Incidental Mutation 'R9059:Hps4'
| ID |
688862 |
| 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 |
068885-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.272)
|
| Stock # |
R9059 (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: 99.9%
- 10x: 99.7%
- 20x: 98.9%
|
| Validation Efficiency |
100% (45/45) |
| 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: 45 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 9030624G23Rik |
A |
T |
12: 24,124,732 (GRCm39) |
D48E |
probably benign |
Het |
| Ablim2 |
A |
G |
5: 35,959,850 (GRCm39) |
T101A |
probably damaging |
Het |
| Acot8 |
A |
G |
2: 164,634,829 (GRCm39) |
S316P |
probably benign |
Het |
| Acta2 |
G |
T |
19: 34,219,155 (GRCm39) |
A349D |
possibly damaging |
Het |
| Adgrv1 |
C |
A |
13: 81,562,692 (GRCm39) |
|
probably null |
Het |
| Ankrd55 |
A |
G |
13: 112,455,073 (GRCm39) |
D57G |
probably damaging |
Het |
| Azin2 |
A |
G |
4: 128,828,440 (GRCm39) |
Y351H |
probably benign |
Het |
| Ccdc142 |
T |
C |
6: 83,079,400 (GRCm39) |
C246R |
probably damaging |
Het |
| Col25a1 |
C |
A |
3: 130,268,499 (GRCm39) |
Q179K |
unknown |
Het |
| Ddx46 |
C |
T |
13: 55,799,921 (GRCm39) |
A277V |
probably benign |
Het |
| Diaph1 |
T |
A |
18: 38,022,798 (GRCm39) |
N792I |
possibly damaging |
Het |
| Dnah11 |
G |
A |
12: 118,094,578 (GRCm39) |
P830L |
probably benign |
Het |
| Dnah3 |
C |
G |
7: 119,684,368 (GRCm39) |
R252S |
probably benign |
Het |
| Dnah5 |
A |
G |
15: 28,245,812 (GRCm39) |
D550G |
probably benign |
Het |
| Dph3 |
T |
C |
14: 31,807,384 (GRCm39) |
N31D |
probably benign |
Het |
| Dsg1c |
A |
T |
18: 20,408,306 (GRCm39) |
T452S |
probably damaging |
Het |
| Dsg4 |
T |
A |
18: 20,604,182 (GRCm39) |
M883K |
possibly damaging |
Het |
| Efcab3 |
T |
C |
11: 104,642,689 (GRCm39) |
V1104A |
possibly damaging |
Het |
| Epn1 |
T |
G |
7: 5,098,067 (GRCm39) |
S293A |
probably benign |
Het |
| Fggy |
T |
A |
4: 95,688,841 (GRCm39) |
Y318* |
probably null |
Het |
| Hip1 |
A |
G |
5: 135,457,597 (GRCm39) |
L703P |
probably benign |
Het |
| Igf2r |
GCAGCCCTCCATAGGCGCCAGCCCTCCATAGGCGC |
GCAGCCCTCCATAGGCGC |
17: 12,970,180 (GRCm39) |
|
probably null |
Het |
| Klk15 |
C |
T |
7: 43,587,790 (GRCm39) |
H73Y |
possibly damaging |
Het |
| Larp4 |
A |
G |
15: 99,889,693 (GRCm39) |
E204G |
probably benign |
Het |
| Lbr |
A |
G |
1: 181,645,119 (GRCm39) |
I511T |
|
Het |
| Lingo3 |
G |
T |
10: 80,670,523 (GRCm39) |
T469K |
probably benign |
Het |
| Lrrc30 |
A |
T |
17: 67,938,798 (GRCm39) |
W261R |
probably damaging |
Het |
| Man2b1 |
T |
C |
8: 85,818,155 (GRCm39) |
V442A |
probably damaging |
Het |
| Mroh3 |
T |
A |
1: 136,109,533 (GRCm39) |
R891S |
probably benign |
Het |
| Mtcl1 |
T |
A |
17: 66,650,606 (GRCm39) |
M1620L |
probably benign |
Het |
| Myo18a |
T |
C |
11: 77,668,899 (GRCm39) |
V253A |
possibly damaging |
Het |
| Or5b101 |
A |
T |
19: 13,005,277 (GRCm39) |
C139S |
probably damaging |
Het |
| Pcdhb22 |
A |
T |
18: 37,652,722 (GRCm39) |
N140Y |
probably damaging |
Het |
| Ppp1r9b |
T |
C |
11: 94,883,254 (GRCm39) |
V294A |
probably benign |
Het |
| Ptk7 |
A |
T |
17: 46,877,117 (GRCm39) |
D980E |
probably damaging |
Het |
| Rdh11 |
T |
A |
12: 79,238,713 (GRCm39) |
|
probably benign |
Het |
| Sec23ip |
T |
G |
7: 128,365,805 (GRCm39) |
L558R |
probably damaging |
Het |
| Slc22a26 |
C |
T |
19: 7,762,559 (GRCm39) |
M460I |
probably benign |
Het |
| Smc1b |
G |
A |
15: 85,004,875 (GRCm39) |
Q400* |
probably null |
Het |
| Spg11 |
T |
C |
2: 121,918,788 (GRCm39) |
E947G |
probably damaging |
Het |
| Stab1 |
T |
C |
14: 30,876,805 (GRCm39) |
I840V |
probably benign |
Het |
| Tlk1 |
T |
C |
2: 70,617,277 (GRCm39) |
T68A |
possibly damaging |
Het |
| Traip |
A |
G |
9: 107,840,549 (GRCm39) |
I273V |
probably benign |
Het |
| Trim30c |
T |
G |
7: 104,031,272 (GRCm39) |
*514C |
probably null |
Het |
| U2surp |
A |
G |
9: 95,363,716 (GRCm39) |
Y615H |
probably damaging |
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 |
|
R9060: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'- AAAAGACAGGACAGTTGTTCCCTG -3'
(R):5'- CACTCAGTTCTTGCAGCTGC -3'
Sequencing Primer
(F):5'- CTGGGCCTGAAGTTCAAATCG -3'
(R):5'- GTTCTTGCAGCTGCCACTGAG -3'
|
| Posted On |
2021-11-19 |
Incidental Mutation