Incidental Mutation 'R6275:Hps1'
ID |
507612 |
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 |
044445-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.214)
|
Stock # |
R6275 (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 42758046 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Glutamic Acid to Glycine
at position 169
(E169G)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000124209
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000026194]
[ENSMUST00000069298]
[ENSMUST00000160455]
[ENSMUST00000162004]
[ENSMUST00000162061]
|
AlphaFold |
no structure available at present |
Predicted Effect |
probably null
Transcript: ENSMUST00000026194
AA Change: E169G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000026194 Gene: ENSMUSG00000025188 AA Change: E169G
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 null
Transcript: ENSMUST00000069298
AA Change: E169G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000071069 Gene: ENSMUSG00000025188 AA Change: E169G
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 |
probably null
Transcript: ENSMUST00000160455
AA Change: E169G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000125662 Gene: ENSMUSG00000025188 AA Change: E169G
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 |
probably null
Transcript: ENSMUST00000162004
AA Change: E169G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000125226 Gene: ENSMUSG00000025188 AA Change: E169G
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 null
Transcript: ENSMUST00000162061
AA Change: E169G
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
SMART Domains |
Protein: ENSMUSP00000124209 Gene: ENSMUSG00000025188 AA Change: E169G
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 |
0.7001 |
Coding Region Coverage |
- 1x: 99.9%
- 3x: 99.7%
- 10x: 98.3%
- 20x: 95.4%
|
Validation Efficiency |
98% (56/57) |
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: 57 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abca7 |
T |
A |
10: 79,833,625 (GRCm39) |
L30H |
probably damaging |
Het |
Abcb6 |
T |
C |
1: 75,149,195 (GRCm39) |
|
probably null |
Het |
Acsbg1 |
T |
A |
9: 54,517,056 (GRCm39) |
M586L |
probably benign |
Het |
Ano6 |
A |
T |
15: 95,811,314 (GRCm39) |
Y159F |
probably damaging |
Het |
C1ql1 |
A |
G |
11: 102,830,575 (GRCm39) |
I254T |
probably damaging |
Het |
Ccdc81 |
T |
C |
7: 89,531,519 (GRCm39) |
D318G |
possibly damaging |
Het |
Ccr7 |
C |
T |
11: 99,036,489 (GRCm39) |
M144I |
probably damaging |
Het |
Cdca3 |
C |
T |
6: 124,809,627 (GRCm39) |
|
probably null |
Het |
Ces1h |
A |
T |
8: 94,099,274 (GRCm39) |
L93I |
probably benign |
Het |
Cntfr |
T |
C |
4: 41,663,216 (GRCm39) |
D197G |
possibly damaging |
Het |
Cyp2d12 |
C |
A |
15: 82,440,859 (GRCm39) |
P126T |
probably benign |
Het |
Dnah10 |
A |
G |
5: 124,862,248 (GRCm39) |
T2225A |
probably damaging |
Het |
Edrf1 |
A |
T |
7: 133,269,311 (GRCm39) |
N1147Y |
possibly damaging |
Het |
Eif1ad15 |
T |
C |
12: 88,287,995 (GRCm39) |
D86G |
possibly damaging |
Het |
Eif1ad16 |
T |
C |
12: 87,985,255 (GRCm39) |
N96S |
probably benign |
Het |
Ermap |
C |
T |
4: 119,035,747 (GRCm39) |
V414M |
probably damaging |
Het |
Fam13a |
A |
G |
6: 58,931,242 (GRCm39) |
I446T |
probably damaging |
Het |
Fgfbp3 |
T |
C |
