Incidental Mutation 'R0421:Hps3'
ID |
37040 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Hps3
|
Ensembl Gene |
ENSMUSG00000027615 |
Gene Name |
HPS3, biogenesis of lysosomal organelles complex 2 subunit 1 |
Synonyms |
Hermansky-Pudlak syndrome 3 |
MMRRC Submission |
038623-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.076)
|
Stock # |
R0421 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
3 |
Chromosomal Location |
20050109-20089478 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
C to A
at 20083480 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Phenylalanine
at position 238
(V238F)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000012580
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000012580]
[ENSMUST00000108321]
|
AlphaFold |
Q91VB4 |
Predicted Effect |
probably benign
Transcript: ENSMUST00000012580
AA Change: V238F
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
SMART Domains |
Protein: ENSMUSP00000012580 Gene: ENSMUSG00000027615 AA Change: V238F
Domain | Start | End | E-Value | Type |
Pfam:HPS3_N
|
3 |
212 |
2.8e-74 |
PFAM |
Pfam:HPS3_Mid
|
255 |
640 |
1.3e-167 |
PFAM |
Pfam:HPS3_C
|
649 |
1000 |
1.8e-175 |
PFAM |
|
Predicted Effect |
probably benign
Transcript: ENSMUST00000108321
AA Change: V106F
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
SMART Domains |
Protein: ENSMUSP00000103957 Gene: ENSMUSG00000027615 AA Change: V106F
Domain | Start | End | E-Value | Type |
Pfam:HPS3_N
|
3 |
87 |
5.6e-25 |
PFAM |
Pfam:HPS3_Mid
|
121 |
508 |
4.2e-161 |
PFAM |
Pfam:HPS3_C
|
517 |
870 |
9.2e-199 |
PFAM |
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000124808
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000126644
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130171
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137408
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000151752
|
Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000155121
|
Meta Mutation Damage Score |
0.0898 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.3%
- 10x: 96.4%
- 20x: 92.7%
|
Validation Efficiency |
97% (67/69) |
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein containing a potential clathrin-binding motif, consensus dileucine signals, and tyrosine-based sorting signals for targeting to vesicles of lysosomal lineage. The encoded protein may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 3. [provided by RefSeq, Apr 2015] PHENOTYPE: Homozygotes for spontaneous null mutations exhibit hypopigmentation and prolonged bleeding associated with a platelet defect. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 69 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abi1 |
G |
A |
2: 22,850,839 (GRCm39) |
T195I |
probably damaging |
Het |
Afap1l1 |
T |
C |
18: 61,884,945 (GRCm39) |
N180S |
probably damaging |
Het |
Arsg |
A |
G |
11: 109,418,592 (GRCm39) |
Y196C |
probably damaging |
Het |
Ascc3 |
G |
T |
10: 50,625,022 (GRCm39) |
V1637L |
probably benign |
Het |
Atp2b2 |
C |
A |
6: 113,790,849 (GRCm39) |
R185L |
probably damaging |
Het |
Ccr9 |
A |
T |
9: 123,608,671 (GRCm39) |
M118L |
probably benign |
Het |
Cdh12 |
A |
T |
15: 21,480,310 (GRCm39) |
|
probably null |
Het |
Cdk13 |
T |
C |
