Incidental Mutation 'R4022:Hps3'
ID |
368266 |
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 |
040956-MU
|
Accession Numbers |
|
Essential gene? |
Probably non essential
(E-score: 0.076)
|
Stock # |
R4022 (G1)
|
Quality Score |
66 |
Status
|
Validated
|
Chromosome |
3 |
Chromosomal Location |
20050109-20089478 bp(-) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
A to G
at 20089425 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Valine to Alanine
at position 2
(V2A)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000012580
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000012580]
[ENSMUST00000108321]
|
AlphaFold |
Q91VB4 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000012580
AA Change: V2A
PolyPhen 2
Score 0.690 (Sensitivity: 0.86; Specificity: 0.92)
|
SMART Domains |
Protein: ENSMUSP00000012580 Gene: ENSMUSG00000027615 AA Change: V2A
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: V2A
PolyPhen 2
Score 0.326 (Sensitivity: 0.90; Specificity: 0.89)
|
SMART Domains |
Protein: ENSMUSP00000103957 Gene: ENSMUSG00000027615 AA Change: V2A
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 |
0.0856 |
Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.5%
- 10x: 97.1%
- 20x: 94.3%
|
Validation Efficiency |
98% (58/59) |
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: 57 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Abo |
T |
A |
2: 26,733,812 (GRCm39) |
Y131F |
probably damaging |
Het |
Adcy4 |
C |
T |
14: 56,012,635 (GRCm39) |
|
probably null |
Het |
Ago3 |
T |
A |
4: 126,262,386 (GRCm39) |
N388I |
probably benign |
Het |
Arfgef2 |
G |
T |
2: 166,715,865 (GRCm39) |
V1385L |
probably benign |
Het |
Camk2a |
A |
T |
18: 61,097,000 (GRCm39) |
K28* |
probably null |
Het |
Ccdc180 |
T |
A |
4: 45,904,560 (GRCm39) |
Y385* |
probably null |
Het |
Cd209g |
A |
T |
8: 4,185,955 (GRCm39) |
Q46L |
possibly damaging |
Het |
Cdh22 |
T |
C |
2: 164,999,173 (GRCm39) |
T220A |
probably benign |
Het |
Cltc |
A |
T |
11: 86,611,174 (GRCm39) |
C562S |
probably damaging |
Het |
Cyp2c55 |
T |
A |
19: 39,023,878 (GRCm39) |
|
probably null |
Het |
Cyp2d34 |
A |
G |
15: 82,502,809 (GRCm39) |
V139A |
probably benign |
Het |
Ddias |
G |
T |
7: 92,510,686 (GRCm39) |
D105E |
possibly damaging |
Het |
Dhx30 |
T |
C |
9: 109,913,465 (GRCm39) |
D1223G |
possibly damaging |
Het |
Dnajb11 |
A |
G |
16: 22,688,196 (GRCm39) |
D238G |
probably damaging |
Het |
Entpd7 |
G |
A |
19: 43,679,597 (GRCm39) |
R50Q |
probably benign |
Het |
Erbb2 |
T |
G |
11: 98,326,123 (GRCm39) |
C966W |
probably benign |
Het |
Exoc1 |
C |
T |
5: 76,697,417 (GRCm39) |
T405I |
possibly damaging |
Het |
Fbxo28 |
T |
C |
1: 182,157,475 (GRCm39) |
N108S |
possibly damaging |
Het |
Fhdc1 |
T |
C |
3: 84,352,409 (GRCm39) |
E157G |
probably benign |
Het |
Gstcd |
C |
T |
3: 132,787,829 (GRCm39) |
V290M |
probably damaging |
Het |
Ilrun |
T |
C |
17: 28,005,236 (GRCm39) |
E107G |
probably damaging |
