Incidental Mutation 'R0763:Hps3'
| ID |
72492 |
| 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 |
038943-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.072)
|
| Stock # |
R0763 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
20050109-20089478 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to G
at 20057443 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Serine
at position 780
(R780S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000103957
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000003714]
[ENSMUST00000012580]
[ENSMUST00000108321]
[ENSMUST00000108328]
[ENSMUST00000108329]
[ENSMUST00000173779]
|
| AlphaFold |
Q91VB4 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000003714
|
| SMART Domains |
Protein: ENSMUSP00000003714
Gene: ENSMUSG00000003617
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Cu-oxidase_3
|
90 |
203 |
5.1e-8 |
PFAM |
|
Pfam:Cu-oxidase
|
220 |
357 |
9.6e-11 |
PFAM |
|
Pfam:Cu-oxidase_2
|
280 |
357 |
1.1e-7 |
PFAM |
|
Pfam:Cu-oxidase_3
|
444 |
556 |
1.4e-7 |
PFAM |
|
Blast:FA58C
|
598 |
673 |
3e-6 |
BLAST |
|
Pfam:Cu-oxidase_3
|
789 |
897 |
2.3e-9 |
PFAM |
|
Pfam:Cu-oxidase_2
|
927 |
1054 |
8.3e-18 |
PFAM |
|
low complexity region
|
1067 |
1078 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000012580
AA Change: R912S
PolyPhen 2
Score 0.960 (Sensitivity: 0.78; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000012580
Gene: ENSMUSG00000027615
AA Change: R912S
| 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 damaging
Transcript: ENSMUST00000108321
AA Change: R780S
PolyPhen 2
Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
|
| SMART Domains |
Protein: ENSMUSP00000103957
Gene: ENSMUSG00000027615
AA Change: R780S
| 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 |
probably benign
Transcript: ENSMUST00000108328
|
| SMART Domains |
Protein: ENSMUSP00000103964
Gene: ENSMUSG00000003617
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Cu-oxidase_3
|
90 |
203 |
5.1e-8 |
PFAM |
|
Pfam:Cu-oxidase
|
220 |
357 |
9.6e-11 |
PFAM |
|
Pfam:Cu-oxidase_2
|
280 |
357 |
1.1e-7 |
PFAM |
|
Pfam:Cu-oxidase_3
|
444 |
556 |
1.4e-7 |
PFAM |
|
Blast:FA58C
|
598 |
673 |
3e-6 |
BLAST |
|
Pfam:Cu-oxidase_3
|
789 |
897 |
2.3e-9 |
PFAM |
|
Pfam:Cu-oxidase_2
|
927 |
1054 |
8.3e-18 |
PFAM |
|
low complexity region
|
1067 |
1078 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000108329
|
| SMART Domains |
Protein: ENSMUSP00000103965
Gene: ENSMUSG00000003617
| Domain | Start | End | E-Value | Type |
|---|
|
Pfam:Cu-oxidase_3
|
89 |
203 |
8.7e-8 |
PFAM |
|
Pfam:Cu-oxidase
|
220 |
357 |
7.8e-12 |
PFAM |
|
Pfam:Cu-oxidase_2
|
242 |
356 |
2.1e-7 |
PFAM |
|
Pfam:Cu-oxidase_3
|
445 |
555 |
4.4e-7 |
PFAM |
|
Blast:FA58C
|
599 |
674 |
3e-6 |
BLAST |
|
Pfam:Cu-oxidase_3
|
793 |
898 |
6.1e-9 |
PFAM |
|
Pfam:Cu-oxidase_2
|
931 |
1055 |
5.2e-18 |
PFAM |
|
low complexity region
|
1068 |
1079 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000130171
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000139446
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000141308
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000173779
|
| SMART Domains |
Protein: ENSMUSP00000133643
Gene: ENSMUSG00000003617
| Domain | Start | End | E-Value | Type |
|---|
|
SCOP:d1gw0a3
|
1 |
37 |
7e-5 |
SMART |
|
| Meta Mutation Damage Score |
0.3325 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.1%
- 20x: 93.8%
|
| Validation Efficiency |
96% (52/54) |
| 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: 50 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abtb1 |
A |
C |
6: 88,815,261 (GRCm39) |
F290V |
probably damaging |
Het |
| Adam26b |
G |
A |
8: 43,973,601 (GRCm39) |
S467L |
probably damaging |
Het |
| Adgrv1 |
T |
A |
13: 81,647,244 (GRCm39) |
I3099F |
probably damaging |
Het |
| Akap6 |
A |
G |
12: 53,188,997 (GRCm39) |
D2137G |
possibly damaging |
Het |
| Arhgdig |