19: 36,896,153 (GRCm39) |
H155R |
possibly damaging |
Het |
Folr1 |
T |
A |
7: 101,508,742 (GRCm39) |
N61I |
probably damaging |
Het |
Fsip1 |
T |
C |
2: 118,035,583 (GRCm39) |
I431V |
probably benign |
Het |
Gm5493 |
A |
T |
17: 22,969,043 (GRCm39) |
E74D |
probably benign |
Het |
H2-Oa |
A |
G |
17: 34,313,540 (GRCm39) |
D197G |
probably benign |
Het |
Il17rc |
A |
T |
6: 113,457,308 (GRCm39) |
M372L |
probably benign |
Het |
Itga10 |
A |
G |
3: 96,565,501 (GRCm39) |
S1042G |
probably benign |
Het |
Jchain |
A |
T |
5: 88,669,212 (GRCm39) |
V147E |
probably damaging |
Het |
Laptm4b |
A |
G |
15: 34,283,473 (GRCm39) |
T211A |
probably benign |
Het |
Mal2 |
T |
C |
15: 54,435,035 (GRCm39) |
|
probably null |
Het |
Mov10l1 |
T |
A |
15: 88,910,823 (GRCm39) |
I1071N |
probably damaging |
Het |
Mpp2 |
T |
A |
11: 101,951,795 (GRCm39) |
Y401F |
probably damaging |
Het |
Myh15 |
A |
G |
16: 48,965,610 (GRCm39) |
T1172A |
probably benign |
Het |
Or51q1 |
T |
A |
7: 103,629,181 (GRCm39) |
S261T |
probably damaging |
Het |
Pcnx1 |
G |
T |
12: 81,965,381 (GRCm39) |
S516I |
probably benign |
Het |
Pidd1 |
C |
T |
7: 141,019,708 (GRCm39) |
A685T |
probably damaging |
Het |
Psg28 |
A |
C |
7: 18,164,365 (GRCm39) |
Y116D |
probably damaging |
Het |
Psmd11 |
T |
C |
11: 80,329,458 (GRCm39) |
|
probably benign |
Het |
Rapgefl1 |
T |
A |
11: 98,741,946 (GRCm39) |
Y637N |
probably damaging |
Het |
Rbm25 |
T |
A |
12: 83,691,206 (GRCm39) |
M66K |
probably damaging |
Het |
Rnf38 |
T |
A |
4: 44,152,408 (GRCm39) |
H52L |
probably benign |
Het |
Rsf1 |
CGGCGGCGG |
CGGCGGCGGTGGCGGCGG |
7: 97,229,130 (GRCm39) |
|
probably benign |
Het |
Sec62 |
A |
G |
3: 30,863,985 (GRCm39) |
Q89R |
probably damaging |
Het |
Serpina6 |
T |
A |
12: 103,614,979 (GRCm39) |
Q289L |
probably benign |
Het |
Sf3b2 |
A |
C |
19: 5,333,678 (GRCm39) |
I640S |
probably damaging |
Het |
Slc13a2 |
CGTTATCTGT |
CGT |
11: 78,294,306 (GRCm39) |
|
probably benign |
Het |
Slc26a11 |
T |
C |
11: 119,250,125 (GRCm39) |
F127L |
probably benign |
Het |
Spata31h1 |
T |
C |
10: 82,121,202 (GRCm39) |
D3936G |
probably damaging |
Het |
Stac3 |
T |
A |
10: 127,343,615 (GRCm39) |
Y252* |
probably null |
Het |
Stoml3 |
G |
A |
3: 53,414,927 (GRCm39) |
A240T |
probably damaging |
Het |
Tanc1 |
A |
T |
2: 59,673,854 (GRCm39) |
H1653L |
probably benign |
Het |
Tll1 |
A |
T |
8: 64,504,401 (GRCm39) |
L665* |
probably null |
Het |
Tnr |
A |
C |
1: 159,688,840 (GRCm39) |
Q434P |
probably damaging |
Het |
Tpgs1 |
C |
A |
10: 79,511,354 (GRCm39) |
D165E |
probably benign |
Het |
Tsc2 |
A |
G |
17: 24,819,394 (GRCm39) |
V1185A |
probably benign |
Het |
Tulp4 |
A |
G |
17: 6,249,011 (GRCm39) |
H203R |
probably damaging |
Het |
Txnl4a |
T |
A |
18: 80,261,980 (GRCm39) |
M72K |
possibly damaging |
Het |
Usp42 |
G |
A |
5: 143,700,727 (GRCm39) |
R1099W |
probably damaging |
Het |
Zfp292 |
G |
A |
4: 34,808,883 (GRCm39) |
A1387V |
possibly damaging |
Het |
Zfp994 |
A |
T |
17: 22,418,972 (GRCm39) |
L659* |
probably null |
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 |
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'- TGAAACTCTCACCCGGAATTCAG -3'
(R):5'- GACAGGAACCTTGGATTGGG -3'
Sequencing Primer
(F):5'- GGAATTCAGTTGCTCACCATGGAAC -3'
(R):5'- GGCCGGACAAGACCAACTTTC -3'
|
Posted On |
2018-03-15 |