Incidental Mutation 'R7120:Hps3'
| ID |
551911 |
| 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 |
045209-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.076)
|
| Stock # |
R7120 (G1)
|
| Quality Score |
225.009 |
|
Status
|
Not validated
|
| Chromosome |
3 |
| Chromosomal Location |
20050109-20089478 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
G to A
at 20065705 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Arginine to Tryptophan
at position 712
(R712W)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000012580
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000003714]
[ENSMUST00000012580]
[ENSMUST00000108321]
[ENSMUST00000108328]
[ENSMUST00000108329]
|
| 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 damaging
Transcript: ENSMUST00000012580
AA Change: R712W
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000012580
Gene: ENSMUSG00000027615
AA Change: R712W
| 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 damaging
Transcript: ENSMUST00000108321
AA Change: R580W
PolyPhen 2
Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
|
| SMART Domains |
Protein: ENSMUSP00000103957
Gene: ENSMUSG00000027615
AA Change: R580W
| 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 |
|
| Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.4%
|
| Validation Efficiency |
|
| 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: 74 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1810062G17Rik |
A |
T |
3: 36,536,016 (GRCm39) |
Q94L |
unknown |
Het |
| 4933411K16Rik |
C |
T |
19: 42,041,112 (GRCm39) |
A81V |
probably benign |
Het |
| Actr3 |
A |
C |
1: 125,331,169 (GRCm39) |
Y273* |
probably null |
Het |
| Aoc1 |
T |
A |
6: 48,883,531 (GRCm39) |
I469N |
probably damaging |
Het |
| Arhgef28 |
A |
T |
13: 98,081,047 (GRCm39) |
L1270Q |
probably damaging |
Het |
| Atp2c1 |
G |
A |
9: 105,297,385 (GRCm39) |
Q780* |
probably null |
Het |
| Bbs10 |
T |
C |
10: 111,135,310 (GRCm39) |
V141A |
possibly damaging |
Het |
| Bivm |
A |
T |
1: 44,165,606 (GRCm39) |
T19S |
probably benign |
Het |
| Cacna1h |
T |
G |
17: 25,610,481 (GRCm39) |
H675P |
probably benign |
Het |
| Cadps |
T |
A |
14: 12,439,919 (GRCm38) |
L1204F |
probably damaging |
Het |
| Cald1 |
T |
C |
6: 34,663,011 (GRCm39) |
|
probably null |
Het |
| Calr |
A |
G |
8: 85,569,457 (GRCm39) |
M357T |
probably damaging |
Het |
| Ccni |
A |
T |
5: 93,331,190 (GRCm39) |
Y260* |
probably null |
Het |
| Csrnp3 |
C |
A |
2: 65,853,354 (GRCm39) |
T594K |
probably damaging |
Het |
| Dek |
A |
T |
13: 47,253,659 (GRCm39) |
M152K |
unknown |
Het |
| Depdc1b |
T |
C |
13: 108,498,781 (GRCm39) |
W155R |
probably benign |
Het |
| Ehd1 |
A |
G |
19: 6,347,591 (GRCm39) |
K315R |
probably benign |
Het |
| Epn3 |
C |
A |
11: 94,383,254 (GRCm39) |
R323S |
probably benign |
Het |
| Fan1 |
T |
A |
7: 64,022,234 (GRCm39) |
N340Y |
probably damaging |
Het |
| Fbxo10 |
T |
A |
4: 45,040,533 (GRCm39) |
K891* |
probably null |
Het |
| Fras1 |
G |
T |
5: 96,900,819 (GRCm39) |
G3013* |
probably null |
Het |
| Gbp2b |
A |
G |
3: 142,312,507 (GRCm39) |
T297A |
probably benign |
Het |
| Gbp7 |
T |
C |
3: 142,249,734 (GRCm39) |
S402P |
probably damaging |
Het |
| Gclc |
T |
C |
9: 77,694,032 (GRCm39) |
Y329H |
probably damaging |
Het |
| Gfpt1 |
A |
G |
6: 87,064,375 (GRCm39) |
H655R |
probably benign |
Het |
| Gm4787 |
C |
A |
12: 81,425,260 (GRCm39) |
M299I |
probably benign |
Het |
| Grb7 |
C |
A |
11: 98,345,817 (GRCm39) |
R532S |
probably benign |
Het |
| Hmcn1 |
A |
T |
1: 150,576,292 (GRCm39) |
I2066N |
probably damaging |
Het |
| Hnrnpll |
T |
C |
17: 80,341,486 (GRCm39) |
T518A |
probably benign |
Het |
| Hspd1 |
A |
G |
1: 55,118,388 (GRCm39) |
V406A |
probably benign |
Het |
| Igkv2-112 |
T |
C |
6: 68,197,510 (GRCm39) |
F61L |
probably benign |
Het |
| Iqcf5 |
G |
A |
9: 106,392,995 (GRCm39) |
R84H |
probably damaging |
Het |
| Itgad |
T |
A |
7: 127,773,146 (GRCm39) |
M1K |
probably null |
Het |
| Kmt2d |
