Incidental Mutation 'R2221:Hps3'
ID |
241473 |
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 |
040223-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.076)
|
Stock # |
R2221 (G1)
|
Quality Score |
225 |
Status
|
Validated
|
Chromosome |
3 |
Chromosomal Location |
20050109-20089478 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to T
at 20056527 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Serine to Arginine
at position 815
(S815R)
|
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 benign
Transcript: ENSMUST00000012580
AA Change: S947R
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
SMART Domains |
Protein: ENSMUSP00000012580 Gene: ENSMUSG00000027615 AA Change: S947R
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: S815R
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
SMART Domains |
Protein: ENSMUSP00000103957 Gene: ENSMUSG00000027615 AA Change: S815R
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 |
0.0898 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 94.8%
|
Validation Efficiency |
100% (58/58) |
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: 56 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Adamtsl1 |
A |
C |
4: 86,306,762 (GRCm39) |
D1392A |
probably benign |
Het |
Afdn |
T |
C |
17: 14,103,999 (GRCm39) |
|
probably benign |
Het |
Aph1b |
A |
T |
9: 66,691,921 (GRCm39) |
M121K |
probably damaging |
Het |
Aspg |
G |
A |
12: 112,080,868 (GRCm39) |
A120T |
probably damaging |
Het |
Bicd1 |
A |
G |
6: 149,418,503 (GRCm39) |
T725A |
probably damaging |
Het |
Cd1d2 |
A |
T |
3: 86,895,847 (GRCm39) |
I292F |
probably damaging |
Het |
Cdcp3 |
A |
T |
7: 130,849,186 (GRCm39) |
|
probably null |
Het |
Cdk13 |
A |
G |
13: 17,894,120 (GRCm39) |
V495A |
probably damaging |
Het |
Cfd |
A |
T |
10: 79,728,039 (GRCm39) |
|
probably null |
Het |
Col9a2 |
C |
G |
4: 120,911,455 (GRCm39) |
R599G |
probably damaging |
Het |
Cradd |
A |
C |
10: 95,011,735 (GRCm39) |
V135G |
probably benign |
Het |
Cry1 |
A |
G |
10: 84,979,617 (GRCm39) |
C460R |
probably damaging |
Het |
Ctu2 |
A |
G |
8: 123,207,649 (GRCm39) |
E375G |
probably damaging |
Het |
Dym |
T |
G |
18: 75,363,236 (GRCm39) |
I580S |
probably damaging |
Het |
Eif3e |
A |
G |
15: 43,114,943 (GRCm39) |
L411P |
possibly damaging |
Het |
Emsy |
T |
C |
7: 98,239,982 (GRCm39) |
E1091G |
possibly damaging |
Het |
Enkur |
A |
G |
2: 21,194,130 (GRCm39) |
|
probably benign |
Het |
Fam184a |
G |
A |
10: 53,531,175 (GRCm39) |
T733M |
probably damaging |
Het |
Frem2 |
G |
A |
3: 53,424,278 (GRCm39) |
A3053V |
probably benign |
Het |
Gbgt1 |
T |
C |
2: 28,388,435 (GRCm39) |
L40P |
probably damaging |
Het |
Gm5174 |
T |
A |
10: 86,492,372 (GRCm39) |
|
noncoding transcript |
Het |
Gys2 |
G |
T |
6: 142,402,148 (GRCm39) |
D230E |
probably damaging |
Het |
Herc2 |
T |
A |
