Incidental Mutation 'R9060:Hps4'
ID |
688921 |
Institutional Source |
Beutler Lab
|
Gene Symbol |
Hps4
|
Ensembl Gene |
ENSMUSG00000042328 |
Gene Name |
HPS4, biogenesis of lysosomal organelles complex 3 subunit 2 |
Synonyms |
BLOC-3, 2010205O06Rik, Hermansky-Pudlak syndrome 4, C130020P05Rik |
MMRRC Submission |
068886-MU
|
Accession Numbers |
|
Essential gene? |
Possibly non essential
(E-score: 0.272)
|
Stock # |
R9060 (G1)
|
Quality Score |
225.009 |
Status
|
Validated
|
Chromosome |
5 |
Chromosomal Location |
112490949-112526280 bp(+) (GRCm39) |
Type of Mutation |
missense |
DNA Base Change (assembly) |
G to A
at 112525905 bp (GRCm39)
|
Zygosity |
Heterozygous |
Amino Acid Change |
Serine to Asparagine
at position 642
(S642N)
|
Ref Sequence |
ENSEMBL: ENSMUSP00000047920
(fasta)
|
Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000035279]
[ENSMUST00000112359]
|
AlphaFold |
Q99KG7 |
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000035279
AA Change: S642N
PolyPhen 2
Score 0.810 (Sensitivity: 0.84; Specificity: 0.93)
|
SMART Domains |
Protein: ENSMUSP00000047920 Gene: ENSMUSG00000042328 AA Change: S642N
Domain | Start | End | E-Value | Type |
low complexity region
|
171 |
180 |
N/A |
INTRINSIC |
low complexity region
|
467 |
486 |
N/A |
INTRINSIC |
low complexity region
|
514 |
529 |
N/A |
INTRINSIC |
|
Predicted Effect |
possibly damaging
Transcript: ENSMUST00000112359
AA Change: S642N
PolyPhen 2
Score 0.810 (Sensitivity: 0.84; Specificity: 0.93)
|
SMART Domains |
Protein: ENSMUSP00000107978 Gene: ENSMUSG00000042328 AA Change: S642N
Domain | Start | End | E-Value | Type |
low complexity region
|
171 |
180 |
N/A |
INTRINSIC |
low complexity region
|
467 |
486 |
N/A |
INTRINSIC |
low complexity region
|
514 |
529 |
N/A |
INTRINSIC |
|
Meta Mutation Damage Score |
0.0638 |
Coding Region Coverage |
- 1x: 100.0%
- 3x: 100.0%
- 10x: 99.8%
- 20x: 99.3%
|
Validation Efficiency |
98% (54/55) |
MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein component of biogenesis of lysosome-related organelles complexes (BLOC). BLOC complexes are important for the formation of endosomal-lysosomal organelles such as melanosomes and platelet dense granules. Mutations in this gene result in subtype 4 of Hermansky-Pudlak syndrome, a form of albinism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012] PHENOTYPE: Homozygotes for a spontaneous null mutation exhibit hypopigmentation, prolonged bleeding associated with a platelet defect, reduced secretion of kidney lysosomal enzymes, and resistance to diet-induced atherosclerosis. [provided by MGI curators]
|
Allele List at MGI |
|
Other mutations in this stock |
Total: 54 list
Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
Acat3 |
A |
C |
17: 13,145,293 (GRCm39) |
V295G |
|
Het |
Agfg1 |
T |
C |
1: 82,872,254 (GRCm39) |
V529A |
possibly damaging |
Het |
Ap1g2 |
G |
A |
14: 55,337,887 (GRCm39) |
P667L |
probably benign |
Het |
Arhgap29 |
T |
A |
3: 121,783,973 (GRCm39) |
S176T |
probably damaging |
Het |
Casq2 |
A |
G |
3: 102,052,619 (GRCm39) |
D377G |
unknown |
Het |
Ccdc14 |
T |
C |
16: 34,517,486 (GRCm39) |
L104P |
probably benign |
Het |
Cep104 |
T |
C |
4: 154,074,281 (GRCm39) |
I511T |
probably damaging |
Het |
Cgn |
A |
G |
3: 94,687,165 (GRCm39) |
Y46H |
probably damaging |
Het |
Cilp |
T |
C |
9: 65,186,302 (GRCm39) |
V799A |
probably benign |
Het |
Col6a1 |
A |
G |
