Incidental Mutation 'IGL03259:Hps5'
ID 414767
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 # IGL03259
Quality Score
Status
Chromosome 7
Chromosomal Location 46409890-46445488 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 46412526 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Glutamine at position 1021 (P1021Q)
Ref Sequence ENSEMBL: ENSMUSP00000103280 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000014562] [ENSMUST00000107653] [ENSMUST00000107654] [ENSMUST00000142663] [ENSMUST00000211347]
AlphaFold P59438
Predicted Effect probably benign
Transcript: ENSMUST00000014562
AA Change: P1054Q

PolyPhen 2 Score 0.393 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000014562
Gene: ENSMUSG00000014418
AA Change: P1054Q

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: P1021Q

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000103280
Gene: ENSMUSG00000014418
AA Change: P1021Q

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 benign
Transcript: ENSMUST00000107654
AA Change: P1054Q

PolyPhen 2 Score 0.393 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000103281
Gene: ENSMUSG00000014418
AA Change: P1054Q

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: ENSMUST00000130365
SMART Domains Protein: ENSMUSP00000114384
Gene: ENSMUSG00000014418

DomainStartEndE-ValueType
low complexity region 92 103 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000138480
Predicted Effect probably benign
Transcript: ENSMUST00000142663
SMART Domains Protein: ENSMUSP00000122887
Gene: ENSMUSG00000014418

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 unknown
Transcript: ENSMUST00000153789
AA Change: P481Q
SMART Domains Protein: ENSMUSP00000119876
Gene: ENSMUSG00000014418
AA Change: P481Q

DomainStartEndE-ValueType
low complexity region 241 252 N/A INTRINSIC
low complexity region 417 426 N/A INTRINSIC
low complexity region 449 461 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000143627
Predicted Effect noncoding transcript
Transcript: ENSMUST00000145776
Predicted Effect probably benign
Transcript: ENSMUST00000211571
Predicted Effect probably benign
Transcript: ENSMUST00000211347
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: 26 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Atp8a1 T C 5: 67,781,349 (GRCm39) probably null Het
Btbd3 T C 2: 138,121,680 (GRCm39) M121T probably damaging Het
Cep192 A T 18: 67,953,483 (GRCm39) N500I probably damaging Het
Clca4a A G 3: 144,663,841 (GRCm39) L534P probably damaging Het
Cyp2d11 C T 15: 82,274,221 (GRCm39) V387M probably damaging Het
Dlgap3 T C 4: 127,094,077 (GRCm39) I443T probably benign Het
Heatr5b T A 17: 79,098,985 (GRCm39) D1305V probably damaging Het
Iqca1 T C 1: 89,980,156 (GRCm39) D637G probably damaging Het
Kank1 A G 19: 25,407,705 (GRCm39) D1233G probably damaging Het
Lad1 A T 1: 135,755,394 (GRCm39) R223S probably benign Het
Ms4a13 A G 19: 11,161,210 (GRCm39) S110P probably damaging Het
Nmd3 T A 3: 69,652,576 (GRCm39) D387E possibly damaging Het
Or1m1 A G 9: 18,666,811 (GRCm39) V40A probably benign Het
Or7a41 C A 10: 78,871,234 (GRCm39) Y201* probably null Het
Or8k3b G T 2: 86,520,894 (GRCm39) Q142K probably benign Het
Pcgf5 T A 19: 36,433,059 (GRCm39) D234E probably benign Het
Pcnx2 T A 8: 126,480,388 (GRCm39) H1973L probably benign Het
Peak1 A G 9: 56,167,251 (GRCm39) F226L probably damaging Het
Pgp A G 17: 24,690,022 (GRCm39) K180R probably damaging Het
Sdk1 A T 5: 141,938,788 (GRCm39) K404* probably null Het
Serinc5 T A 13: 92,827,500 (GRCm39) V272D probably damaging Het
Slc4a5 A G 6: 83,247,979 (GRCm39) H395R probably damaging Het
Spice1 T A 16: 44,176,530 (GRCm39) V40D probably damaging Het
Syne2 A G 12: 76,035,853 (GRCm39) I3713M probably benign Het
Vmn1r58 A T 7: 5,414,086 (GRCm39) L48* probably null Het
Vwa7 A G 17: 35,239,002 (GRCm39) probably null 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
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
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 2016-08-02