7: 55,818,766 (GRCm39) |
|
probably null |
Het |
Igf1r |
C |
A |
7: 67,851,710 (GRCm39) |
S983R |
probably damaging |
Het |
Itsn1 |
T |
A |
16: 91,650,656 (GRCm39) |
|
probably benign |
Het |
Kcnc2 |
A |
G |
10: 112,292,431 (GRCm39) |
N91D |
probably damaging |
Het |
Kif28 |
C |
A |
1: 179,560,676 (GRCm39) |
A210S |
possibly damaging |
Het |
Klri2 |
T |
A |
6: 129,717,272 (GRCm39) |
Q37L |
probably damaging |
Het |
Lrrc38 |
T |
A |
4: 143,096,419 (GRCm39) |
C243* |
probably null |
Het |
Map3k5 |
T |
C |
10: 19,943,666 (GRCm39) |
V590A |
possibly damaging |
Het |
Mdn1 |
C |
A |
4: 32,763,306 (GRCm39) |
F5135L |
probably benign |
Het |
Megf11 |
G |
A |
9: 64,567,713 (GRCm39) |
G401S |
possibly damaging |
Het |
Mst1r |
T |
C |
9: 107,785,547 (GRCm39) |
F402L |
probably damaging |
Het |
Ntrk3 |
T |
C |
7: 77,848,600 (GRCm39) |
I759V |
probably damaging |
Het |
Nup188 |
T |
C |
2: 30,226,936 (GRCm39) |
|
probably benign |
Het |
Or4a71 |
C |
T |
2: 89,358,281 (GRCm39) |
V158I |
probably benign |
Het |
Or8b12i |
T |
C |
9: 20,082,388 (GRCm39) |
S160G |
possibly damaging |
Het |
Prdm2 |
T |
C |
4: 142,861,469 (GRCm39) |
N607S |
possibly damaging |
Het |
Prl2a1 |
T |
A |
13: 27,990,369 (GRCm39) |
|
probably null |
Het |
Serpina9 |
T |
A |
12: 103,964,523 (GRCm39) |
I305F |
probably damaging |
Het |
Setx |
GTGGCT |
GT |
2: 29,044,073 (GRCm39) |
1814 |
probably null |
Het |
Slc19a1 |
C |
T |
10: 76,878,320 (GRCm39) |
T285I |
probably benign |
Het |
Snap91 |
T |
C |
9: 86,674,580 (GRCm39) |
T544A |
possibly damaging |
Het |
Srgap3 |
A |
G |
6: 112,923,454 (GRCm39) |
S2P |
probably damaging |
Het |
Tcof1 |
A |
G |
18: 60,970,973 (GRCm39) |
V210A |
possibly damaging |
Het |
Tex261 |
A |
G |
6: 83,748,497 (GRCm39) |
I136T |
probably benign |
Het |
Trpa1 |
A |
T |
1: 14,973,480 (GRCm39) |
F279L |
probably null |
Het |
Ttc39b |
T |
C |
4: 83,150,999 (GRCm39) |
N532S |
probably benign |
Het |
Ttn |
T |
C |
2: 76,572,438 (GRCm39) |
T26152A |
probably damaging |
Het |
Ube2w |
A |
G |
1: 16,668,183 (GRCm39) |
S97P |
possibly damaging |
Het |
Vmn1r25 |
A |
C |
6: 57,956,223 (GRCm39) |
L22R |
probably damaging |
Het |
Vmn1r64 |
T |
C |
7: 5,887,448 (GRCm39) |
I32V |
probably benign |
Het |
Vmn2r112 |
T |
G |
17: 22,820,214 (GRCm39) |
M29R |
possibly damaging |
Het |
Vmn2r71 |
T |
A |
7: 85,273,301 (GRCm39) |
M705K |
probably benign |
Het |
Vps13b |
G |
A |
15: 35,884,743 (GRCm39) |
V3139I |
probably benign |
Het |
Zfp628 |
T |
C |
7: 4,923,830 (GRCm39) |
V684A |
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 |
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 |
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'- TAGATGACTCTTGCACCCTGGG -3'
(R):5'- TAAGTTTCATCAGGAGCCTCGC -3'
Sequencing Primer
(F):5'- GGTACCTCACCTGACATCATGG -3'
(R):5'- CCTTGTTATAACAGAGGTGCTTC -3'
|
Posted On |
2014-10-15 |