Incidental Mutation 'R8996:Hps4'
| ID |
684714 |
| 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 |
068827-MU
|
| Accession Numbers |
|
| Essential gene? |
Possibly non essential
(E-score: 0.292)
|
| Stock # |
R8996 (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% (43/43) |
| 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: 43 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| Abcb1a |
A |
G |
5: 8,769,069 (GRCm39) |
I764V |
probably benign |
Het |
| Adgrv1 |
GTT |
GT |
13: 81,553,457 (GRCm39) |
|
probably null |
Het |
| Alcam |
T |
C |
16: 52,126,114 (GRCm39) |
I68V |
probably benign |
Het |
| Atp8b2 |
A |
G |
3: 89,850,696 (GRCm39) |
L75P |
probably damaging |
Het |
| B3gnt6 |
T |
C |
7: 97,842,799 (GRCm39) |
N387S |
probably benign |
Het |
| Btn2a2 |
T |
C |
13: 23,662,831 (GRCm39) |
E373G |
probably damaging |
Het |
| Cfap65 |
G |
A |
1: 74,941,347 (GRCm39) |
H1831Y |
probably benign |
Het |
| Cftr |
T |
A |
6: 18,255,945 (GRCm39) |
C564* |
probably null |
Het |
| Chd6 |
A |
G |
2: 160,823,543 (GRCm39) |
W1276R |
probably damaging |
Het |
| Csmd1 |
T |
C |
8: 15,971,105 (GRCm39) |
E3070G |
possibly damaging |
Het |
| Cxcr4 |
A |
G |
1: 128,517,538 (GRCm39) |
I41T |
possibly damaging |
Het |
| Dnhd1 |
T |
A |
7: 105,323,242 (GRCm39) |
N583K |
probably damaging |
Het |
| Fignl1 |
G |
T |
11: 11,752,953 (GRCm39) |
P34Q |
probably damaging |
Het |
| Frg2f1 |
T |
C |
4: 119,388,085 (GRCm39) |
D138G |
probably damaging |
Het |
| Gabra4 |
A |
T |
5: 71,729,046 (GRCm39) |
M578K |
possibly damaging |
Het |
| Gnb5 |
T |
C |
9: 75,251,805 (GRCm39) |
V351A |
probably benign |
Het |
| H2-Ob |
A |
T |
17: 34,462,531 (GRCm39) |
I245F |
probably damaging |
Het |
| Igkv4-54 |
A |
T |
6: 69,608,774 (GRCm39) |
Y48* |
probably null |
Het |
| Kdm7a |
A |
C |
6: 39,129,786 (GRCm39) |
H463Q |
probably benign |
Het |
| L3mbtl4 |
A |
G |
17: 68,769,997 (GRCm39) |
T256A |
probably benign |
Het |
| Lhpp |
A |
G |
7: 132,212,484 (GRCm39) |
D17G |
probably damaging |
Het |
| Mis18bp1 |
C |
T |
12: 65,180,632 (GRCm39) |
V950I |
probably benign |
Het |
| Mms22l |
T |
A |
4: 24,598,884 (GRCm39) |
|
probably null |
Het |
| Mrgpra4 |
T |
C |
7: 47,630,945 (GRCm39) |
T219A |
probably benign |
Het |
| Nptx1 |
G |
A |
11: 119,438,394 (GRCm39) |
R8C |
unknown |
Het |
| Plcxd1 |
A |
G |
5: 110,250,444 (GRCm39) |
T262A |
probably benign |
Het |
| Sf1 |
G |
A |
19: 6,426,441 (GRCm39) |
G221S |
|
Het |
| Shkbp1 |
A |
G |
7: 27,042,844 (GRCm39) |
V531A |
possibly damaging |
Het |
| Slc12a3 |
A |
T |
8: 95,056,063 (GRCm39) |
E66D |
probably benign |
Het |
| Slc14a1 |
A |
T |
18: 78,156,911 (GRCm39) |
I198K |
possibly damaging |
Het |
| Spag8 |
T |
C |
4: 43,651,998 (GRCm39) |
E362G |
probably damaging |
Het |
| Speer4c1 |
T |
A |
5: 15,915,886 (GRCm39) |
I161L |
probably benign |
Het |
| Stk3 |
A |
G |
15: 34,945,208 (GRCm39) |
S427P |
possibly damaging |
Het |
| Stt3b |
T |
C |
9: 115,073,065 (GRCm39) |
K814E |
unknown |
Het |
| Synpo |
T |
A |
18: 60,737,230 (GRCm39) |
I239F |
possibly damaging |
Het |
| Tcf7l1 |
G |
T |
6: 72,765,563 (GRCm39) |
R97S |
possibly damaging |
Het |
| Trav15-2-dv6-2 |
T |
A |
14: 53,887,247 (GRCm39) |
Y56N |
probably benign |
Het |
| Ttc39c |
A |
G |
18: 12,820,136 (GRCm39) |
N112S |
probably benign |
Het |
| Usp14 |
T |
C |
18: 10,000,521 (GRCm39) |
K380E |
probably benign |
Het |
| Usp17lb |
C |
T |
7: 104,490,889 (GRCm39) |
A13T |
probably benign |
Het |
| Usp4 |
G |
A |
9: 108,268,909 (GRCm39) |
R921H |
probably damaging |
Het |
| Xndc1 |
A |
G |
7: 101,722,518 (GRCm39) |
D61G |
probably damaging |
Het |
| Zfp1006 |
G |
A |
8: 129,946,016 (GRCm39) |
P270S |
possibly 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 |
|
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'- GAAAAGACAGGACAGTTGTTCC -3'
(R):5'- ACTCAGTTCTTGCAGCTGCC -3'
Sequencing Primer
(F):5'- CTGGGCCTGAAGTTCAAATCG -3'
(R):5'- GTTCTTGCAGCTGCCACTGAG -3'
|
| Posted On |
2021-10-11 |
Incidental Mutation