T |
C |
17: 26,419,275 (GRCm39) |
Y48C |
probably damaging |
Het |
| Astn1 |
A |
G |
1: 158,337,460 (GRCm39) |
I389V |
possibly damaging |
Het |
| Atp8a1 |
T |
C |
5: 67,817,226 (GRCm39) |
D920G |
probably benign |
Het |
| BC016579 |
T |
A |
16: 45,449,818 (GRCm39) |
N200I |
probably damaging |
Het |
| Casc3 |
T |
C |
11: 98,722,144 (GRCm39) |
Y661H |
probably damaging |
Het |
| Cep120 |
A |
C |
18: 53,854,809 (GRCm39) |
V442G |
probably benign |
Het |
| Cfap65 |
A |
G |
1: 74,943,841 (GRCm39) |
Y1557H |
probably damaging |
Het |
| Chd2 |
G |
T |
7: 73,097,022 (GRCm39) |
Q1485K |
possibly damaging |
Het |
| Cntrl |
T |
C |
2: 35,061,078 (GRCm39) |
F1967L |
probably benign |
Het |
| Csmd1 |
G |
A |
8: 17,077,300 (GRCm39) |
T119M |
possibly damaging |
Het |
| Dnah9 |
T |
C |
11: 66,046,356 (GRCm39) |
H64R |
probably benign |
Het |
| Ep400 |
T |
C |
5: 110,813,703 (GRCm39) |
R2899G |
probably damaging |
Het |
| Foxl2 |
A |
C |
9: 98,838,086 (GRCm39) |
T125P |
probably damaging |
Het |
| Foxred1 |
A |
T |
9: 35,118,769 (GRCm39) |
|
probably null |
Het |
| H2-Eb1 |
T |
A |
17: 34,533,133 (GRCm39) |
|
probably benign |
Het |
| Heatr3 |
T |
C |
8: 88,884,869 (GRCm39) |
S378P |
probably damaging |
Het |
| Hectd4 |
T |
C |
5: 121,445,096 (GRCm39) |
|
probably benign |
Het |
| Ifi44 |
G |
A |
3: 151,455,135 (GRCm39) |
A30V |
probably damaging |
Het |
| Il12rb1 |
G |
A |
8: 71,265,934 (GRCm39) |
|
probably benign |
Het |
| Invs |
G |
A |
4: 48,392,628 (GRCm39) |
G281R |
possibly damaging |
Het |
| Itgax |
C |
A |
7: 127,747,112 (GRCm39) |
|
probably benign |
Het |
| Jade1 |
G |
T |
3: 41,568,218 (GRCm39) |
C762F |
possibly damaging |
Het |
| Lama1 |
C |
T |
17: 68,079,813 (GRCm39) |
P1229S |
probably damaging |
Het |
| Mmp15 |
C |
A |
8: 96,094,856 (GRCm39) |
D243E |
probably benign |
Het |
| Mug2 |
A |
G |
6: 122,052,253 (GRCm39) |
T1004A |
probably benign |
Het |
| Myh14 |
A |
T |
7: 44,314,791 (GRCm39) |
V44E |
probably damaging |
Het |
| N4bp2l1 |
C |
A |
5: 150,517,869 (GRCm39) |
R11S |
possibly damaging |
Het |
| Notch4 |
T |
A |
17: 34,784,306 (GRCm39) |
C36* |
probably null |
Het |
| Nwd1 |
A |
G |
8: 73,397,672 (GRCm39) |
D637G |
probably damaging |
Het |
| Ogfod1 |
T |
C |
8: 94,782,264 (GRCm39) |
I238T |
probably benign |
Het |
| Pakap |
G |
A |
4: 57,688,441 (GRCm39) |
E95K |
probably damaging |
Het |
| Papln |
A |
G |
12: 83,838,639 (GRCm39) |
D1256G |
possibly damaging |
Het |
| Ppp1r26 |
T |
C |
2: 28,340,379 (GRCm39) |
L3P |
probably damaging |
Het |
| Rbm10 |
C |
T |
X: 20,503,903 (GRCm39) |
|
probably benign |
Het |
| Slc17a5 |
A |
T |
9: 78,460,372 (GRCm39) |
|
probably benign |
Het |
| Slc25a17 |
A |
G |
15: 81,207,907 (GRCm39) |
|
probably benign |
Het |
| Socs4 |
T |
C |
14: 47,528,112 (GRCm39) |
F349S |
probably damaging |
Het |
| Spata31f1a |
A |
G |
4: 42,851,238 (GRCm39) |
V306A |
probably damaging |
Het |
| Tchhl1 |
A |
C |
3: 93,378,878 (GRCm39) |
E527D |
probably benign |
Het |
| Tm7sf3 |
A |
G |
6: 146,507,787 (GRCm39) |
L425S |
possibly damaging |
Het |
| Tmem266 |
G |
T |
9: 55,322,239 (GRCm39) |
V112L |
probably damaging |
Het |
| Tmem30c |
T |
A |
16: 57,090,539 (GRCm39) |
I223F |
possibly damaging |
Het |
| Tomm70a |
G |
A |
16: 56,942,535 (GRCm39) |
G104D |
probably benign |
Het |
| Ttc17 |
G |
T |
2: 94,163,148 (GRCm39) |
A834E |
probably benign |
Het |
| Ttn |
C |
T |
2: 76,561,534 (GRCm39) |
V20664M |
probably damaging |
Het |
| Zbed5 |
T |
C |
5: 129,931,020 (GRCm39) |
V323A |
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 |
|
|
R0421:Hps3
|
UTSW |
3 |
20,083,480 (GRCm39) |
missense |
probably benign |
0.00 |
|
R0524:Hps3
|
UTSW |
3 |
20,066,940 (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'- TTCAACGCAAAATGTGGATACGCC -3'
(R):5'- CTCATCTGTAGCCCTTCATTGGACG -3'
Sequencing Primer
(F):5'- ctgactgctcctgagttcc -3'
(R):5'- GGACGTAGCCTCCATTATTCCG -3'
|
| Posted On |
2013-09-30 |
Incidental Mutation