Incidental Mutation 'R2101:Hps3'
| ID |
230482 |
| 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 |
040105-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.072)
|
| Stock # |
R2101 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
3 |
| Chromosomal Location |
20050109-20089478 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
C to A
at 20066947 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Valine to Phenylalanine
at position 540
(V540F)
|
| 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 |
possibly damaging
Transcript: ENSMUST00000012580
AA Change: V672F
PolyPhen 2
Score 0.899 (Sensitivity: 0.82; Specificity: 0.94)
|
| SMART Domains |
Protein: ENSMUSP00000012580
Gene: ENSMUSG00000027615
AA Change: V672F
| 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 |
possibly damaging
Transcript: ENSMUST00000108321
AA Change: V540F
PolyPhen 2
Score 0.950 (Sensitivity: 0.79; Specificity: 0.95)
|
| SMART Domains |
Protein: ENSMUSP00000103957
Gene: ENSMUSG00000027615
AA Change: V540F
| 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: ENSMUST00000141308
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000155121
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000139446
|
| Meta Mutation Damage Score |
0.1795 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.4%
- 20x: 95.6%
|
| Validation Efficiency |
100% (67/67) |
| 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: 65 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abtb2 |
G |
A |
2: 103,397,207 (GRCm39) |
A46T |
probably benign |
Het |
| Agap3 |
T |
A |
5: 24,692,797 (GRCm39) |
L47Q |
probably damaging |
Het |
| Apaf1 |
T |
G |
10: 90,895,942 (GRCm39) |
I377L |
probably benign |
Het |
| Astn2 |
G |
A |
4: 65,499,923 (GRCm39) |
R937* |
probably null |
Het |
| Cacnb1 |
A |
C |
11: 97,896,554 (GRCm39) |
V369G |
probably damaging |
Het |
| Cdc42bpa |
G |
T |
1: 179,974,533 (GRCm39) |
V1464L |
probably benign |
Het |
| Cdkn2aip |
A |
T |
8: 48,166,036 (GRCm39) |
M90K |
probably damaging |
Het |
| Chd3 |
A |
T |
11: 69,239,877 (GRCm39) |
D1650E |
probably benign |
Het |
| Chd9 |
C |
T |
8: 91,760,615 (GRCm39) |
P2120L |
probably benign |
Het |
| Clca3a2 |
T |
C |
3: 144,783,699 (GRCm39) |
T639A |
probably damaging |
Het |
| Cluh |
G |
T |
11: 74,551,328 (GRCm39) |
|
probably benign |
Het |
| Cnga1 |
C |
T |
5: 72,776,404 (GRCm39) |
V20I |
possibly damaging |
Het |
| Col11a2 |
A |
T |
17: 34,271,143 (GRCm39) |
D528V |
probably damaging |
Het |
| Cyfip2 |
A |
G |
11: 46,133,270 (GRCm39) |
L810P |
probably damaging |
Het |
| D430041D05Rik |
A |
G |
2: 103,979,175 (GRCm39) |
V2084A |
probably damaging |
Het |
| Dcc |
G |
A |
18: 71,943,941 (GRCm39) |
H237Y |
possibly damaging |
Het |
| Ddx60 |
T |
A |
8: 62,393,679 (GRCm39) |
F38L |
probably damaging |
Het |
| Dio2 |
T |
C |
12: 90,696,597 (GRCm39) |
*130W |
probably null |
Het |
| Dock5 |
G |
T |
14: 68,031,459 (GRCm39) |
F990L |
probably benign |
Het |
| Dpy19l1 |
A |
T |
9: 24,393,331 (GRCm39) |
V146E |
probably damaging |
Het |
| Dscam |
T |
C |
16: 96,411,549 (GRCm39) |
T1776A |
probably benign |
Het |
| Enpep |
C |
T |
3: 129,092,587 (GRCm39) |
S532N |
probably benign |
Het |
| Gdf6 |
A |
G |
4: 9,860,025 (GRCm39) |
D369G |
probably damaging |
Het |
| Gtf2b |
T |
C |
3: 142,477,144 (GRCm39) |
|
probably benign |
Het |
| Hmbox1 |
A |
G |
14: 65,066,028 (GRCm39) |
|
