Incidental Mutation 'R4823:Hps3'
| ID |
371267 |
| 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 |
042439-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.072)
|
| Stock # |
R4823 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
20050109-20089478 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 20066890 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Tyrosine to Histidine
at position 559
(Y559H)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000103957
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000003714]
[ENSMUST00000012580]
[ENSMUST00000108321]
|
| 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: Y691H
PolyPhen 2
Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)
|
| SMART Domains |
Protein: ENSMUSP00000012580
Gene: ENSMUSG00000027615
AA Change: Y691H
| 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: Y559H
PolyPhen 2
Score 0.026 (Sensitivity: 0.95; Specificity: 0.81)
|
| SMART Domains |
Protein: ENSMUSP00000103957
Gene: ENSMUSG00000027615
AA Change: Y559H
| 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: ENSMUST00000139446
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000141308
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000155121
|
| Meta Mutation Damage Score |
0.0898 |
| Coding Region Coverage |
- 1x: 99.1%
- 3x: 98.5%
- 10x: 96.8%
- 20x: 94.1%
|
| Validation Efficiency |
98% (96/98) |
| 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: 88 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2310003L06Rik |
G |
A |
5: 88,120,457 (GRCm39) |
D405N |
probably benign |
Het |
| 4921517D22Rik |
T |
G |
13: 59,838,718 (GRCm39) |
E38A |
probably damaging |
Het |
| 4930433I11Rik |
A |
T |
7: 40,642,786 (GRCm39) |
I152F |
probably benign |
Het |
| Aass |
A |
T |
6: 23,107,690 (GRCm39) |
D364E |
probably benign |
Het |
| Adamts2 |
A |
G |
11: 50,628,014 (GRCm39) |
D238G |
probably benign |
Het |
| Albfm1 |
T |
A |
5: 90,714,362 (GRCm39) |
L124H |
probably benign |
Het |
| Aoc1l1 |
A |
G |
6: 48,952,195 (GRCm39) |
D40G |
probably damaging |
Het |
| Aplf |
G |
A |
6: 87,623,237 (GRCm39) |
L302F |
probably damaging |
Het |
| Apol7b |
G |
T |
15: 77,311,982 (GRCm39) |
|
probably benign |
Het |
| Arhgef12 |
A |
G |
9: 42,931,992 (GRCm39) |
V165A |
probably benign |
Het |
| Ascc3 |
T |
C |
10: 50,589,329 (GRCm39) |
S1017P |
probably damaging |
Het |
| B230104I21Rik |
T |
A |
4: 154,434,204 (GRCm39) |
|
probably benign |
Het |
| Bfsp2 |
C |
A |
9: 103,357,082 (GRCm39) |
C115F |
probably damaging |
Het |
| Bhmt2 |
A |
T |
13: 93,799,798 (GRCm39) |
W213R |
probably benign |
Het |
| Capn5 |
A |
T |
7: 97,775,648 (GRCm39) |
V431E |
probably damaging |
Het |
| Ccdc88c |
A |
G |
12: 100,896,802 (GRCm39) |
Y1390H |
probably damaging |
Het |
| Ccr3 |
A |
G |
9: 123,828,718 (GRCm39) |
T18A |
probably damaging |
Het |
| Cdh5 |
T |
C |
8: 104,869,301 (GRCm39) |
