Incidental Mutation 'R4457:Hps5'
| ID |
329949 |
| Institutional Source |
Beutler Lab
|
| Gene Symbol |
Hps5
|
| Ensembl Gene |
ENSMUSG00000014418 |
| Gene Name |
HPS5, biogenesis of lysosomal organelles complex 2 subunit 2 |
| Synonyms |
Hermansky-Pudlak syndrome 5, ru-2, ru2, ruby eye 2 |
| MMRRC Submission |
041717-MU
|
| Accession Numbers |
|
| Essential gene? |
Probably non essential
(E-score: 0.113)
|
| Stock # |
R4457 (G1)
|
| Quality Score |
225 |
|
Status
|
Validated
|
| Chromosome |
7 |
| Chromosomal Location |
46409890-46445488 bp(-) (GRCm39) |
| Type of Mutation |
missense |
| DNA Base Change (assembly) |
A to T
at 46433037 bp (GRCm39)
|
| Zygosity |
Heterozygous |
| Amino Acid Change |
Cysteine to Serine
at position 228
(C228S)
|
| Ref Sequence |
ENSEMBL: ENSMUSP00000122887
(fasta)
|
| Gene Model |
predicted gene model for transcript(s):
[ENSMUST00000014562]
[ENSMUST00000107653]
[ENSMUST00000107654]
[ENSMUST00000123725]
[ENSMUST00000142663]
[ENSMUST00000152759]
[ENSMUST00000211347]
|
| AlphaFold |
P59438 |
| Predicted Effect |
probably benign
Transcript: ENSMUST00000014562
AA Change: C228S
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000014562
Gene: ENSMUSG00000014418
AA Change: C228S
| Domain | Start | End | E-Value | Type |
|---|
|
SCOP:d1jjub_
|
44 |
192 |
3e-8 |
SMART |
|
Blast:WD40
|
63 |
103 |
7e-21 |
BLAST |
|
Blast:WD40
|
111 |
151 |
1e-19 |
BLAST |
|
low complexity region
|
429 |
449 |
N/A |
INTRINSIC |
|
low complexity region
|
775 |
786 |
N/A |
INTRINSIC |
|
low complexity region
|
989 |
998 |
N/A |
INTRINSIC |
|
low complexity region
|
1021 |
1033 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000107653
AA Change: C228S
PolyPhen 2
Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)
|
| SMART Domains |
Protein: ENSMUSP00000103280
Gene: ENSMUSG00000014418
AA Change: C228S
| Domain | Start | End | E-Value | Type |
|---|
|
SCOP:d1jjub_
|
44 |
192 |
3e-8 |
SMART |
|
Blast:WD40
|
63 |
103 |
6e-21 |
BLAST |
|
Blast:WD40
|
111 |
151 |
1e-19 |
BLAST |
|
low complexity region
|
396 |
416 |
N/A |
INTRINSIC |
|
low complexity region
|
742 |
753 |
N/A |
INTRINSIC |
|
low complexity region
|
956 |
965 |
N/A |
INTRINSIC |
|
low complexity region
|
988 |
1000 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000107654
AA Change: C228S
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000103281
Gene: ENSMUSG00000014418
AA Change: C228S
| Domain | Start | End | E-Value | Type |
|---|
|
SCOP:d1jjub_
|
44 |
192 |
3e-8 |
SMART |
|
Blast:WD40
|
63 |
103 |
7e-21 |
BLAST |
|
Blast:WD40
|
111 |
151 |
1e-19 |
BLAST |
|
low complexity region
|
429 |
449 |
N/A |
INTRINSIC |
|
low complexity region
|
775 |
786 |
N/A |
INTRINSIC |
|
low complexity region
|
989 |
998 |
N/A |
INTRINSIC |
|
low complexity region
|
1021 |
1033 |
N/A |
INTRINSIC |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000123725
|
| SMART Domains |