10: 76,557,711 (GRCm39) |
V175A |
probably benign |
Het |
Dclk1 |
C |
A |
3: 55,163,575 (GRCm39) |
D222E |
probably benign |
Het |
Dnah10 |
G |
T |
5: 124,905,141 (GRCm39) |
C4058F |
probably damaging |
Het |
Dnai4 |
A |
T |
4: 102,947,750 (GRCm39) |
D175E |
probably benign |
Het |
Elmod3 |
A |
T |
6: 72,543,790 (GRCm39) |
Y334N |
probably damaging |
Het |
Enah |
C |
A |
1: 181,749,817 (GRCm39) |
A341S |
probably damaging |
Het |
Eomes |
T |
C |
9: 118,311,364 (GRCm39) |
*396Q |
probably null |
Het |
Epb41l1 |
T |
A |
2: 156,345,679 (GRCm39) |
Y227* |
probably null |
Het |
Epha5 |
A |
T |
5: 84,218,977 (GRCm39) |
D765E |
probably benign |
Het |
Fat3 |
T |
C |
9: 15,910,782 (GRCm39) |
N1740S |
possibly damaging |
Het |
Fhip2a |
C |
T |
19: 57,361,450 (GRCm39) |
H125Y |
probably damaging |
Het |
Galnt9 |
G |
A |
5: 110,737,710 (GRCm39) |
R222H |
possibly damaging |
Het |
Gm19410 |
A |
G |
8: 36,269,480 (GRCm39) |
D1105G |
probably damaging |
Het |
Hoxa13 |
T |
A |
6: 52,236,897 (GRCm39) |
Y121F |
probably damaging |
Het |
Jag1 |
T |
G |
2: 136,931,204 (GRCm39) |
T643P |
probably damaging |
Het |
Limd1 |
T |
A |
9: 123,309,514 (GRCm39) |
S404R |
probably benign |
Het |
Micall2 |
A |
T |
5: 139,705,035 (GRCm39) |
S100T |
probably damaging |
Het |
Miga2 |
T |
A |
2: 30,271,735 (GRCm39) |
L419Q |
probably damaging |
Het |
Ms4a13 |
A |
C |
19: 11,168,950 (GRCm39) |
I25S |
|
Het |
Nnmt |
T |
C |
9: 48,503,367 (GRCm39) |
T220A |
probably benign |
Het |
Nrg3 |
G |
A |
14: 38,734,052 (GRCm39) |
T278I |
probably damaging |
Het |
Nup98 |
A |
G |
7: 101,783,895 (GRCm39) |
W1146R |
probably damaging |
Het |
Or13a28 |
T |
G |
7: 140,217,695 (GRCm39) |
L27R |
|
Het |
Or5m10 |
T |
C |
2: 85,717,920 (GRCm39) |
Y259H |
probably benign |
Het |
Pacsin3 |
T |
C |
2: 91,091,557 (GRCm39) |
F85L |
probably benign |
Het |
Padi4 |
T |
A |
4: 140,477,953 (GRCm39) |
D465V |
probably damaging |
Het |
Pakap |
A |
G |
4: 57,855,412 (GRCm39) |
E247G |
probably damaging |
Het |
Pclo |
A |
T |
5: 14,726,599 (GRCm39) |
Y1819F |
unknown |
Het |
Pitpnm1 |
C |
A |
19: 4,156,869 (GRCm39) |
T464N |
probably damaging |
Het |
Rnf214 |
T |
C |
9: 45,809,772 (GRCm39) |
|
probably benign |
Het |
Rrs1 |
G |
A |
1: 9,616,677 (GRCm39) |
G310D |
probably damaging |
Het |
Rsf1 |
CGGCGGCGG |
CGGCGGCGGGGGCGGCGG |
7: 97,229,130 (GRCm39) |
|
probably benign |
Het |
Slc35e3 |
A |
G |
10: 117,581,688 (GRCm39) |
|
probably null |
Het |
Slc47a2 |
T |
C |
11: 61,227,699 (GRCm39) |
I142V |
probably benign |
Het |
Slc8a3 |
G |
A |
12: 81,260,852 (GRCm39) |
R626C |
probably benign |
Het |
Spart |
T |
C |
3: 55,032,275 (GRCm39) |
S370P |
probably benign |
Het |
Spata31e1 |
G |
A |
13: 49,940,087 (GRCm39) |
S541F |
probably damaging |
Het |
Spmap2 |
G |
T |
10: 79,420,571 (GRCm39) |
L189I |
probably damaging |
Het |
Tle3 |
T |
A |
9: 61,282,821 (GRCm39) |
M67K |
probably damaging |
Het |
Tmco1 |
C |
T |
1: 167,136,132 (GRCm39) |
|
probably benign |
Het |
Ubr3 |
T |
A |
2: 69,839,489 (GRCm39) |
Y1534* |
probably null |
Het |
Usp13 |
T |
C |
3: 32,965,812 (GRCm39) |
|
probably null |
Het |
Vmn2r97 |
T |
C |
17: 19,134,585 (GRCm39) |
M1T |
probably null |
Het |
Zc3h7a |
G |
A |
16: 10,969,047 (GRCm39) |
T438I |
probably damaging |
Het |
Zfhx2 |
A |
G |
14: 55,311,803 (GRCm39) |
V297A |
probably benign |
Het |
|
Other mutations in Hps4 |
Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
IGL01485:Hps4
|
