Incidental Mutation 'R1435:Hps1'
ID |
159493 |
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 |
039490-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.214)
|
Stock # |
R1435 (G1)
|
Quality Score |
124 |
Status
|
Not validated
|
Chromosome |
19 |
Chromosomal Location |
42743544-42768417 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
T to C
at 42750714 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Serine to Glycine
at position 398
(S398G)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000071069
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000026194]
[ENSMUST00000069298]
[ENSMUST00000160455]
[ENSMUST00000162061]
[ENSMUST00000162004]
|
AlphaFold |
no structure available at present |
Predicted Effect |
probably benign
Transcript: ENSMUST00000026194
AA Change: S390G
PolyPhen 2
Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)
|
SMART Domains |
Protein: ENSMUSP00000026194 Gene: ENSMUSG00000025188 AA Change: S390G
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: S398G
PolyPhen 2
Score 0.043 (Sensitivity: 0.94; Specificity: 0.83)
|
SMART Domains |
Protein: ENSMUSP00000071069 Gene: ENSMUSG00000025188 AA Change: S398G
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 benign
Transcript: ENSMUST00000160455
AA Change: S398G
PolyPhen 2
Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)
|
SMART Domains |
Protein: ENSMUSP00000125662 Gene: ENSMUSG00000025188 AA Change: S398G
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 |
noncoding transcript
Transcript: ENSMUST00000161761
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000162061
AA Change: S390G
PolyPhen 2
Score 0.020 (Sensitivity: 0.95; Specificity: 0.80)
|
SMART Domains |
Protein: ENSMUSP00000124209 Gene: ENSMUSG00000025188 AA Change: S390G
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: S390G
PolyPhen 2
Score 0.023 (Sensitivity: 0.95; Specificity: 0.81)
|
SMART Domains |
Protein: ENSMUSP00000125226 Gene: ENSMUSG00000025188 AA Change: S390G
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: 98.7%
- 3x: 97.5%
- 10x: 93.0%
- 20x: 81.3%
|
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: 67 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Acadvl |
T |
G |
11: 69,905,642 (GRCm39) |
T62P |
probably benign |
Het |
Amz1 |
A |
T |
5: 140,733,921 (GRCm39) |
N166Y |
probably damaging |
Het |
Anxa6 |
T |
C |
11: 54,882,236 (GRCm39) |
Q518R |
probably benign |
Het |
Aox3 |
G |
A |
1: 58,202,605 (GRCm39) |
|
probably null |
Het |
Arid1a |
C |
T |
4: 133,408,009 (GRCm39) |
R2166Q |
unknown |
Het |
Asb4 |
T |
G |
6: 5,398,410 (GRCm39) |
I125S |
probably benign |
Het |
Aspscr1 |
T |
C |
11: 120,580,048 (GRCm39) |
S196P |
probably benign |
Het |
Atxn3 |
A |
G |
12: 101,908,460 (GRCm39) |
F131L |
probably benign |
Het |
B3gnt5 |
T |
A |
16: 19,587,924 (GRCm39) |
Y48N |
probably damaging |
Het |
Bglap3 |
A |
G |
3: 88,276,453 (GRCm39) |
M35T |
possibly damaging |
Het |
Cabp1 |
A |
T |
5: 115,311,267 (GRCm39) |
D79E |
probably damaging |
Het |
Cemip2 |
A |
T |
19: 21,822,070 (GRCm39) |
Q1155L |
probably benign |
Het |
Chd2 |
C |
T |
7: 73,102,884 (GRCm39) |
R1367Q |
probably damaging |
Het |
Clec5a |
T |
A |
6: 40,561,358 (GRCm39) |
Q29L |
probably damaging |
Het |
Cmtr2 |
T |
C |
8: 110,947,711 (GRCm39) |
L7P |
probably benign |
Het |
Cnbd1 |
T |
C |
4: 18,907,026 (GRCm39) |
I183V |
probably benign |
Het |
Col7a1 |
G |
A |
9: 108,792,341 (GRCm39) |
G1297D |
unknown |
Het |
Csnk1g3 |
G |
A |
18: 54,039,746 (GRCm39) |
|
probably null |
Het |
Cyp4a32 |
A |
T |
4: 115,463,863 (GRCm39) |
N134I |
probably damaging |
Het |
Cyp4f16 |
CTATG |
CTATGTATG |
17: 32,769,708 (GRCm39) |
|
probably null |
Het |
Dst |
G |
A |
1: 34,153,026 (GRCm39) |
V56M |
probably damaging |
Het |
Engase |
A |
T |
11: 118,375,727 (GRCm39) |
