Incidental Mutation 'R0107:Hps3'
| ID |
33308 |
| 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 |
038393-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.076)
|
| Stock # |
R0107 (G1)
|
| Quality Score |
91 |
|
Status
|
Validated
(trace)
|
| Chromosome |
3 |
| Chromosomal Location |
20050109-20089478 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to C
at 20084960 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Leucine to Arginine
at position 76
(L76R)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000012580
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000012580]
[ENSMUST00000108321]
|
| AlphaFold |
Q91VB4 |
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000012580
AA Change: L76R
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000012580
Gene: ENSMUSG00000027615
AA Change: L76R
| 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
|
| SMART Domains |
Protein: ENSMUSP00000103957
Gene: ENSMUSG00000027615
| 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: ENSMUST00000133094
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000137408
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000155121
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000151752
|
| Meta Mutation Damage Score |
0.6467 |
| Coding Region Coverage |
- 1x: 99.0%
- 3x: 98.1%
- 10x: 95.8%
- 20x: 90.6%
|
| Validation Efficiency |
99% (71/72) |
| 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: 63 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Aadacl2fm2 |
T |
A |
3: 59,659,737 (GRCm39) |
L397I |
possibly damaging |
Het |
| Abca1 |
A |
G |
4: 53,080,834 (GRCm39) |
V825A |
probably benign |
Het |
| Adamts7 |
T |
C |
9: 90,062,773 (GRCm39) |
I409T |
possibly damaging |
Het |
| Adck1 |
T |
C |
12: 88,413,426 (GRCm39) |
W253R |
possibly damaging |
Het |
| Afg3l2 |
A |
G |
18: 67,564,836 (GRCm39) |
F213L |
probably damaging |
Het |
| Ankle2 |
T |
C |
5: 110,400,893 (GRCm39) |
V743A |
probably benign |
Het |
| Ankrd34c |
C |
T |
9: 89,611,537 (GRCm39) |
R268H |
probably benign |
Het |
| Arb2a |
A |
G |
13: 78,050,933 (GRCm39) |
D145G |
probably damaging |
Het |
| Bcl2 |
G |
A |
1: 106,640,292 (GRCm39) |
R107C |
probably damaging |
Het |
| Ccdc7b |
T |
G |
8: 129,904,678 (GRCm39) |
|
probably benign |
Het |
| Cd320 |
A |
T |
17: 34,067,059 (GRCm39) |
M169L |
probably benign |
Het |
| Chn1 |
A |
G |
2: 73,445,028 (GRCm39) |
Y338H |
probably damaging |
Het |
| Chuk |
T |
A |
19: 44,085,358 (GRCm39) |
S263C |
probably damaging |
Het |
| Dennd4b |
C |
A |
3: 90,180,043 (GRCm39) |
P663T |
possibly damaging |
Het |
| Dnajc24 |
T |
G |
2: 105,832,259 (GRCm39) |
|
probably benign |
Het |
| Fbn2 |
A |
G |
18: 58,189,275 (GRCm39) |
V1617A |
probably benign |
Het |
| Fermt2 |
T |
C |
14: 45,702,279 (GRCm39) |
N502D |
probably damaging |
Het |
| Frrs1 |
A |
T |
3: 116,690,365 (GRCm39) |
I3F |
probably damaging |
Het |
| Fut1 |
C |
A |
7: 45,268,270 (GRCm39) |
Q20K |
possibly damaging |
Het |
| Gbf1 |
T |
C |
19: 46,273,267 (GRCm39) |
V1709A |
probably benign |
Het |
| Gfra3 |
G |
T |
18: 34,844,359 (GRCm39) |
H60Q |
probably benign |
Het |
| Gm10750 |
T |
A |
2: 148,857,973 (GRCm39) |
M93L |
unknown |
Het |
| Hmcn1 |
T |
A |
1: 150,462,766 (GRCm39) |
I5124L |
probably benign |
Het |
| Ifrd1 |
T |
A |
12: 40,264,080 (GRCm39) |
Q105L |