Protein: ENSMUSP00000116770
Gene: ENSMUSG00000014418
| Domain | Start | End | E-Value | Type |
|---|
|
SCOP:d1tbga_
|
24 |
107 |
5e-4 |
SMART |
|
Blast:WD40
|
63 |
103 |
1e-22 |
BLAST |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000142663
AA Change: C228S
PolyPhen 2
Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
|
| SMART Domains |
Protein: ENSMUSP00000122887
Gene: ENSMUSG00000014418
AA Change: C228S
| Domain | Start | End | E-Value | Type |
|---|
|
SCOP:d1jjub_
|
44 |
192 |
8e-8 |
SMART |
|
Blast:WD40
|
63 |
103 |
9e-20 |
BLAST |
|
Blast:WD40
|
111 |
151 |
2e-19 |
BLAST |
|
low complexity region
|
429 |
449 |
N/A |
INTRINSIC |
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000145776
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000152759
|
| SMART Domains |
Protein: ENSMUSP00000115786
Gene: ENSMUSG00000014418
| Domain | Start | End | E-Value | Type |
|---|
|
SCOP:d1jjub_
|
44 |
192 |
2e-8 |
SMART |
|
Blast:WD40
|
63 |
103 |
1e-21 |
BLAST |
|
Blast:WD40
|
111 |
151 |
2e-20 |
BLAST |
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000211471
|
| Predicted Effect |
noncoding transcript
Transcript: ENSMUST00000211528
|
| Predicted Effect |
probably benign
Transcript: ENSMUST00000211347
|
| Meta Mutation Damage Score |
0.0746 |
| Coding Region Coverage |
- 1x: 99.2%
- 3x: 98.6%
- 10x: 97.2%
- 20x: 95.1%
|
| Validation Efficiency |
97% (62/64) |
| MGI Phenotype |
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. This protein interacts with Hermansky-Pudlak syndrome 6 protein and may interact with the cytoplasmic domain of integrin, alpha-3. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 5. Multiple transcript variants encoding two distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes have hypopigmented eyes and hair, impaired secretion of lysosomal enzymes by renal proximal tubules and reduced clotting due to a platelet dense granule defect. Homozygotes for one allele are less susceptible to diet-induced atherosclerosis. [provided by MGI curators]
|
| Allele List at MGI |
|
| Other mutations in this stock |
Total: 60 list
| Gene | Ref | Var | Chr/Loc | Mutation | Predicted Effect | Zygosity |
|---|
| 1110008E08Rik |
A |
G |
16: 90,351,260 (GRCm39) |
|
noncoding transcript |
Het |
| 1700025G04Rik |
T |
C |
1: 151,796,805 (GRCm39) |
R87G |
probably damaging |
Het |
| 9030619P08Rik |
T |
A |
15: 75,303,249 (GRCm39) |
|
noncoding transcript |
Het |
| Akap13 |
A |
G |
7: 75,389,213 (GRCm39) |
D2377G |
probably damaging |
Het |
| Arhgef5 |
T |
C |
6: 43,251,027 (GRCm39) |
S593P |
probably damaging |
Het |
| Atp4a |
G |
A |
7: 30,419,650 (GRCm39) |
R671Q |
probably benign |
Het |
| Cdkn2d |
C |
G |
9: 21,202,185 (GRCm39) |
V21L |
probably benign |
Het |
| Cfap73 |
T |
C |
5: 120,768,215 (GRCm39) |
K181R |
possibly damaging |
Het |
| Chn1 |
A |
G |
2: 73,443,427 (GRCm39) |
I383T |
probably damaging |
Het |
| Cmtr2 |
A |
