Incidental Mutation 'R2305:Hps4'
| ID |
244554 |
| 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 |
040304-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.292)
|
| Stock # |
R2305 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
5 |
| Chromosomal Location |
112490949-112526280 bp(+) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to G
at 112494527 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Isoleucine to Valine
at position 37
(I37V)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000107978
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000031289]
[ENSMUST00000035279]
[ENSMUST00000112359]
[ENSMUST00000146510]
|
| AlphaFold |
Q99KG7 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000031289
|
| SMART Domains |
Protein: ENSMUSP00000031289
Gene: ENSMUSG00000029346
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
13 |
54 |
N/A |
INTRINSIC |
|
Pfam:SRR1
|
109 |
164 |
2.1e-25 |
PFAM |
|
| Predicted Effect |
probably damaging
Transcript: ENSMUST00000035279
AA Change: I37V
PolyPhen 2
Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000047920
Gene: ENSMUSG00000042328
AA Change: I37V
| 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 |
probably damaging
Transcript: ENSMUST00000112359
AA Change: I37V
PolyPhen 2
Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)
|
| SMART Domains |
Protein: ENSMUSP00000107978
Gene: ENSMUSG00000042328
AA Change: I37V
| 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 |
noncoding transcript
Transcript: ENSMUST00000133708
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000146510
|
| SMART Domains |
Protein: ENSMUSP00000119870
Gene: ENSMUSG00000029346
| Domain | Start | End | E-Value | Type |
|---|
|
low complexity region
|
12 |
53 |
N/A |
INTRINSIC |
|
Pfam:SRR1
|
109 |
162 |
1.8e-20 |
PFAM |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000156083
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000175718
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000176737
|
| Meta Mutation Damage Score |
0.1112 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.3%
- 20x: 94.8%
|
| Validation Efficiency |
100% (32/32) |
| 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: 30 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Acvr1c |
C |
A |
2: 58,171,711 (GRCm39) |
D295Y |
probably damaging |
Het |
| Adamts7 |
A |
G |
9: 90,062,764 (GRCm39) |
D406G |
probably benign |
Het |
| Ankhd1 |
T |
C |
18: 36,775,979 (GRCm39) |
S1443P |
possibly damaging |
Het |
| Casp8ap2 |
A |
T |
4: 32,646,411 (GRCm39) |
K1828I |
probably damaging |
Het |
| Cep135 |
T |
C |
5: 76,743,236 (GRCm39) |
|
probably benign |
Het |
| Cyp3a57 |
A |
G |
5: 145,318,090 (GRCm39) |
D357G |
probably damaging |
Het |
| Defb21 |
T |
A |
2: 152,416,791 (GRCm39) |
L89Q |
possibly damaging |
Het |
| Dnah5 |
A |
T |
15: 28,387,913 (GRCm39) |
E3124V |
probably benign |
Het |
| Efcab7 |
A |
G |
4: 99,719,718 (GRCm39) |
T67A |
possibly damaging |
Het |
| Exo1 |
C |
T |
1: 175,716,327 (GRCm39) |
P148L |
probably damaging |
Het |
| Krt9 |
T |
A |
11: 100,083,942 (GRCm39) |
M30L |
unknown |
Het |
| Med25 |
C |
A |
7: 44,535,314 (GRCm39) |
R37L |
possibly damaging |
Het |
| Or10ak12 |
T |
G |
4: 118,666,058 (GRCm39) |
Q318H |
probably benign |
Het |
| Or5an10 |
T |
C |
19: 12,276,451 (GRCm39) |
E15G |
probably benign |
Het |
| Phf3 |
G |
A |
1: 30,844,556 (GRCm39) |
Q1468* |
probably null |
Het |
| Phkb |
A |
G |
8: 86,770,431 (GRCm39) |
K900R |
possibly damaging |
Het |
| Pirb |
G |
A |
7: 3,715,990 (GRCm39) |
H755Y |
probably benign |
Het |
| Polq |
A |
T |
16: 36,882,699 (GRCm39) |
N1342I |
probably damaging |
Het |
| Polr2b |
T |
A |
5: 77,468,284 (GRCm39) |
|
probably benign |
Het |
| Pus1 |
C |
A |
5: 110,922,826 (GRCm39) |
M232I |
probably benign |
Het |
| Serpina3a |
C |
A |
12: 104,082,787 (GRCm39) |
Q187K |
probably benign |
Het |
| Slit1 |
G |
A |
19: 41,599,455 (GRCm39) |
P1032L |
probably benign |
Het |
| Syne1 |
C |
T |
10: 4,997,573 (GRCm39) |
E465K |
probably damaging |
Het |
| Tektl1 |
T |
C |
10: 78,584,336 (GRCm39) |
T360A |
probably damaging |
Het |
| Tlk2 |
T |
G |
11: 105,132,417 (GRCm39) |
I217R |
possibly damaging |
Het |
| Tlr4 |
A |
G |
4: 66,758,338 (GRCm39) |
D377G |
probably damaging |
Het |
| Tmtc1 |
T |
C |
6: 148,146,195 (GRCm39) |
D866G |
probably damaging |
Het |
| Tubd1 |
T |
A |
11: 86,446,017 (GRCm39) |
I219N |
probably benign |
Het |
| Ugt3a1 |
C |
A |
15: 9,351,203 (GRCm39) |
P71T |
probably benign |
Het |
| Vmn1r64 |
A |
G |
7: 5,887,535 (GRCm39) |
S3P |
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 |
|
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 |
|
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'- TCTTCCTGGCAACTGAGCAC -3'
(R):5'- CCTTGGGAATTTAAGATCCAGACAGG -3'
Sequencing Primer
(F):5'- TGGCAACTGAGCACCAAGC -3'
(R):5'- TCCAGACAGGAGGACAGCC -3'
|
| Posted On |
2014-10-30 |
Incidental Mutation