probably benign |
Het |
| Hsd3b6 |
T |
A |
3: 98,713,553 (GRCm39) |
I249F |
possibly damaging |
Het |
| Hunk |
T |
A |
16: 90,229,388 (GRCm39) |
|
probably null |
Het |
| Kidins220 |
T |
A |
12: 25,107,422 (GRCm39) |
L1625Q |
probably damaging |
Het |
| Krt1 |
C |
T |
15: 101,754,622 (GRCm39) |
G543S |
unknown |
Het |
| Myo10 |
T |
A |
15: 25,722,345 (GRCm39) |
L186Q |
probably benign |
Het |
| N4bp2 |
T |
A |
5: 65,948,224 (GRCm39) |
W285R |
probably damaging |
Het |
| Nat8l |
T |
C |
5: 34,155,716 (GRCm39) |
L124P |
probably damaging |
Het |
| Nemp2 |
T |
C |
1: 52,680,225 (GRCm39) |
|
probably null |
Het |
| Nkain2 |
G |
A |
10: 32,205,813 (GRCm39) |
T74I |
possibly damaging |
Het |
| Nol4 |
A |
G |
18: 22,956,466 (GRCm39) |
S239P |
probably damaging |
Het |
| Or4c118 |
T |
A |
2: 88,975,301 (GRCm39) |
E22V |
probably benign |
Het |
| Pcbp3 |
T |
C |
10: 76,625,589 (GRCm39) |
I152V |
possibly damaging |
Het |
| Pcp4l1 |
G |
T |
1: 171,003,174 (GRCm39) |
P10Q |
probably damaging |
Het |
| Pla1a |
T |
C |
16: 38,235,730 (GRCm39) |
N135D |
probably damaging |
Het |
| Plb1 |
T |
A |
5: 32,507,004 (GRCm39) |
M1193K |
probably damaging |
Het |
| Prc1 |
T |
C |
7: 79,962,032 (GRCm39) |
V73A |
probably benign |
Het |
| Prkd2 |
T |
A |
7: 16,603,490 (GRCm39) |
W807R |
probably damaging |
Het |
| Prp2rt |
G |
T |
13: 97,235,730 (GRCm39) |
R6S |
probably damaging |
Het |
| Ptprb |
C |
T |
10: 116,150,943 (GRCm39) |
|
probably benign |
Het |
| Rb1cc1 |
A |
G |
1: 6,319,559 (GRCm39) |
I993V |
probably benign |
Het |
| Rbp3 |
C |
T |
14: 33,677,975 (GRCm39) |
T641M |
probably damaging |
Het |
| Rev3l |
T |
C |
10: 39,704,092 (GRCm39) |
V2046A |
probably benign |
Het |
| Rnpep |
G |
T |
1: 135,199,355 (GRCm39) |
N334K |
probably damaging |
Het |
| Sarm1 |
G |
A |
11: 78,366,115 (GRCm39) |
P695S |
probably damaging |
Het |
| Sf3a3 |
C |
T |
4: 124,612,136 (GRCm39) |
T131I |
possibly damaging |
Het |
| Slc38a10 |
A |
T |
11: 120,023,567 (GRCm39) |
V283E |
probably damaging |
Het |
| Slco6c1 |
A |
T |
1: 97,000,595 (GRCm39) |
L552* |
probably null |
Het |
| Tas2r136 |
T |
C |
6: 132,754,495 (GRCm39) |
M211V |
probably benign |
Het |
| Tax1bp3 |
G |
A |
11: 73,071,947 (GRCm39) |
D65N |
probably damaging |
Het |
| Tdrd5 |
A |
G |
1: 156,129,209 (GRCm39) |
F167S |
probably damaging |
Het |
| Tfeb |
G |
A |
17: 48,100,590 (GRCm39) |
V269M |
probably damaging |
Het |
| Tspan12 |
A |
T |
6: 21,799,887 (GRCm39) |
F153L |
probably benign |
Het |
| Txnrd1 |
T |
G |
10: 82,717,573 (GRCm39) |
L186V |
probably damaging |
Het |
| Upk1b |
A |
T |
16: 38,600,499 (GRCm39) |
C160* |
probably null |
Het |
| Uty |
T |
C |
Y: 1,176,541 (GRCm39) |
Q172R |
probably damaging |
Het |
| Vmn1r23 |
T |
C |
6: 57,903,437 (GRCm39) |
K114E |
possibly damaging |
Het |
| Vmn2r99 |
T |
G |
17: 19,598,253 (GRCm39) |
N92K |
probably damaging |
Het |
| Vstm2a |
T |
A |
11: 16,213,191 (GRCm39) |
M192K |
probably benign |
Het |
| Zc3h12c |
A |
G |
9: 52,027,721 (GRCm39) |
V547A |
probably benign |
Het |
| Zfp944 |
T |
A |
17: 22,558,809 (GRCm39) |
N146I |
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 |
|
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'- CTAAAGTTCCATCTAACACTGTCTG -3'
(R):5'- CCTGTTTCCTATTGGCTAACGG -3'
Sequencing Primer
(F):5'- ACACTGTCTGTTTTCTGTTACTAAG -3'
(R):5'- TAGCAGCAAAAGTGGCTC -3'
|
| Posted On |
2014-09-18 |
Incidental Mutation