G |
8: 110,948,884 (GRCm39) |
D398G |
probably benign |
Het |
| Dnah12 |
T |
C |
14: 26,537,464 (GRCm39) |
Y2238H |
probably damaging |
Het |
| Dnah7c |
A |
G |
1: 46,779,781 (GRCm39) |
N3161S |
probably damaging |
Het |
| Dnah8 |
C |
A |
17: 31,032,125 (GRCm39) |
H4148Q |
probably benign |
Het |
| Ehbp1l1 |
T |
C |
19: 5,766,321 (GRCm39) |
S397G |
possibly damaging |
Het |
| Eya4 |
A |
T |
10: 22,992,566 (GRCm39) |
S462R |
probably damaging |
Het |
| Fam227b |
T |
A |
2: 125,988,188 (GRCm39) |
|
probably benign |
Het |
| Frrs1 |
G |
A |
3: 116,690,377 (GRCm39) |
V7I |
probably benign |
Het |
| Fsip2 |
G |
T |
2: 82,821,120 (GRCm39) |
A5618S |
possibly damaging |
Het |
| Gja10 |
A |
T |
4: 32,601,073 (GRCm39) |
M437K |
probably benign |
Het |
| Gm2840 |
T |
G |
5: 96,322,187 (GRCm39) |
|
noncoding transcript |
Het |
| Gm4956 |
A |
G |
1: 21,368,319 (GRCm39) |
|
noncoding transcript |
Het |
| Gria4 |
A |
G |
9: 4,427,074 (GRCm39) |
W789R |
probably damaging |
Het |
| Hoxb5 |
A |
G |
11: 96,194,546 (GRCm39) |
D36G |
probably damaging |
Het |
| Hspa4 |
A |
T |
11: 53,171,395 (GRCm39) |
C270S |
probably damaging |
Het |
| Htra4 |
C |
A |
8: 25,528,674 (GRCm39) |
A73S |
possibly damaging |
Het |
| Ikzf2 |
T |
C |
1: 69,723,347 (GRCm39) |
|
probably benign |
Het |
| Ivl |
G |
A |
3: 92,479,673 (GRCm39) |
H131Y |
probably benign |
Het |
| Kat6a |
A |
G |
8: 23,422,129 (GRCm39) |
|
probably null |
Het |
| Lamp3 |
T |
A |
16: 19,492,279 (GRCm39) |
M322L |
probably benign |
Het |
| Letmd1 |
T |
C |
15: 100,373,011 (GRCm39) |
V37A |
possibly damaging |
Het |
| Mslnl |
G |
A |
17: 25,961,908 (GRCm39) |
V128M |
probably damaging |
Het |
| Myh1 |
G |
A |
11: 67,111,441 (GRCm39) |
G1627R |
probably benign |
Het |
| Myo9b |
A |
G |
8: 71,743,643 (GRCm39) |
I235V |
probably damaging |
Het |
| Ndor1 |
A |
G |
2: 25,138,128 (GRCm39) |
|
probably null |
Het |
| Ndufa12 |
A |
T |
10: 94,056,680 (GRCm39) |
K136M |
probably damaging |
Het |
| Or2t49 |
A |
G |
11: 58,392,944 (GRCm39) |
L146P |
probably damaging |
Het |
| Or4a78 |
A |
T |
2: 89,497,427 (GRCm39) |
S268T |
probably benign |
Het |
| Or51g2 |
C |
T |
7: 102,622,734 (GRCm39) |
S155N |
probably damaging |
Het |
| Or5d44 |
A |
G |
2: 88,141,173 (GRCm39) |
|
probably benign |
Het |
| Pcdha2 |
A |
G |
18: 37,073,599 (GRCm39) |
D410G |
probably damaging |
Het |
| Pcyox1l |
T |
A |
18: 61,830,939 (GRCm39) |
N311I |
probably benign |
Het |
| Pif1 |
A |
G |
9: 65,495,058 (GRCm39) |
|
probably benign |
Het |
| Pkp1 |
CTCTTCTT |
CTCTT |
1: 135,803,362 (GRCm39) |
|
probably null |
Het |
| Pogz |
G |
A |
3: 94,763,374 (GRCm39) |
V49I |
probably benign |
Het |
| Rab36 |
G |
A |
10: 74,880,328 (GRCm39) |
V63I |
probably damaging |
Het |
| Rnf4 |
A |
G |
5: 34,508,705 (GRCm39) |
Y189C |
probably benign |
Het |
| Rpl31-ps17 |
C |
T |
12: 54,748,397 (GRCm39) |
|
noncoding transcript |
Het |
| Sgms2 |
A |
C |
3: 131,118,665 (GRCm39) |
