Incidental Mutation 'R9330:Hps4'
| ID |
706787 |
| 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 |
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.292)
|
| Stock # |
R9330 (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: 99.0%
|
| Validation Efficiency |
100% (52/52) |
| 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: 52 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 2900026A02Rik |
T |
A |
5: 113,330,833 (GRCm39) |
D1127V |
probably benign |
Het |
| Ajap1 |
A |
G |
4: 153,516,961 (GRCm39) |
S127P |
probably damaging |
Het |
| Cdon |
T |
A |
9: 35,400,275 (GRCm39) |
Y996* |
probably null |
Het |
| Cnr2 |
A |
G |
4: 135,644,312 (GRCm39) |
D130G |
probably damaging |
Het |
| Cyp2j12 |
A |
G |
4: 95,994,791 (GRCm39) |
V344A |
probably damaging |
Het |
| Cyp4a32 |
T |
A |
4: 115,478,635 (GRCm39) |
C456S |
probably damaging |
Het |
| Dipk1a |
A |
T |
5: 108,059,583 (GRCm39) |
D123E |
probably benign |
Het |
| Dsc1 |
T |
A |
18: 20,243,214 (GRCm39) |
T80S |
possibly damaging |
Het |
| Esyt2 |
G |
A |
12: 116,305,765 (GRCm39) |
V332I |
probably benign |
Het |
| Fcgbpl1 |
C |
T |
7: 27,856,410 (GRCm39) |
H2066Y |
probably benign |
Het |
| G2e3 |
C |
T |
12: 51,403,928 (GRCm39) |
Q161* |
probably null |
Het |
| Galnt18 |
C |
A |
7: 111,071,271 (GRCm39) |
R566L |
probably benign |
Het |
| Gatb |
C |
T |
3: 85,559,801 (GRCm39) |
P542S |
probably benign |
Het |
| Gpt |
G |
A |
15: 76,581,215 (GRCm39) |
R53H |
possibly damaging |
Het |
| Herpud2 |
T |
C |
9: 25,036,246 (GRCm39) |
E138G |
probably damaging |
Het |
| Hivep1 |
A |
G |
13: 42,317,713 (GRCm39) |
Y2063C |
probably damaging |
Het |
| Hoxd12 |
T |
A |
2: 74,505,733 (GRCm39) |
Y101* |
probably null |
Het |
| Lama4 |
T |
C |
10: 38,954,722 (GRCm39) |
F1092L |
probably damaging |
Het |
| Lrp1b |
A |
G |
2: 41,012,993 (GRCm39) |
S1985P |
|
Het |
| Malrd1 |
C |
T |
2: 16,260,089 (GRCm39) |
P2103L |
unknown |
Het |
| Mbnl1 |
C |
A |
3: 60,511,168 (GRCm39) |
N41K |
possibly damaging |
Het |
| Muc16 |
T |
C |
9: 18,552,332 (GRCm39) |
N4654D |
probably benign |
Het |
| Mug1 |
A |
G |
6: 121,859,723 (GRCm39) |
T1241A |
probably benign |
Het |
| Ncam1 |
T |
C |
9: 49,456,097 (GRCm39) |
D507G |
probably benign |
Het |
| Nfxl1 |
A |
T |
5: 72,681,451 (GRCm39) |
D693E |
probably benign |
Het |
| Npr1 |
A |
T |
3: 90,365,979 (GRCm39) |
I604N |
possibly damaging |
Het |
| Obscn |
G |
A |
11: 58,971,047 (GRCm39) |
H2280Y |
possibly damaging |
Het |
| Or5b105 |
T |
A |
19: 13,080,588 (GRCm39) |
I27F |
probably benign |
Het |
| Or7c70 |
T |
C |
10: 78,683,153 (GRCm39) |
T199A |
probably benign |
Het |
| Pcdh10 |
T |
C |
3: 45,335,618 (GRCm39) |
V644A |
probably damaging |
Het |
| Pgk2 |
T |
A |
17: 40,519,078 (GRCm39) |
I117F |
probably benign |
Het |
| Pinx1 |
T |
A |
14: 64,109,777 (GRCm39) |
S110T |
probably benign |
Het |
| Pira1 |
A |
T |
7: 3,742,234 (GRCm39) |
C98S |
probably damaging |
Het |
| Psmd1 |
A |
G |
1: 86,061,490 (GRCm39) |
Y900C |
probably damaging |
Het |
| Rab3a |
C |
T |
8: 71,209,881 (GRCm39) |
R149C |
probably damaging |
Het |
| Samsn1 |
T |
A |
16: 75,673,433 (GRCm39) |
N148Y |
probably damaging |
Het |
| Sin3a |
C |
T |
9: 57,032,481 (GRCm39) |
R1142C |
probably damaging |
Het |
| Snrnp27 |
A |
G |
6: 86,653,184 (GRCm39) |
C145R |
probably benign |
Het |
| Sorl1 |
A |
C |
9: 41,979,229 (GRCm39) |
V423G |
probably damaging |
Het |
| Sptlc3 |
G |
T |
2: 139,388,423 (GRCm39) |
M138I |
probably benign |
Het |
| Tex15 |
T |
A |
8: 34,065,143 (GRCm39) |
F1524L |
probably benign |
Het |
| Tln2 |
T |
C |
9: 67,229,213 (GRCm39) |
N113D |
possibly damaging |
Het |
| Tmco1 |
C |
T |
1: 167,136,132 (GRCm39) |
|
probably benign |
Het |
| Tnfsf14 |
T |
A |
17: 57,501,020 (GRCm39) |
D17V |
probably damaging |
Het |
| Trmt44 |
T |
C |
5: 35,727,264 (GRCm39) |
D317G |
probably damaging |
Het |
| Trpc2 |
T |
C |
7: 101,739,764 (GRCm39) |
F563L |
probably benign |
Het |
| Ubox5 |
T |
C |
2: 130,442,165 (GRCm39) |
K174R |
probably benign |
Het |
| Vrk3 |
T |
C |
7: 44,424,910 (GRCm39) |
S442P |
probably damaging |
Het |
| Wdr64 |
A |
T |
1: 175,554,024 (GRCm39) |
T185S |
possibly damaging |
Het |
| Wfdc15a |
A |
T |
2: 164,041,632 (GRCm39) |
C64S |
probably damaging |
Het |
| Zfp688 |
A |
G |
7: 127,021,077 (GRCm39) |
Y34H |
probably damaging |
Het |
| Zfp808 |
A |
T |
13: 62,319,974 (GRCm39) |
H401L |
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 |
|
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 |
|
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 |
2022-04-18 |
Incidental Mutation