13: 17,937,755 (GRCm39) |
S763G |
probably damaging |
Het |
Cenpk |
C |
A |
13: 104,378,911 (GRCm39) |
N177K |
probably benign |
Het |
Cfap43 |
T |
G |
19: 47,824,014 (GRCm39) |
N119T |
probably benign |
Het |
Chrna6 |
T |
C |
8: 27,898,415 (GRCm39) |
E101G |
probably null |
Het |
Clasp2 |
G |
A |
9: 113,683,370 (GRCm39) |
R400H |
probably benign |
Het |
Col6a6 |
T |
C |
9: 105,661,405 (GRCm39) |
M235V |
probably benign |
Het |
Ddx49 |
A |
T |
8: 70,748,282 (GRCm39) |
L291Q |
probably damaging |
Het |
Dhrs7 |
A |
T |
12: 72,699,860 (GRCm39) |
|
probably benign |
Het |
Dnah5 |
A |
T |
15: 28,229,687 (GRCm39) |
K107M |
possibly damaging |
Het |
Dsg2 |
C |
T |
18: 20,712,448 (GRCm39) |
R151C |
probably damaging |
Het |
Dsn1 |
T |
C |
2: 156,847,789 (GRCm39) |
T2A |
possibly damaging |
Het |
Edem3 |
A |
G |
1: 151,668,189 (GRCm39) |
|
probably benign |
Het |
Eif3c |
T |
C |
7: 126,162,884 (GRCm39) |
N133S |
possibly damaging |
Het |
F10 |
A |
G |
8: 13,095,097 (GRCm39) |
K85E |
probably benign |
Het |
Fbn2 |
T |
A |
18: 58,160,876 (GRCm39) |
|
probably benign |
Het |
Gtpbp10 |
A |
T |
5: 5,607,290 (GRCm39) |
H50Q |
probably benign |
Het |
Hephl1 |
A |
G |
9: 14,970,456 (GRCm39) |
F1013L |
probably benign |
Het |
Kcna10 |
A |
C |
3: 107,101,820 (GRCm39) |
K150N |
probably damaging |
Het |
Kirrel1 |
C |
T |
3: 86,990,914 (GRCm39) |
G636D |
probably damaging |
Het |
Kndc1 |
G |
A |
7: 139,488,912 (GRCm39) |
R189H |
probably damaging |
Het |
Knop1 |
C |
T |
7: 118,454,852 (GRCm39) |
E50K |
possibly damaging |
Het |
Kplce |
T |
C |
3: 92,776,291 (GRCm39) |
T131A |
probably damaging |
Het |
Kpna7 |
T |
A |
5: 144,926,551 (GRCm39) |
H467L |
possibly damaging |
Het |
Lcn4 |
T |
C |
2: 26,558,661 (GRCm39) |
N142D |
possibly damaging |
Het |
Map3k3 |
T |
C |
11: 106,039,741 (GRCm39) |
|
probably benign |
Het |
Mdn1 |
A |
G |
4: 32,684,707 (GRCm39) |
T806A |
probably benign |
Het |
Nbeal1 |
T |
A |
1: 60,307,598 (GRCm39) |
N1703K |
probably benign |
Het |
Neurl4 |
T |
C |
11: 69,799,360 (GRCm39) |
V914A |
probably damaging |
Het |
Niban1 |
T |
A |
1: 151,584,833 (GRCm39) |
|
probably benign |
Het |
Nop56 |
T |
C |
2: 130,118,692 (GRCm39) |
S275P |
possibly damaging |
Het |
Or1j20 |
A |
G |
2: 36,759,653 (GRCm39) |
E25G |
possibly damaging |
Het |
Or52ac1 |
A |
G |
7: 104,245,929 (GRCm39) |
V153A |
probably benign |
Het |
Or7e174 |
A |
G |
9: 20,012,771 (GRCm39) |
K239E |
probably damaging |
Het |
Otof |
A |
C |
5: 30,528,912 (GRCm39) |
I1827S |
possibly damaging |
Het |
Pappa2 |
A |
T |
1: 158,675,650 (GRCm39) |
I1032N |
probably damaging |
Het |
Pcdh7 |
A |
G |
5: 57,877,402 (GRCm39) |
E319G |
probably damaging |
Het |
Pcdhb11 |
T |
A |
18: 37,555,533 (GRCm39) |
S288T |
probably benign |
Het |
Phip |
A |
T |
9: 82,808,510 (GRCm39) |
D488E |
probably damaging |
Het |
Pla2g7 |
A |
T |
17: 43,922,303 (GRCm39) |
H394L |
probably damaging |
Het |
Plk3 |
A |
G |
4: 116,990,641 (GRCm39) |
V69A |
probably damaging |
Het |
Prob1 |
C |
A |
18: 35,786,083 (GRCm39) |
A724S |
possibly damaging |
Het |
Prune2 |
T |
C |
19: 17,100,675 (GRCm39) |
F2060L |
probably benign |
Het |
Rgl3 |
G |
A |
9: 21,887,328 (GRCm39) |
R498C |
probably benign |
Het |
Rnf213 |
A |
C |
11: 119,338,083 (GRCm39) |
N3362H |
