Incidental Mutation 'R8050:Hps3'
| ID |
618971 |
| 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 |
067487-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.076)
|
| Stock # |
R8050 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
3 |
| Chromosomal Location |
20050109-20089478 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
T to C
at 20057492 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Histidine to Arginine
at position 896
(H896R)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000012580
(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 benign
Transcript: ENSMUST00000012580
AA Change: H896R
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000012580
Gene: ENSMUSG00000027615
AA Change: H896R
| 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: H764R
PolyPhen 2
Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
|
| SMART Domains |
Protein: ENSMUSP00000103957
Gene: ENSMUSG00000027615
AA Change: H764R
| 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 |
probably benign
Transcript: ENSMUST00000173779
|
| SMART Domains |
Protein: ENSMUSP00000133643
Gene: ENSMUSG00000003617
| Domain | Start | End | E-Value | Type |
|---|
|
SCOP:d1gw0a3
|
1 |
37 |
7e-5 |
SMART |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.7%
- 20x: 99.2%
|
| 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 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: 67 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2410002F23Rik |
T |
A |
7: 43,900,677 (GRCm39) |
V194E |
possibly damaging |
Het |
| Adgrv1 |
T |
C |
13: 81,561,296 (GRCm39) |
N5406S |
probably damaging |
Het |
| Arhgef38 |
T |
A |
3: 132,843,323 (GRCm39) |
R416* |
probably null |
Het |
| Asb7 |
T |
A |
7: 66,328,932 (GRCm39) |
Q36L |
probably benign |
Het |
| Bbof1 |
G |
A |
12: 84,457,991 (GRCm39) |
M85I |
probably benign |
Het |
| Bin1 |
T |
G |
18: 32,539,198 (GRCm39) |
F44V |
probably damaging |
Het |
| Bnc2 |
C |
A |
4: 84,210,573 (GRCm39) |
V599L |
probably benign |
Het |
| Bnip3l |
A |
G |
14: 67,226,651 (GRCm39) |
S181P |
probably damaging |
Het |
| Btnl9 |
A |
G |
11: 49,066,442 (GRCm39) |
L374P |
probably benign |
Het |
| Cd109 |
T |
C |
9: 78,571,633 (GRCm39) |
I424T |
probably benign |
Het |
| Cdhr2 |
G |
A |
13: 54,882,035 (GRCm39) |
V1162M |
probably damaging |
Het |
| Dgkb |
G |
A |
12: 38,174,216 (GRCm39) |
E181K |
probably benign |
Het |
| Dnase1 |
A |
T |
16: 3,855,861 (GRCm39) |
D64V |
probably damaging |
Het |
| E130308A19Rik |
T |
C |
4: 59,719,767 (GRCm39) |
I433T |
probably damaging |
Het |
| Ecsit |
C |
T |
9: 21,987,592 (GRCm39) |
R149H |
probably benign |
Het |
| Eif1ad8 |
G |
A |
12: 87,563,911 (GRCm39) |
R82Q |
possibly damaging |
Het |
| Enpep |
A |
T |
3: 129,099,165 (GRCm39) |
V437E |
probably damaging |
Het |
| Esrp1 |
A |
T |
4: 11,338,767 (GRCm39) |
V679D |
probably damaging |
Het |
| Fa2h |
T |
A |
8: 112,074,817 (GRCm39) |
|
probably null |
Het |
| Fabp1 |
G |
A |
6: 71,176,956 (GRCm39) |
E16K |
probably damaging |
Het |
| Fstl5 |
T |
A |
3: 76,614,810 (GRCm39) |
S624T |
probably benign |
Het |
| Gemin5 |
G |
A |
11: 58,019,686 (GRCm39) |
R1128W |
probably benign |
Het |
| H2bc8 |
T |
C |
13: 23,755,841 (GRCm39) |
S79P |
probably damaging |
Het |
| Hsf1 |
T |
A |
15: 76,382,481 (GRCm39) |
I284K |
probably benign |
Het |
| Igkv3-2 |
T |
A |
6: 70,675,988 (GRCm39) |
I99N |
probably damaging |
Het |
| Iqub |
T |
A |
6: 24,503,784 (GRCm39) |
I163F |
possibly damaging |
Het |
| Jak2 |
T |