Y273D |
probably damaging |
Het |
| Slc25a10 |
G |
A |
11: 120,387,915 (GRCm39) |
V203I |
probably benign |
Het |
| Slc4a2 |
T |
A |
5: 24,639,328 (GRCm39) |
|
probably benign |
Het |
| Tbc1d13 |
A |
G |
2: 30,025,450 (GRCm39) |
|
probably benign |
Het |
| Tdrd7 |
A |
G |
4: 46,007,526 (GRCm39) |
N526S |
probably benign |
Het |
| Tet2 |
C |
T |
3: 133,191,324 (GRCm39) |
D1037N |
possibly damaging |
Het |
| Thrb |
T |
A |
14: 18,011,187 (GRCm38) |
W188R |
probably damaging |
Het |
| Ttn |
T |
C |
2: 76,777,257 (GRCm39) |
M1382V |
probably benign |
Het |
| Usp9y |
T |
A |
Y: 1,394,078 (GRCm39) |
I551L |
possibly damaging |
Het |
| Vwde |
T |
C |
6: 13,196,100 (GRCm39) |
I308M |
probably damaging |
Het |
| Zan |
T |
C |
5: 137,409,778 (GRCm39) |
I3488V |
unknown |
Het |
| Zgrf1 |
A |
T |
3: 127,389,578 (GRCm39) |
I375F |
probably damaging |
Het |
| Zic4 |
A |
G |
9: 91,261,315 (GRCm39) |
K183R |
probably damaging |
Het |
|
| Other mutations in Hps5 |
| Allele | Source | Chr | Coord | Type | Predicted Effect | PPH Score |
|---|
|
IGL00089:Hps5
|
APN |
7 |
46,425,362 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL00543:Hps5
|
APN |
7 |
46,427,497 (GRCm39) |
missense |
probably benign |
0.37 |
|
IGL01090:Hps5
|
APN |
7 |
46,437,751 (GRCm39) |
missense |
probably benign |
0.02 |
|
IGL01351:Hps5
|
APN |
7 |
46,410,856 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL01479:Hps5
|
APN |
7 |
46,412,366 (GRCm39) |
critical splice donor site |
probably null |
|
|
IGL02056:Hps5
|
APN |
7 |
46,437,606 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02117:Hps5
|
APN |
7 |
46,432,940 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL02210:Hps5
|
APN |
7 |
46,435,994 (GRCm39) |
missense |
probably benign |
0.03 |
|
IGL02967:Hps5
|
APN |
7 |
46,418,804 (GRCm39) |
missense |
possibly damaging |
0.69 |
|
IGL03046:Hps5
|
APN |
7 |
46,426,463 (GRCm39) |
splice site |
probably benign |
|
|
IGL03187:Hps5
|
APN |
7 |
46,422,631 (GRCm39) |
missense |
probably damaging |
1.00 |
|
IGL03259:Hps5
|
APN |
7 |
46,412,526 (GRCm39) |
missense |
probably damaging |
0.99 |
|
dorian_gray
|
UTSW |
7 |
46,784,145 (GRCm38) |
unclassified |
probably benign |
|
|
smoky
|
UTSW |
7 |
46,418,775 (GRCm39) |
nonsense |
probably null |
|
|
Titan
|
UTSW |
7 |
46,432,893 (GRCm39) |
critical splice donor site |
probably null |
|
|
toffee
|
UTSW |
7 |
46,777,075 (GRCm38) |
intron |
probably benign |
|
|
wombat
|
UTSW |
7 |
46,433,058 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0068:Hps5
|
UTSW |
7 |
46,426,466 (GRCm39) |
splice site |
probably benign |
|
|
R0068:Hps5
|
UTSW |
7 |
46,426,466 (GRCm39) |
splice site |
probably benign |
|
|
R0141:Hps5
|
UTSW |
7 |
46,438,605 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R0383:Hps5
|
UTSW |
7 |
46,418,712 (GRCm39) |
splice site |
probably null |
|
|
R0402:Hps5
|
UTSW |
7 |
46,440,333 (GRCm39) |
splice site |