probably damaging |
Het |
Sbds |
A |
G |
5: 130,282,774 (GRCm39) |
|
probably benign |
Het |
Scn9a |
T |
C |
2: 66,373,621 (GRCm39) |
S453G |
probably benign |
Het |
Sh3rf3 |
T |
C |
10: 58,819,897 (GRCm39) |
L236P |
probably damaging |
Het |
Skint1 |
A |
G |
4: 111,876,211 (GRCm39) |
N44S |
possibly damaging |
Het |
Slc5a1 |
T |
A |
5: 33,291,996 (GRCm39) |
I141N |
probably damaging |
Het |
Tlcd3b |
G |
A |
7: 126,424,187 (GRCm39) |
V44M |
probably damaging |
Het |
Trank1 |
T |
A |
9: 111,220,907 (GRCm39) |
I2548N |
probably damaging |
Het |
Tsc22d2 |
G |
A |
3: 58,324,749 (GRCm39) |
|
probably benign |
Het |
Unc13c |
T |
A |
9: 73,840,492 (GRCm39) |
I120F |
possibly damaging |
Het |
Vmn2r11 |
T |
G |
5: 109,207,294 (GRCm39) |
I9L |
probably benign |
Het |
Vmn2r58 |
T |
G |
7: 41,514,628 (GRCm39) |
N114H |
probably benign |
Het |
Vps53 |
A |
G |
11: 75,973,496 (GRCm39) |
L166P |
probably damaging |
Het |
Zfp119a |
T |
A |
17: 56,172,248 (GRCm39) |
K532* |
probably null |
Het |
Zfp472 |
A |
G |
17: 33,194,897 (GRCm39) |
T11A |
possibly damaging |
Het |
Zfp512b |
T |
A |
2: 181,230,051 (GRCm39) |
K87* |
probably null |
Het |
Zfp518b |
G |
A |
5: 38,831,918 (GRCm39) |
P29L |
probably damaging |
Het |
Zfp599 |
A |
G |
9: 22,161,843 (GRCm39) |
|
probably benign |
Het |
Zic2 |
CCCACCACCACCATCACCACCACCACC |
CCCACCATCACCACCACCACC |
14: 122,713,776 (GRCm39) |
|
probably benign |
Het |
|
Other mutations in Hps3 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL00545:Hps3
|
APN |
3 |
20,073,971 (GRCm39) |
missense |
possibly damaging |
0.94 |
IGL00846:Hps3
|
APN |
3 |
20,079,956 (GRCm39) |
missense |
probably benign |
0.00 |
IGL01320:Hps3
|
APN |
3 |
20,084,633 (GRCm39) |
missense |
probably benign |
0.12 |
IGL01364:Hps3
|
APN |
3 |
20,057,469 (GRCm39) |
missense |
possibly damaging |
0.58 |
IGL01751:Hps3
|
APN |
3 |
20,065,130 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL01843:Hps3
|
APN |
3 |
20,083,165 (GRCm39) |
missense |
probably benign |
0.05 |
IGL02294:Hps3
|
APN |
3 |
20,068,212 (GRCm39) |
missense |
probably damaging |
1.00 |
IGL02581:Hps3
|
APN |
3 |
20,057,385 (GRCm39) |
intron |
probably benign |
|
Blue
|
UTSW |
3 |
20,084,960 (GRCm39) |
missense |
probably damaging |
1.00 |
earl_grey
|
UTSW |
3 |
20,017,173 (GRCm38) |
intron |
probably benign |
|
gandalf
|
UTSW |
3 |
20,066,960 (GRCm39) |
nonsense |
probably null |
|
pam_gray
|
UTSW |
3 |
20,017,173 (GRCm38) |
intron |
probably benign |
|
R0107:Hps3
|
UTSW |
3 |
20,084,960 (GRCm39) |
missense |
probably damaging |
1.00 |
R0245:Hps3
|
UTSW |
3 |
20,066,960 (GRCm39) |
nonsense |
probably null |
|
R0524:Hps3
|
UTSW |
3 |
20,066,940 (GRCm39) |
missense |
probably damaging |
1.00 |
R0763:Hps3
|
UTSW |
3 |
20,057,443 (GRCm39) |
missense |
probably damaging |
1.00 |
R1795:Hps3
|
UTSW |
3 |
20,066,859 (GRCm39) |
critical splice donor site |
probably null |
|
R1864:Hps3
|
UTSW |
3 |
20,074,123 (GRCm39) |
critical splice acceptor site |
probably null |
|
R2029:Hps3
|
UTSW |
3 |
20,084,691 (GRCm39) |
missense |
probably benign |
0.01 |
R2101:Hps3
|
UTSW |
3 |
20,066,947 (GRCm39) |
missense |
possibly damaging |
0.95 |
R2221:Hps3
|
UTSW |
3 |
20,056,527 (GRCm39) |
missense |
probably benign |
|
R2268:Hps3
|
UTSW |
3 |