C |
19: 29,275,732 (GRCm39) |
I724T |
probably damaging |
Het |
| Kbtbd3 |
A |
T |
9: 4,330,408 (GRCm39) |
T261S |
probably benign |
Het |
| Kctd20 |
G |
T |
17: 29,171,732 (GRCm39) |
|
probably null |
Het |
| Kif28 |
C |
T |
1: 179,537,014 (GRCm39) |
V490M |
probably benign |
Het |
| Kif9 |
T |
C |
9: 110,348,208 (GRCm39) |
L677P |
probably damaging |
Het |
| Klhl18 |
T |
C |
9: 110,257,829 (GRCm39) |
Y537C |
probably damaging |
Het |
| Mmut |
T |
A |
17: 41,254,784 (GRCm39) |
I331K |
probably benign |
Het |
| Myo5a |
T |
A |
9: 75,089,228 (GRCm39) |
S1119R |
probably damaging |
Het |
| Napepld |
C |
A |
5: 21,870,319 (GRCm39) |
E366D |
probably benign |
Het |
| Nbea |
A |
G |
3: 55,895,402 (GRCm39) |
V1540A |
probably damaging |
Het |
| Neb |
T |
A |
2: 52,111,738 (GRCm39) |
I130L |
probably benign |
Het |
| Opcml |
T |
C |
9: 28,724,640 (GRCm39) |
V146A |
probably damaging |
Het |
| Or2g7 |
T |
C |
17: 38,378,370 (GRCm39) |
S103P |
probably damaging |
Het |
| Or2r11 |
A |
T |
6: 42,437,764 (GRCm39) |
L63H |
probably damaging |
Het |
| Or7e178 |
C |
T |
9: 20,225,941 (GRCm39) |
D92N |
probably damaging |
Het |
| Pappa2 |
A |
C |
1: 158,675,970 (GRCm39) |
C925W |
probably damaging |
Het |
| Parp12 |
T |
A |
6: 39,066,038 (GRCm39) |
N562Y |
probably damaging |
Het |
| Patj |
C |
A |
4: 98,427,201 (GRCm39) |
H1198Q |
probably benign |
Het |
| Pcyox1 |
T |
A |
6: 86,366,128 (GRCm39) |
K362M |
possibly damaging |
Het |
| Pcyt2 |
T |
C |
11: 120,501,765 (GRCm39) |
Y350C |
probably benign |
Het |
| Pkd1 |
A |
T |
17: 24,784,617 (GRCm39) |
T388S |
probably benign |
Het |
| Prl3d1 |
T |
A |
13: 27,284,011 (GRCm39) |
Y193* |
probably null |
Het |
| Psme1 |
A |
T |
14: 55,817,056 (GRCm39) |
D15V |
possibly damaging |
Het |
| Qrsl1 |
G |
A |
10: 43,750,631 (GRCm39) |
R476C |
probably damaging |
Het |
| Ranbp2 |
A |
G |
10: 58,315,441 (GRCm39) |
N2054D |
probably damaging |
Het |
| Serpinb1c |
T |
A |
13: 33,066,052 (GRCm39) |
K298* |
probably null |
Het |
| Slc22a27 |
A |
T |
19: 7,857,532 (GRCm39) |
M355K |
probably benign |
Het |
| Spp1 |
T |
A |
5: 104,588,280 (GRCm39) |
H227Q |
probably benign |
Het |
| Stam2 |
T |
A |
2: 52,609,785 (GRCm39) |
N75I |
probably damaging |
Het |
| Tacc1 |
T |
C |
8: 25,659,230 (GRCm39) |
T579A |
probably benign |
Het |
| Tbx3 |
A |
G |
5: 119,821,132 (GRCm39) |
D734G |
probably benign |
Het |
| Tmem233 |
G |
T |
5: 116,221,141 (GRCm39) |
S35* |
probably null |
Het |
| Trim43c |
A |
T |
9: 88,722,390 (GRCm39) |
E12V |
probably damaging |
Het |
| Trio |
A |
G |
15: 27,891,540 (GRCm39) |
S463P |
unknown |
Het |
| Uggt2 |
A |
T |
14: 119,263,834 (GRCm39) |
D1065E |
probably damaging |
Het |
| Usp1 |
A |
G |
4: 98,817,150 (GRCm39) |
N114S |
probably benign |
Het |
| Usp34 |
A |
G |
11: 23,396,787 (GRCm39) |
E2377G |
|
Het |
| Virma |
T |
A |
4: 11,528,643 (GRCm39) |
H1243Q |
probably benign |
Het |
| Vmn2r3 |
A |
T |
3: 64,178,714 (GRCm39) |
V517D |
probably damaging |
Het |
| Zfp931 |
T |
C |
2: 177,709,889 (GRCm39) |
K166E |
probably damaging |
Het |
| Zp3 |
T |
A |
5: 136,011,604 (GRCm39) |
Y141N |
probably damaging |
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 |
|
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 |
|
|
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'- CCCTCATTCTGCAGATAAGCC -3'
(R):5'- CCAGGGCCATATTCATGTTTTC -3'
Sequencing Primer
(F):5'- TTCTGCAGATAAGCCAAGCAAAG -3'
(R):5'- TGGCAAAGTGGGATTTTATTATTTTG -3'
|
| Posted On |
2020-01-23 |
Incidental Mutation