Incidental Mutation 'IGL02117:Hps5'
ID 280432
Institutional Source Australian Phenomics Network (link to record)
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
Accession Numbers
Essential gene? Probably non essential (E-score: 0.104) question?
Stock # IGL02117
Quality Score
Status
Chromosome 7
Chromosomal Location 46409890-46445488 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 46432940 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Serine at position 260 (F260S)
Ref Sequence ENSEMBL: ENSMUSP00000122887 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000014562] [ENSMUST00000107653] [ENSMUST00000107654] [ENSMUST00000123725] [ENSMUST00000142663] [ENSMUST00000211347] [ENSMUST00000152759]
AlphaFold P59438
Predicted Effect probably damaging
Transcript: ENSMUST00000014562
AA Change: F260S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000014562
Gene: ENSMUSG00000014418
AA Change: F260S

DomainStartEndE-ValueType
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 damaging
Transcript: ENSMUST00000107653
AA Change: F260S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000103280
Gene: ENSMUSG00000014418
AA Change: F260S

DomainStartEndE-ValueType
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 damaging
Transcript: ENSMUST00000107654
AA Change: F260S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000103281
Gene: ENSMUSG00000014418
AA Change: F260S

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
SCOP:d1tbga_ 24 107 5e-4 SMART
Blast:WD40 63 103 1e-22 BLAST
Predicted Effect probably damaging
Transcript: ENSMUST00000142663
AA Change: F260S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000122887
Gene: ENSMUSG00000014418
AA Change: F260S

DomainStartEndE-ValueType
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 noncoding transcript
Transcript: ENSMUST00000211528
Predicted Effect probably benign
Transcript: ENSMUST00000211347
Predicted Effect probably benign
Transcript: ENSMUST00000211471
Predicted Effect probably benign
Transcript: ENSMUST00000152759
SMART Domains Protein: ENSMUSP00000115786
Gene: ENSMUSG00000014418

DomainStartEndE-ValueType
SCOP:d1jjub_ 44 192 2e-8 SMART
Blast:WD40 63 103 1e-21 BLAST
Blast:WD40 111 151 2e-20 BLAST
Coding Region Coverage
Validation Efficiency
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: 45 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4921509C19Rik T A 2: 151,315,466 (GRCm39) M71L probably benign Het
Abcb11 A G 2: 69,154,169 (GRCm39) probably benign Het
Ago4 T C 4: 126,410,645 (GRCm39) T249A probably benign Het
Ahr A T 12: 35,562,922 (GRCm39) C92* probably null Het
Arhgap17 G A 7: 122,885,996 (GRCm39) probably benign Het
Arid1a G T 4: 133,420,126 (GRCm39) T992K unknown Het
Camk2a A G 18: 61,111,061 (GRCm39) I83M probably damaging Het
Ccdc154 T C 17: 25,386,792 (GRCm39) probably null Het
Chtf18 T C 17: 25,941,177 (GRCm39) H607R possibly damaging Het
Col25a1 T C 3: 130,313,422 (GRCm39) probably benign Het
Col9a1 C T 1: 24,276,574 (GRCm39) Q530* probably null Het
Cryl1 G T 14: 57,523,904 (GRCm39) D219E probably damaging Het
Cul3 A T 1: 80,300,781 (GRCm39) probably benign Het
Cul9 C A 17: 46,851,301 (GRCm39) R373L probably benign Het
Exo1 A G 1: 175,721,309 (GRCm39) Y316C possibly damaging Het
Fam114a1 G A 5: 65,187,465 (GRCm39) V408M probably benign Het
Hmcn2 A T 2: 31,347,185 (GRCm39) S4792C possibly damaging Het
Hrh4 T C 18: 13,155,477 (GRCm39) S339P probably benign Het
Ist1 A T 8: 110,405,584 (GRCm39) L152Q probably damaging Het
Marco A G 1: 120,418,683 (GRCm39) V190A probably benign Het
Mdn1 T C 4: 32,709,364 (GRCm39) V1711A probably benign Het
Mmp9 A G 2: 164,791,644 (GRCm39) Y179C probably damaging Het
Mrgprb5 A G 7: 47,818,742 (GRCm39) probably benign Het
Mrgprx1 G T 7: 47,671,371 (GRCm39) C125* probably null Het
Msh6 A G 17: 88,298,234 (GRCm39) probably benign Het
Myot C A 18: 44,488,177 (GRCm39) R441S probably benign Het
Or11g7 A G 14: 50,691,399 (GRCm39) R297G possibly damaging Het
Paf1 A G 7: 28,098,115 (GRCm39) probably benign Het
Pde11a A G 2: 75,821,606 (GRCm39) L891P probably damaging Het
Prkar2a T A 9: 108,596,460 (GRCm39) I135N probably damaging Het
Rap1gap C T 4: 137,454,355 (GRCm39) T646M probably damaging Het
Rgs7bp T C 13: 105,088,087 (GRCm39) D229G possibly damaging Het
Rhobtb3 C T 13: 76,025,547 (GRCm39) S523N probably damaging Het
Setd7 A T 3: 51,428,826 (GRCm39) Y335N probably damaging Het
Setdb2 C T 14: 59,639,764 (GRCm39) R709Q probably damaging Het
Socs4 T C 14: 47,528,264 (GRCm39) Y400H probably damaging Het
Spag16 A T 1: 69,909,479 (GRCm39) H192L probably damaging Het
Ssh1 A T 5: 114,084,541 (GRCm39) C566* probably null Het
Stap1 T G 5: 86,234,552 (GRCm39) I98S possibly damaging Het
Tgs1 C T 4: 3,585,836 (GRCm39) H238Y probably damaging Het
Tifab T C 13: 56,324,275 (GRCm39) Y56C probably benign Het
Tssk2 A G 16: 17,717,653 (GRCm39) E352G probably benign Het
Vmn2r57 A T 7: 41,049,874 (GRCm39) V625D probably benign Het
Wbp1l T C 19: 46,632,876 (GRCm39) Y75H probably benign Het
Wnt5a T C 14: 28,228,077 (GRCm39) probably benign Het
Other mutations in Hps5
AlleleSourceChrCoordTypePredicted EffectPPH 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
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
R4457:Hps5 UTSW 7 46,433,037 (GRCm39) missense probably benign 0.00
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
Posted On 2015-04-16