probably benign |
|
|
R0684:Hps5
|
UTSW |
7 |
46,432,893 (GRCm39) |
critical splice donor site |
probably null |
|
|
R1159:Hps5
|
UTSW |
7 |
46,421,978 (GRCm39) |
splice site |
probably null |
|
|
R1938:Hps5
|
UTSW |
7 |
46,422,691 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R2058:Hps5
|
UTSW |
7 |
46,417,475 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R3613:Hps5
|
UTSW |
7 |
46,426,298 (GRCm39) |
critical splice donor site |
probably null |
|
|
R3881:Hps5
|
UTSW |
7 |
46,421,420 (GRCm39) |
missense |
possibly damaging |
0.54 |
|
R3882:Hps5
|
UTSW |
7 |
46,421,420 (GRCm39) |
missense |
possibly damaging |
0.54 |
|
R3914:Hps5
|
UTSW |
7 |
46,432,950 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4095:Hps5
|
UTSW |
7 |
46,425,218 (GRCm39) |
missense |
probably benign |
0.01 |
|
R4739:Hps5
|
UTSW |
7 |
46,436,013 (GRCm39) |
missense |
probably benign |
|
|
R4838:Hps5
|
UTSW |
7 |
46,437,778 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R4934:Hps5
|
UTSW |
7 |
46,418,775 (GRCm39) |
nonsense |
probably null |
|
|
R5876:Hps5
|
UTSW |
7 |
46,438,620 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R6056:Hps5
|
UTSW |
7 |
46,416,521 (GRCm39) |
missense |
probably benign |
0.00 |
|
R6129:Hps5
|
UTSW |
7 |
46,421,198 (GRCm39) |
missense |
probably benign |
|
|
R6878:Hps5
|
UTSW |
7 |
46,433,058 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R7912:Hps5
|
UTSW |
7 |
46,418,826 (GRCm39) |
missense |
probably benign |
0.15 |
|
R7977:Hps5
|
UTSW |
7 |
46,418,475 (GRCm39) |
missense |
probably benign |
0.03 |
|
R7987:Hps5
|
UTSW |
7 |
46,418,475 (GRCm39) |
missense |
probably benign |
0.03 |
|
R8131:Hps5
|
UTSW |
7 |
46,421,312 (GRCm39) |
missense |
probably benign |
0.00 |
|
R8243:Hps5
|
UTSW |
7 |
46,436,066 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R8245:Hps5
|
UTSW |
7 |
46,418,485 (GRCm39) |
nonsense |
probably null |
|
|
R8878:Hps5
|
UTSW |
7 |
46,421,345 (GRCm39) |
missense |
probably benign |
0.07 |
|
R9050:Hps5
|
UTSW |
7 |
46,422,607 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9186:Hps5
|
UTSW |
7 |
46,438,370 (GRCm39) |
missense |
probably damaging |
1.00 |
|
R9278:Hps5
|
UTSW |
7 |
46,440,397 (GRCm39) |
missense |
probably benign |
0.00 |
|
R9290:Hps5
|
UTSW |
7 |
46,424,331 (GRCm39) |
missense |
probably damaging |
0.97 |
|
R9303:Hps5
|
UTSW |
7 |
46,438,619 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R9305:Hps5
|
UTSW |
7 |
46,438,619 (GRCm39) |
missense |
possibly damaging |
0.94 |
|
R9650:Hps5
|
UTSW |
7 |
46,425,354 (GRCm39) |
missense |
probably damaging |
1.00 |
|
X0021:Hps5
|
UTSW |
7 |
46,412,517 (GRCm39) |
missense |
probably damaging |
1.00 |
|
| Predicted Primers |
PCR Primer
(F):5'- GTCTCCAGGAAGTCCCATGTAG -3'
(R):5'- GGTAACCATCCGTGCCATTG -3'
Sequencing Primer
(F):5'- TAGCGGCTACCTTGCAGTGATC -3'
(R):5'- CTAGTGTAGTACTGGCAGAGC -3'
|
| Posted On |
2015-07-21 |
Incidental Mutation