Het |
Itsn2 |
G |
A |
12: 4,674,927 (GRCm39) |
R23H |
probably damaging |
Het |
Kirrel1 |
C |
T |
3: 86,996,458 (GRCm39) |
M380I |
probably null |
Het |
Lax1 |
C |
T |
1: 133,610,774 (GRCm39) |
G105S |
probably benign |
Het |
Lin7c |
G |
T |
2: 109,726,790 (GRCm39) |
|
probably null |
Het |
Lrrn2 |
T |
C |
1: 132,866,852 (GRCm39) |
V639A |
probably benign |
Het |
Luzp1 |
T |
C |
4: 136,269,504 (GRCm39) |
S576P |
probably benign |
Het |
Mast4 |
G |
T |
13: 102,990,377 (GRCm39) |
A48E |
probably damaging |
Het |
Mast4 |
G |
A |
13: 102,875,829 (GRCm39) |
R1112* |
probably null |
Het |
Mat2a |
G |
A |
6: 72,413,227 (GRCm39) |
R168C |
probably damaging |
Het |
Megf8 |
T |
C |
7: 25,037,200 (GRCm39) |
V700A |
probably damaging |
Het |
Mroh2a |
G |
C |
1: 88,173,764 (GRCm39) |
A871P |
probably damaging |
Het |
Myh2 |
G |
T |
11: 67,070,230 (GRCm39) |
E421* |
probably null |
Het |
Or12d2 |
T |
A |
17: 37,625,165 (GRCm39) |
I37L |
probably benign |
Het |
Or5k17 |
T |
C |
16: 58,746,483 (GRCm39) |
I150M |
possibly damaging |
Het |
Pecam1 |
T |
C |
11: 106,545,986 (GRCm39) |
N693D |
probably benign |
Het |
Ppip5k1 |
C |
T |
2: 121,168,108 (GRCm39) |
R715H |
probably damaging |
Het |
Prune2 |
A |
G |
19: 16,977,384 (GRCm39) |
T40A |
probably damaging |
Het |
Ranbp17 |
G |
A |
11: 33,429,189 (GRCm39) |
A352V |
probably benign |
Het |
Reln |
T |
C |
5: 22,432,628 (GRCm39) |
Q124R |
probably benign |
Het |
Rnf17 |
C |
T |
14: 56,697,458 (GRCm39) |
H451Y |
probably damaging |
Het |
Ryr3 |
C |
G |
2: 112,506,218 (GRCm39) |
R3443P |
probably damaging |
Het |
Sall3 |
T |
A |
18: 81,013,055 (GRCm39) |
E1127V |
probably benign |
Het |
Sertad3 |
A |
G |
7: 27,176,120 (GRCm39) |
N185D |
probably damaging |
Het |
Sox1 |
A |
G |
8: 12,446,719 (GRCm39) |
Y120C |
probably damaging |
Het |
Spag17 |
A |
T |
3: 99,956,546 (GRCm39) |
I881F |
probably benign |
Het |
Spart |
G |
T |
3: 55,025,157 (GRCm39) |
V251L |
probably damaging |
Het |
Stard9 |
A |
G |
2: 120,534,636 (GRCm39) |
E3631G |
probably benign |
Het |
Syde2 |
A |
G |
3: 145,721,480 (GRCm39) |
T848A |
probably benign |
Het |
Tmem11 |
T |
C |
11: 60,756,154 (GRCm39) |
D12G |
possibly damaging |
Het |
Trim28 |
T |
C |
7: 12,762,485 (GRCm39) |
|
probably benign |
Het |
Tsen2 |
T |
A |
6: 115,524,948 (GRCm39) |
V49E |
probably damaging |
Het |
Tspan1 |
C |
T |
4: 116,024,232 (GRCm39) |
M10I |
probably benign |
Het |
Uncx |
A |
T |
5: 139,532,444 (GRCm39) |
T170S |
probably damaging |
Het |
Usp24 |
T |
C |
4: 106,236,421 (GRCm39) |
|
probably benign |
Het |
Vmn1r84 |
T |
C |
7: 12,095,857 (GRCm39) |
I267V |
probably benign |
Het |
Zfp488 |
T |
A |
14: 33,693,110 (GRCm39) |
M18L |
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 |
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'- TCTGCGGTCGCTAAAACAAC -3'
(R):5'- ATCTGTCCAGAAGCAGCAAAG -3'
Sequencing Primer
(F):5'- TTCGCTGTAGGCCATGC -3'
(R):5'- TCTGTCCAGAAGCAGCAAAGTTAAC -3'
|
Posted On |
2016-01-15 |