S676P |
probably benign |
Het |
| Ceacam5 |
A |
G |
7: 17,491,669 (GRCm39) |
T680A |
possibly damaging |
Het |
| Cebpd |
G |
A |
16: 15,705,978 (GRCm39) |
G264S |
probably benign |
Het |
| Cfd |
T |
C |
10: 79,726,782 (GRCm39) |
V8A |
probably benign |
Het |
| Cops9 |
C |
T |
1: 92,569,588 (GRCm39) |
|
probably benign |
Het |
| Cpne6 |
T |
C |
14: 55,754,467 (GRCm39) |
Y533H |
probably damaging |
Het |
| Cyp2c67 |
T |
A |
19: 39,604,168 (GRCm39) |
H396L |
probably benign |
Het |
| Cyp2j9 |
G |
A |
4: 96,456,972 (GRCm39) |
P500S |
possibly damaging |
Het |
| Cyp4a12a |
A |
T |
4: 115,184,610 (GRCm39) |
|
probably null |
Het |
| Dbt |
G |
A |
3: 116,317,036 (GRCm39) |
D71N |
probably damaging |
Het |
| Ddx41 |
G |
T |
13: 55,679,868 (GRCm39) |
Q440K |
probably benign |
Het |
| Elovl4 |
A |
G |
9: 83,662,738 (GRCm39) |
F174S |
probably damaging |
Het |
| Emcn |
C |
G |
3: 137,129,187 (GRCm39) |
P193R |
probably damaging |
Het |
| Etnk1 |
T |
C |
6: 143,113,364 (GRCm39) |
|
probably null |
Het |
| Fads3 |
A |
C |
19: 10,019,252 (GRCm39) |
S53R |
probably damaging |
Het |
| Fam193a |
A |
G |
5: 34,616,372 (GRCm39) |
E849G |
probably damaging |
Het |
| Fat3 |
A |
G |
9: 15,907,803 (GRCm39) |
V2733A |
probably benign |
Het |
| Frem3 |
T |
A |
8: 81,340,587 (GRCm39) |
M960K |
probably benign |
Het |
| Frmd6 |
A |
T |
12: 70,919,349 (GRCm39) |
I62L |
probably benign |
Het |
| Glmp |
T |
C |
3: 88,232,530 (GRCm39) |
|
probably benign |
Het |
| Gm17421 |
T |
C |
12: 113,333,161 (GRCm39) |
|
noncoding transcript |
Het |
| Gm27013 |
T |
A |
6: 130,499,186 (GRCm39) |
|
noncoding transcript |
Het |
| Gtf2ird1 |
A |
G |
5: 134,424,576 (GRCm39) |
V390A |
probably damaging |
Het |
| Hsh2d |
G |
A |
8: 72,954,304 (GRCm39) |
D229N |
probably benign |
Het |
| Itpr3 |
A |
G |
17: 27,304,121 (GRCm39) |
D114G |
probably benign |
Het |
| Jmjd4 |
G |
A |
11: 59,346,406 (GRCm39) |
A408T |
probably benign |
Het |
| Kcnh4 |
G |
T |
11: 100,646,000 (GRCm39) |
A316D |
probably damaging |
Het |
| Klrg1 |
T |
A |
6: 122,250,492 (GRCm39) |
|
probably null |
Het |
| Lancl2 |
T |
A |
6: 57,709,262 (GRCm39) |
Y355N |
probably damaging |
Het |
| Ltb |
T |
C |
17: 35,414,206 (GRCm39) |
S115P |
probably benign |
Het |
| Mccc2 |
T |
G |
13: 100,136,762 (GRCm39) |
R64S |
probably benign |
Het |
| Mgam2-ps |
T |
A |
6: 40,809,596 (GRCm39) |
|
noncoding transcript |
Het |
| Mrrf |
T |
G |
2: 36,038,042 (GRCm39) |
N104K |
possibly damaging |
Het |
| Nipa1 |
C |
A |
7: 55,629,436 (GRCm39) |
V226L |
possibly damaging |
Het |
| Numa1 |
T |
A |
7: 101,645,244 (GRCm39) |
L290Q |
probably damaging |
Het |
| Ofcc1 |
T |
A |
13: 40,433,949 (GRCm39) |
H52L |
probably damaging |
Het |
| Ogfod3 |
G |
A |
11: 121,086,027 (GRCm39) |
A189V |
probably benign |
Het |
| Or14c39 |
T |
A |
7: 86,343,796 (GRCm39) |
I44N |
probably damaging |
Het |
| Or5b21 |
A |
T |