20,067,099 (GRCm39) |
splice site |
probably benign |
|
R2520:Hps3
|
UTSW |
3 |
20,083,194 (GRCm39) |
missense |
probably damaging |
1.00 |
R3809:Hps3
|
UTSW |
3 |
20,072,976 (GRCm39) |
missense |
probably damaging |
1.00 |
R3888:Hps3
|
UTSW |
3 |
20,057,387 (GRCm39) |
critical splice donor site |
probably null |
|
R3942:Hps3
|
UTSW |
3 |
20,051,103 (GRCm39) |
missense |
probably damaging |
1.00 |
R4022:Hps3
|
UTSW |
3 |
20,089,425 (GRCm39) |
missense |
possibly damaging |
0.69 |
R4156:Hps3
|
UTSW |
3 |
20,083,393 (GRCm39) |
missense |
probably damaging |
1.00 |
R4739:Hps3
|
UTSW |
3 |
20,084,574 (GRCm39) |
critical splice acceptor site |
probably null |
|
R4823:Hps3
|
UTSW |
3 |
20,066,890 (GRCm39) |
missense |
probably benign |
0.03 |
R4912:Hps3
|
UTSW |
3 |
20,068,337 (GRCm39) |
missense |
probably damaging |
1.00 |
R5307:Hps3
|
UTSW |
3 |
20,066,865 (GRCm39) |
missense |
possibly damaging |
0.89 |
R5859:Hps3
|
UTSW |
3 |
20,063,034 (GRCm39) |
missense |
probably benign |
0.02 |
R6140:Hps3
|
UTSW |
3 |
20,051,151 (GRCm39) |
missense |
probably damaging |
1.00 |
R6183:Hps3
|
UTSW |
3 |
20,063,032 (GRCm39) |
missense |
probably benign |
0.04 |
R6971:Hps3
|
UTSW |
3 |
20,065,699 (GRCm39) |
missense |
probably damaging |
1.00 |
R6981:Hps3
|
UTSW |
3 |
20,076,984 (GRCm39) |
missense |
probably damaging |
1.00 |
R7120:Hps3
|
UTSW |
3 |
20,065,705 (GRCm39) |
missense |
probably damaging |
1.00 |
R7146:Hps3
|
UTSW |
3 |
20,063,050 (GRCm39) |
missense |
probably damaging |
1.00 |
R7223:Hps3
|
UTSW |
3 |
20,084,583 (GRCm39) |
missense |
probably benign |
0.05 |
R7448:Hps3
|
UTSW |
3 |
20,089,329 (GRCm39) |
missense |
probably damaging |
0.99 |
R7452:Hps3
|
UTSW |
3 |
20,065,592 (GRCm39) |
missense |
probably damaging |
1.00 |
R7560:Hps3
|
UTSW |
3 |
20,084,616 (GRCm39) |
missense |
probably benign |
0.29 |
R7659:Hps3
|
UTSW |
3 |
20,076,978 (GRCm39) |
nonsense |
probably null |
|
R7769:Hps3
|
UTSW |
3 |
20,072,972 (GRCm39) |
splice site |
probably null |
|
R8050:Hps3
|
UTSW |
3 |
20,057,492 (GRCm39) |
missense |
probably benign |
|
R8242:Hps3
|
UTSW |
3 |
20,068,290 (GRCm39) |
missense |
possibly damaging |
0.59 |
R8802:Hps3
|
UTSW |
3 |
20,074,070 (GRCm39) |
missense |
probably damaging |
1.00 |
R8822:Hps3
|
UTSW |
3 |
20,057,391 (GRCm39) |
missense |
probably benign |
|
R8945:Hps3
|
UTSW |
3 |
20,068,224 (GRCm39) |
missense |
probably damaging |
0.99 |
R9111:Hps3
|
UTSW |
3 |
20,084,575 (GRCm39) |
critical splice acceptor site |
probably null |
|
R9131:Hps3
|
UTSW |
3 |
20,083,350 (GRCm39) |
missense |
probably damaging |
0.98 |
R9645:Hps3
|
UTSW |
3 |
20,084,831 (GRCm39) |
missense |
probably benign |
0.01 |
R9728:Hps3
|
UTSW |
3 |
20,065,128 (GRCm39) |
missense |
probably benign |
0.06 |
X0021:Hps3
|
UTSW |
3 |
20,084,913 (GRCm39) |
missense |
probably benign |
0.14 |
X0066:Hps3
|
UTSW |
3 |
20,070,152 (GRCm39) |
missense |
probably damaging |
1.00 |
Z1177:Hps3
|
UTSW |
3 |
20,063,065 (GRCm39) |
missense |
probably damaging |
1.00 |
|
Predicted Primers |
PCR Primer
(F):5'- TGCCGCTCAGCTATACTTACCACTTT -3'
(R):5'- GGGTTTCCACTCTGTGTTCTCATAGTC -3'
Sequencing Primer
(F):5'- TATCTGGAGCAAAACGTCTGTG -3'
(R):5'- gggaagaaggcagtaagcag -3'
|
Protein Function and Prediction |
|
Posted On |
2013-05-09 |