T32S |
probably damaging |
Het |
Fam117b |
T |
C |
1: 60,008,222 (GRCm39) |
I352T |
possibly damaging |
Het |
Golga4 |
C |
A |
9: 118,364,508 (GRCm39) |
D290E |
probably benign |
Het |
Gtf2a1l |
C |
A |
17: 89,001,743 (GRCm39) |
H153N |
probably damaging |
Het |
Hivep1 |
C |
A |
13: 42,311,519 (GRCm39) |
T1253N |
probably damaging |
Het |
Il1r2 |
T |
A |
1: 40,144,459 (GRCm39) |
F49I |
probably damaging |
Het |
Iqsec1 |
A |
G |
6: 90,649,006 (GRCm39) |
S808P |
probably damaging |
Het |
Lrrk1 |
A |
G |
7: 65,922,776 (GRCm39) |
L289P |
probably damaging |
Het |
Magi2 |
T |
A |
5: 20,563,943 (GRCm39) |
D358E |
probably damaging |
Het |
Man2b2 |
A |
G |
5: 36,970,411 (GRCm39) |
W832R |
probably damaging |
Het |
Mfsd4a |
G |
T |
1: 131,995,494 (GRCm39) |
T46K |
probably damaging |
Het |
N4bp3 |
G |
A |
11: 51,535,167 (GRCm39) |
R341W |
probably damaging |
Het |
Odad2 |
T |
A |
18: 7,222,646 (GRCm39) |
H541L |
probably benign |
Het |
Or51f2 |
T |
C |
7: 102,526,974 (GRCm39) |
S216P |
probably damaging |
Het |
Or8s5 |
A |
T |
15: 98,238,209 (GRCm39) |
H220Q |
possibly damaging |
Het |
Otof |
A |
G |
5: 30,536,039 (GRCm39) |
L1353S |
probably benign |
Het |
Pcsk5 |
A |
T |
19: 17,541,246 (GRCm39) |
C844* |
probably null |
Het |
Pdk2 |
T |
C |
11: 94,922,721 (GRCm39) |
Y153C |
probably damaging |
Het |
Pes1 |
T |
C |
11: 3,926,075 (GRCm39) |
V292A |
probably benign |
Het |
Pex14 |
T |
C |
4: 149,047,984 (GRCm39) |
T198A |
probably benign |
Het |
Phactr4 |
G |
A |
4: 132,104,559 (GRCm39) |
T256I |
probably benign |
Het |
Pnpla2 |
G |
A |
7: 141,037,324 (GRCm39) |
R109H |
probably benign |
Het |
Polh |
G |
A |
17: 46,505,181 (GRCm39) |
T145I |
probably damaging |
Het |
Polr3d |
A |
T |
14: 70,677,479 (GRCm39) |
V299E |
probably benign |
Het |
Polr3e |
C |
T |
7: 120,540,011 (GRCm39) |
T586M |
probably benign |
Het |
Rbm20 |
T |
A |
19: 53,802,588 (GRCm39) |
F365L |
probably benign |
Het |
Resf1 |
A |
G |
6: 149,227,580 (GRCm39) |
T209A |
probably benign |
Het |
Rnf213 |
G |
T |
11: 119,326,831 (GRCm39) |
C1606F |
probably damaging |
Het |
Sipa1l2 |
A |
G |
8: 126,195,464 (GRCm39) |
V758A |
probably damaging |
Het |
Slc22a16 |
T |
A |
10: 40,463,603 (GRCm39) |
M451K |
probably damaging |
Het |
Slc28a1 |
T |
C |
7: 80,803,265 (GRCm39) |
S359P |
probably damaging |
Het |
Slc45a1 |
G |
T |
4: 150,728,505 (GRCm39) |
F99L |
probably damaging |
Het |
Sp3 |
A |
T |
2: 72,768,500 (GRCm39) |
N754K |
possibly damaging |
Het |
Taf4b |
A |
T |
18: 14,940,466 (GRCm39) |
Q315L |
probably damaging |
Het |
Tcstv2a |
T |
A |
13: 120,725,524 (GRCm39) |
W63R |
probably damaging |
Het |
Tmprss15 |
A |
T |
16: 78,818,342 (GRCm39) |
N544K |
probably benign |
Het |
Tnfsf13b |
A |
G |
8: 10,085,358 (GRCm39) |
I283V |
probably benign |
Het |
Tnfsf14 |
T |
A |
17: 57,497,605 (GRCm39) |
E209V |
possibly damaging |
Het |
Uckl1 |
T |
G |
2: 181,214,926 (GRCm39) |
S283R |
probably benign |
Het |
Ush1g |
T |
C |
11: 115,209,294 (GRCm39) |
D300G |
probably damaging |
Het |
Virma |
C |
T |
4: 11,528,621 (GRCm39) |
A1286V |
probably damaging |
Het |
Vmn2r114 |
ATTT |
ATT |
17: 23,509,906 (GRCm39) |
|
probably null |
Het |
Vmn2r59 |
A |
T |
7: 41,695,629 (GRCm39) |
M261K |
possibly damaging |
Het |
Vwf |
A |
T |
6: 125,619,212 (GRCm39) |
K1297* |
probably null |
Het |
Zdbf2 |
G |
A |
1: 63,342,199 (GRCm39) |
E193K |
possibly damaging |
Het |
Zfp759 |
T |
G |
13: 67,286,830 (GRCm39) |
I127S |
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 |
|
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 |
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'- GTGACAATACCTGAATCTCCTGCCC -3'
(R):5'- TTCAAGTTGTGGATGAGCCTGGAC -3'
Sequencing Primer
(F):5'- TGCCCAACTCGATTCTTGATAAAC -3'
(R):5'- GGATCTTCCTGGATGCCAAC -3'
|
Posted On |
2014-03-14 |