19: 12,839,180 (GRCm39) |
I14F |
probably benign |
Het |
| Or5d46 |
A |
G |
2: 88,170,179 (GRCm39) |
D90G |
probably damaging |
Het |
| Or9i1b |
G |
A |
19: 13,897,022 (GRCm39) |
V213I |
probably benign |
Het |
| P2ry12 |
G |
A |
3: 59,125,318 (GRCm39) |
S119L |
probably benign |
Het |
| Pde7b |
T |
A |
10: 20,314,531 (GRCm39) |
N192Y |
probably damaging |
Het |
| Pfkl |
T |
C |
10: 77,833,428 (GRCm39) |
N258S |
probably damaging |
Het |
| Phykpl |
G |
A |
11: 51,477,420 (GRCm39) |
A71T |
probably damaging |
Het |
| Ppp1r16a |
T |
C |
15: 76,577,393 (GRCm39) |
|
probably benign |
Het |
| Pramel15 |
T |
C |
4: 144,099,781 (GRCm39) |
N328S |
possibly damaging |
Het |
| Pramel32 |
T |
C |
4: 88,547,452 (GRCm39) |
K160R |
probably damaging |
Het |
| Prune2 |
C |
T |
19: 17,097,868 (GRCm39) |
T1124M |
probably damaging |
Het |
| Rapgef6 |
A |
G |
11: 54,585,326 (GRCm39) |
I1570V |
probably benign |
Het |
| Rbm34 |
T |
C |
8: 127,697,655 (GRCm39) |
S19G |
probably benign |
Het |
| Rnf10 |
T |
C |
5: 115,393,501 (GRCm39) |
|
probably null |
Het |
| Rnf34 |
A |
G |
5: 122,988,365 (GRCm39) |
|
probably null |
Het |
| Setd4 |
A |
G |
16: 93,386,838 (GRCm39) |
S287P |
probably benign |
Het |
| Shc3 |
C |
T |
13: 51,605,606 (GRCm39) |
V225I |
probably benign |
Het |
| Sipa1l3 |
C |
T |
7: 29,070,427 (GRCm39) |
V1030I |
probably damaging |
Het |
| Siva1 |
G |
T |
12: 112,611,498 (GRCm39) |
R33L |
probably damaging |
Het |
| Slc4a5 |
C |
T |
6: 83,249,115 (GRCm39) |
T573I |
probably damaging |
Het |
| Sorcs1 |
C |
T |
19: 50,666,578 (GRCm39) |
R110Q |
possibly damaging |
Het |
| Sorcs1 |
T |
C |
19: 50,218,740 (GRCm39) |
I581V |
possibly damaging |
Het |
| Sorl1 |
T |
C |
9: 41,903,617 (GRCm39) |
D1545G |
probably damaging |
Het |
| Tas2r124 |
T |
G |
6: 132,732,509 (GRCm39) |
S273A |
probably damaging |
Het |
| Tcf15 |
T |
C |
2: 151,985,813 (GRCm39) |
F90L |
probably damaging |
Het |
| Trim59 |
G |
A |
3: 68,944,453 (GRCm39) |
R296C |
probably benign |
Het |
| Tulp1 |
A |
T |
17: 28,572,546 (GRCm39) |
D229E |
probably benign |
Het |
| Ush1c |
T |
A |
7: 45,845,157 (GRCm39) |
N886I |
probably benign |
Het |
| Usp9y |
A |
T |
Y: 1,444,559 (GRCm39) |
S127T |
probably damaging |
Het |
| Vmn1r19 |
T |
A |
6: 57,382,219 (GRCm39) |
Y257* |
probably null |
Het |
| Vmn2r109 |
A |
T |
17: 20,774,153 (GRCm39) |
Y401N |
probably damaging |
Het |
| Vmn2r69 |
A |
C |
7: 85,060,508 (GRCm39) |
S359A |
probably benign |
Het |
| Zfp37 |
A |
T |
4: 62,109,740 (GRCm39) |
N479K |
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 |
|
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 |
|
|
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'- TGTGGTACAGTGATGATGAAAGATC -3'
(R):5'- AGCAAAAGTGGCTCAGATATTCC -3'
Sequencing Primer
(F):5'- TTCCATTTGACAGATCTAAAGTTCC -3'
(R):5'- GCTCAGATATTCCACATGGCTGAG -3'
|
| Posted On |
2016-03-01 |
Incidental Mutation