APN |
5 |
112,512,377 (GRCm39) |
splice site |
probably benign |
|
IGL02331:Hps4
|
APN |
5 |
112,517,402 (GRCm39) |
missense |
probably benign |
0.03 |
IGL02410:Hps4
|
APN |
5 |
112,518,093 (GRCm39) |
missense |
probably benign |
0.07 |
IGL02821:Hps4
|
APN |
5 |
112,523,307 (GRCm39) |
missense |
probably benign |
0.02 |
R0748:Hps4
|
UTSW |
5 |
112,522,780 (GRCm39) |
missense |
probably damaging |
1.00 |
R1487:Hps4
|
UTSW |
5 |
112,525,865 (GRCm39) |
nonsense |
probably null |
|
R1891:Hps4
|
UTSW |
5 |
112,517,422 (GRCm39) |
splice site |
probably null |
|
R2010:Hps4
|
UTSW |
5 |
112,517,342 (GRCm39) |
missense |
probably damaging |
1.00 |
R2305:Hps4
|
UTSW |
5 |
112,494,527 (GRCm39) |
missense |
probably damaging |
0.99 |
R3196:Hps4
|
UTSW |
5 |
112,512,429 (GRCm39) |
missense |
probably damaging |
1.00 |
R4274:Hps4
|
UTSW |
5 |
112,522,896 (GRCm39) |
intron |
probably benign |
|
R4878:Hps4
|
UTSW |
5 |
112,523,234 (GRCm39) |
missense |
probably benign |
0.12 |
R4988:Hps4
|
UTSW |
5 |
112,526,019 (GRCm39) |
utr 3 prime |
probably benign |
|
R5843:Hps4
|
UTSW |
5 |
112,497,296 (GRCm39) |
critical splice donor site |
probably null |
|
R5896:Hps4
|
UTSW |
5 |
112,517,351 (GRCm39) |
missense |
probably benign |
0.02 |
R6318:Hps4
|
UTSW |
5 |
112,494,495 (GRCm39) |
missense |
probably damaging |
1.00 |
R7381:Hps4
|
UTSW |
5 |
112,523,324 (GRCm39) |
missense |
possibly damaging |
0.86 |
R7781:Hps4
|
UTSW |
5 |
112,518,388 (GRCm39) |
missense |
probably benign |
0.14 |
R8112:Hps4
|
UTSW |
5 |
112,517,977 (GRCm39) |
missense |
probably benign |
0.17 |
R8996:Hps4
|
UTSW |
5 |
112,525,905 (GRCm39) |
missense |
possibly damaging |
0.81 |
R9058:Hps4
|
UTSW |
5 |
112,525,905 (GRCm39) |
missense |
possibly damaging |
0.81 |
R9059:Hps4
|
UTSW |
5 |
112,525,905 (GRCm39) |
missense |
possibly damaging |
0.81 |
R9103:Hps4
|
UTSW |
5 |
112,525,905 (GRCm39) |
missense |
possibly damaging |
0.81 |
R9105:Hps4
|
UTSW |
5 |
112,525,905 (GRCm39) |
missense |
possibly damaging |
0.81 |
R9106:Hps4
|
UTSW |
5 |
112,525,905 (GRCm39) |
missense |
possibly damaging |
0.81 |
R9175:Hps4
|
UTSW |
5 |
112,525,905 (GRCm39) |
missense |
possibly damaging |
0.81 |
R9210:Hps4
|
UTSW |
5 |
112,497,227 (GRCm39) |
missense |
possibly damaging |
0.78 |
R9226:Hps4
|
UTSW |
5 |
112,525,905 (GRCm39) |
missense |
possibly damaging |
0.81 |
R9227:Hps4
|
UTSW |
5 |
112,525,905 (GRCm39) |
missense |
possibly damaging |
0.81 |
R9229:Hps4
|
UTSW |
5 |
112,525,905 (GRCm39) |
missense |
possibly damaging |
0.81 |
R9230:Hps4
|
UTSW |
5 |
112,525,905 (GRCm39) |
missense |
possibly damaging |
0.81 |
R9232:Hps4
|
UTSW |
5 |
112,525,905 (GRCm39) |
missense |
possibly damaging |
0.81 |
R9233:Hps4
|
UTSW |
5 |
112,525,905 (GRCm39) |
missense |
possibly damaging |
0.81 |
R9234:Hps4
|
UTSW |
5 |
112,525,905 (GRCm39) |
missense |
possibly damaging |
0.81 |
R9236:Hps4
|
UTSW |
5 |
112,525,905 (GRCm39) |
missense |
possibly damaging |
0.81 |
R9330:Hps4
|
UTSW |
5 |
112,525,905 (GRCm39) |
missense |
possibly damaging |
0.81 |
R9459:Hps4
|
UTSW |
5 |
112,522,875 (GRCm39) |
missense |
probably benign |
0.30 |
Z1177:Hps4
|
UTSW |
5 |
112,518,243 (GRCm39) |
missense |
probably damaging |
0.99 |
|
Predicted Primers |
PCR Primer
(F):5'- TGAAAAGACAGGACAGTTGTTCCC -3'
(R):5'- TCAGTTCTTGCAGCTGCCAC -3'
Sequencing Primer
(F):5'- CTGGGCCTGAAGTTCAAATCG -3'
(R):5'- TCTTGCAGCTGCCACTGAGG -3'
|
Posted On |
2021-11-19 |