probably damaging |
Het |
| Irs2 |
A |
T |
8: 11,054,691 (GRCm39) |
V1247E |
probably damaging |
Het |
| Itgal |
T |
C |
7: 126,927,731 (GRCm39) |
|
probably benign |
Het |
| Ivns1abp |
A |
T |
1: 151,237,321 (GRCm39) |
N495I |
probably damaging |
Het |
| Kank1 |
T |
A |
19: 25,407,730 (GRCm39) |
|
probably benign |
Het |
| Mroh8 |
T |
C |
2: 157,067,388 (GRCm39) |
Q657R |
probably benign |
Het |
| Mthfd1l |
T |
C |
10: 3,991,838 (GRCm39) |
Y597H |
probably benign |
Het |
| Myom1 |
G |
A |
17: 71,384,360 (GRCm39) |
V692I |
probably damaging |
Het |
| Or13a17 |
A |
T |
7: 140,271,258 (GRCm39) |
M147L |
probably benign |
Het |
| Or1j18 |
T |
G |
2: 36,624,730 (GRCm39) |
Y132* |
probably null |
Het |
| Or7g20 |
A |
G |
9: 18,946,629 (GRCm39) |
D70G |
probably damaging |
Het |
| Palmd |
A |
T |
3: 116,717,725 (GRCm39) |
H257Q |
probably damaging |
Het |
| Pcnx2 |
A |
T |
8: 126,480,325 (GRCm39) |
V1994D |
probably benign |
Het |
| Phkb |
G |
A |
8: 86,743,560 (GRCm39) |
G553S |
probably benign |
Het |
| Plekha5 |
G |
A |
6: 140,537,473 (GRCm39) |
R646K |
possibly damaging |
Het |
| Ptprn |
A |
T |
1: 75,232,356 (GRCm39) |
L453M |
probably damaging |
Het |
| Ptprz1 |
T |
A |
6: 23,000,569 (GRCm39) |
D886E |
probably damaging |
Het |
| Rcn1 |
T |
A |
2: 105,225,126 (GRCm39) |
I110F |
possibly damaging |
Het |
| Scn1a |
T |
A |
2: 66,154,977 (GRCm39) |
T661S |
probably benign |
Het |
| Slc6a19 |
A |
G |
13: 73,832,176 (GRCm39) |
Y467H |
possibly damaging |
Het |
| Slc9c1 |
T |
A |
16: 45,395,783 (GRCm39) |
D611E |
probably benign |
Het |
| Slitrk6 |
T |
C |
14: 110,989,395 (GRCm39) |
E104G |
possibly damaging |
Het |
| Spag17 |
A |
T |
3: 99,958,103 (GRCm39) |
K920N |
possibly damaging |
Het |
| St3gal5 |
A |
G |
6: 72,119,133 (GRCm39) |
S82G |
probably benign |
Het |
| Tlk1 |
T |
C |
2: 70,544,333 (GRCm39) |
*767W |
probably null |
Het |
| Tln2 |
A |
G |
9: 67,277,988 (GRCm39) |
V342A |
probably damaging |
Het |
| Tmem104 |
T |
A |
11: 115,093,006 (GRCm39) |
M132K |
probably damaging |
Het |
| Tmem184c |
A |
G |
8: 78,323,702 (GRCm39) |
S387P |
possibly damaging |
Het |
| Tmtc1 |
A |
G |
6: 148,327,411 (GRCm39) |
V34A |
possibly damaging |
Het |
| Trim46 |
A |
G |
3: 89,143,640 (GRCm39) |
F596S |
probably damaging |
Het |
| Unc79 |
T |
A |
12: 103,100,784 (GRCm39) |
D1870E |
possibly damaging |
Het |
| Utp20 |
T |
C |
10: 88,614,253 (GRCm39) |
T1234A |
probably benign |
Het |
| Vmn1r31 |
T |
A |
6: 58,449,728 (GRCm39) |
T46S |
probably benign |
Het |
| Vps13a |
A |
T |
19: 16,669,188 (GRCm39) |
L1341Q |
probably benign |
Het |
| Wdr72 |
A |
T |
9: 74,117,715 (GRCm39) |
D821V |
probably damaging |
Het |
| Zfhx4 |
T |
C |
3: 5,464,042 (GRCm39) |
L1400P |
probably damaging |
Het |
| Zfp217 |
T |
A |
2: 169,956,794 (GRCm39) |
K735* |
probably null |
Het |
| Zfp235 |
A |
G |
7: 23,836,541 (GRCm39) |
Q29R |
probably damaging |
Het |
| Zfp628 |
A |
G |
7: 4,923,167 (GRCm39) |
Y463C |
probably damaging |
Het |
| Zkscan4 |
A |
G |
13: 21,668,751 (GRCm39) |
T401A |
possibly 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 |
|
|
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 |
|
|
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'- AGTCAAATGCATCACGTACCTTCCG -3'
(R):5'- CACACCTCAGAGGCTGTTGCTTAG -3'
|
| Posted On |
2013-05-09 |
Incidental Mutation