A |
G |
15: 98,758,946 (GRCm39) |
S1292P |
unknown |
Het |
| Macc1 |
C |
A |
12: 119,409,480 (GRCm39) |
Q83K |
possibly damaging |
Het |
| Map3k4 |
G |
T |
17: 12,490,354 (GRCm39) |
A359E |
probably damaging |
Het |
| Mfap3 |
T |
A |
11: 57,419,043 (GRCm39) |
C68S |
probably damaging |
Het |
| Mipep |
C |
T |
14: 61,112,696 (GRCm39) |
R660C |
possibly damaging |
Het |
| Morc2b |
A |
T |
17: 33,354,787 (GRCm39) |
L995Q |
probably damaging |
Het |
| Mrc1 |
A |
G |
2: 14,313,508 (GRCm39) |
N913S |
probably damaging |
Het |
| N4bp1 |
C |
A |
8: 87,587,495 (GRCm39) |
C481F |
probably benign |
Het |
| Nae1 |
A |
G |
8: 105,252,910 (GRCm39) |
|
probably null |
Het |
| Nup214 |
T |
A |
2: 31,941,054 (GRCm39) |
V29E |
probably benign |
Het |
| Or1e30 |
A |
T |
11: 73,677,940 (GRCm39) |
M59L |
probably damaging |
Het |
| Or8c11 |
T |
C |
9: 38,289,945 (GRCm39) |
L250P |
probably damaging |
Het |
| Orai1 |
A |
G |
5: 123,167,535 (GRCm39) |
E236G |
possibly damaging |
Het |
| P2rx7 |
A |
G |
5: 122,819,357 (GRCm39) |
Y593C |
probably benign |
Het |
| Pcbp2 |
A |
G |
15: 102,383,113 (GRCm39) |
D77G |
possibly damaging |
Het |
| Pcdha8 |
G |
A |
18: 37,126,840 (GRCm39) |
V441M |
possibly damaging |
Het |
| Peg10 |
CCACATCAGGATCCACATCAGGATGCACATCAGCATCAGGATCCCCATCAGGATGCACATCAGGATCCACATCAGGATGCACATCAG |
CCACATCAGGATCCACATCAGGATGCACATCAG |
6: 4,756,398 (GRCm39) |
|
probably benign |
Het |
| Plaa |
A |
G |
4: 94,470,919 (GRCm39) |
S406P |
possibly damaging |
Het |
| Plekhh1 |
C |
A |
12: 79,117,713 (GRCm39) |
P903Q |
probably benign |
Het |
| Plekhh3 |
T |
C |
11: 101,059,064 (GRCm39) |
E92G |
probably damaging |
Het |
| Ptpn9 |
T |
C |
9: 56,967,166 (GRCm39) |
F463S |
probably damaging |
Het |
| Ptprn2 |
A |
C |
12: 116,835,676 (GRCm39) |
E337A |
probably benign |
Het |
| Rubcn |
C |
T |
16: 32,656,839 (GRCm39) |
R527Q |
probably damaging |
Het |
| Samd3 |
C |
T |
10: 26,106,864 (GRCm39) |
T73M |
possibly damaging |
Het |
| Sfxn4 |
T |
A |
19: 60,840,477 (GRCm39) |
K173* |
probably null |
Het |
| Son |
CATGGACTCCCAGATGTTAGCAACTAGCTCTATGGACTCCCAGATGTTAGCAACTAGCTCTATGGACTCCCAGATGTTAGCAACCAGCAGTATGGACTCCCAGATGTTAGCAACCAGCAGTATGGACTCCCAGATGTTAGCAACCAGCTCCATGGACTCCCAGATGTTAGCAAC |
CATGGACTCCCAGATGTTAGCAACTAGCTCTATGGACTCCCAGATGTTAGCAACCAGCAGTATGGACTCCCAGATGTTAGCAACCAGCAGTATGGACTCCCAGATGTTAGCAACCAGCTCCATGGACTCCCAGATGTTAGCAAC |
16: 91,453,579 (GRCm39) |
|
probably benign |
Het |
| Son |
T |
G |
16: 91,467,414 (GRCm39) |
N2258K |
unknown |
Het |
| Sspo |
A |
T |
6: 48,442,505 (GRCm39) |
H2000L |
probably benign |
Het |
| Syne1 |
C |
T |
10: 5,243,971 (GRCm39) |
S2731N |
probably benign |
Het |
| Syt6 |
T |
C |
3: 103,494,673 (GRCm39) |
Y213H |
probably damaging |
Het |
| Tkt |
A |
G |
14: 30,281,779 (GRCm39) |
N99S |
probably benign |
Het |
| Tlcd3b |
T |
C |
7: 126,428,505 (GRCm39) |
L221P |
probably damaging |
Het |
| Tmem258 |
G |
A |
19: 10,181,602 (GRCm39) |
|
probably benign |
Het |
| Tnks1bp1 |
T |
C |
2: 84,902,441 (GRCm39) |
S1702P |
probably damaging |
Het |
| Tpte |
A |
G |
8: 22,817,689 (GRCm39) |
D225G |
probably damaging |
Het |
| Trak1 |
T |
A |
9: 121,289,564 (GRCm39) |
F625L |
probably benign |
Het |
| Ttc33 |
G |
T |
15: 5,241,488 (GRCm39) |
C77F |
probably benign |
Het |
| Ugt1a2 |
A |
G |
1: 88,128,522 (GRCm39) |
H55R |
probably damaging |
Het |
| Vmn1r169 |
G |
T |
7: 23,277,444 (GRCm39) |
V279L |
probably benign |
Het |
| Vmn2r25 |
T |
C |
6: 123,805,394 (GRCm39) |
K488E |
possibly damaging |
Het |
| Vmn2r8 |
A |
T |
5: 108,956,504 (GRCm39) |
D39E |
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 |
|
|
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 |
|
|
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 |
|
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'- CCTTTGGTTTCTATCAGACAACTCAG -3'
(R):5'- GGAACATCTCAAAGCTTAGTTCC -3'
Sequencing Primer
(F):5'- CAGAAAAATTACATTTCCAACTGGAC -3'
(R):5'- CGAGAAAGATAATATTCTTCTTGGGG -3'
|
| Posted On |
2019-05-15 |
Incidental Mutation