |
9: 44,701,819 (GRCm39) |
T283I |
probably damaging |
Het |
| Ldb2 |
G |
A |
5: 44,956,757 (GRCm39) |
Q27* |
probably null |
Het |
| Lmcd1 |
T |
A |
6: 112,306,770 (GRCm39) |
I314N |
probably damaging |
Het |
| Lypd9 |
T |
G |
11: 58,337,129 (GRCm39) |
S115R |
probably damaging |
Het |
| Mctp2 |
C |
A |
7: 71,879,081 (GRCm39) |
V259L |
probably benign |
Het |
| Midn |
T |
G |
10: 79,990,234 (GRCm39) |
S302A |
probably damaging |
Het |
| Ncor2 |
A |
G |
5: 125,106,291 (GRCm39) |
V797A |
|
Het |
| Npm2 |
A |
G |
14: 70,885,768 (GRCm39) |
S146P |
probably damaging |
Het |
| Npr1 |
G |
A |
3: 90,372,201 (GRCm39) |
R204C |
probably damaging |
Het |
| Or2w2 |
G |
A |
13: 21,757,999 (GRCm39) |
S209L |
probably benign |
Het |
| Or52n3 |
T |
A |
7: 104,530,862 (GRCm39) |
V316D |
possibly damaging |
Het |
| Or6e1 |
C |
T |
14: 54,520,070 (GRCm39) |
G94D |
probably benign |
Het |
| Paip2b |
A |
C |
6: 83,791,738 (GRCm39) |
M48R |
probably damaging |
Het |
| Pcsk2 |
T |
A |
2: 143,642,990 (GRCm39) |
H422Q |
probably damaging |
Het |
| Pdzph1 |
G |
C |
17: 59,187,715 (GRCm39) |
Y1168* |
probably null |
Het |
| Peli2 |
G |
A |
14: 48,490,130 (GRCm39) |
E201K |
possibly damaging |
Het |
| Prelp |
T |
C |
1: 133,842,878 (GRCm39) |
N89S |
probably damaging |
Het |
| Rapgef3 |
T |
C |
15: 97,646,538 (GRCm39) |
N799S |
probably benign |
Het |
| Rel |
C |
T |
11: 23,695,626 (GRCm39) |
R219H |
probably damaging |
Het |
| Relch |
T |
A |
1: 105,654,179 (GRCm39) |
F873L |
possibly damaging |
Het |
| Rimbp3 |
T |
C |
16: 17,028,771 (GRCm39) |
S732P |
probably benign |
Het |
| Rock1 |
A |
G |
18: 10,070,626 (GRCm39) |
F1196S |
probably damaging |
Het |
| Ryr3 |
G |
A |
2: 112,466,137 (GRCm39) |
R4795W |
probably damaging |
Het |
| Ryr3 |
A |
G |
2: 112,690,069 (GRCm39) |
V1180A |
probably benign |
Het |
| Scn11a |
T |
C |
9: 119,645,586 (GRCm39) |
I123V |
probably benign |
Het |
| Sema4b |
G |
C |
7: 79,870,248 (GRCm39) |
E475D |
probably damaging |
Het |
| Serinc2 |
C |
A |
4: 130,149,172 (GRCm39) |
M343I |
probably damaging |
Het |
| Serinc5 |
G |
T |
13: 92,844,544 (GRCm39) |
V429F |
probably benign |
Het |
| Tnfsf10 |
G |
A |
3: 27,389,451 (GRCm39) |
V171M |
probably benign |
Het |
| Zfp27 |
T |
C |
7: 29,594,013 (GRCm39) |
K651E |
probably benign |
Het |
| Zfp438 |
A |
G |
18: 5,213,383 (GRCm39) |
I525T |
possibly 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 |
|
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 |
|
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'- TGCCTTCCAAAGAACTCTACAGTC -3'
(R):5'- TCTCTTCCTGTAAGGCCTGG -3'
Sequencing Primer
(F):5'- GAACTCTACAGTCCAAGGCAAG -3'
(R):5'- CCTGTAAGGCCTGGGTCTTG -3'
|
| Posted On |
2021-04-30 |
Incidental Mutation