Incidental Mutation 'IGL01351:Hps5'
ID 75366
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 # IGL01351
Quality Score
Status
Chromosome 7
Chromosomal Location 46409890-46445488 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 46410856 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Isoleucine at position 1113 (M1113I)
Ref Sequence ENSEMBL: ENSMUSP00000103281 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000014562] [ENSMUST00000107653] [ENSMUST00000107654] [ENSMUST00000142663] [ENSMUST00000211347]
AlphaFold P59438
Predicted Effect probably damaging
Transcript: ENSMUST00000014562
AA Change: M1113I

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000014562
Gene: ENSMUSG00000014418
AA Change: M1113I

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: M1080I

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000103280
Gene: ENSMUSG00000014418
AA Change: M1080I

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: M1113I

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000103281
Gene: ENSMUSG00000014418
AA Change: M1113I

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 noncoding transcript
Transcript: ENSMUST00000145776
Predicted Effect probably benign
Transcript: ENSMUST00000211347
Predicted Effect probably benign
Transcript: ENSMUST00000211571
Predicted Effect probably benign
Transcript: ENSMUST00000153789
SMART Domains Protein: ENSMUSP00000119876
Gene: ENSMUSG00000014418

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
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: 38 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca13 T C 11: 9,217,565 (GRCm39) S336P probably benign Het
Abca9 T C 11: 110,039,729 (GRCm39) Y428C probably damaging Het
Alpk1 T C 3: 127,466,011 (GRCm39) Q1165R probably damaging Het
Angel2 C A 1: 190,665,310 (GRCm39) N80K probably benign Het
Bmp6 T C 13: 38,653,610 (GRCm39) S226P probably damaging Het
Ccar2 T C 14: 70,383,311 (GRCm39) T229A probably benign Het
Cdh12 G A 15: 21,237,989 (GRCm39) V75M probably damaging Het
Cdh6 G T 15: 13,034,326 (GRCm39) A778E possibly damaging Het
Corin A T 5: 72,496,334 (GRCm39) C540S probably damaging Het
Cyfip1 C A 7: 55,547,991 (GRCm39) Y530* probably null Het
Dock10 T G 1: 80,570,876 (GRCm39) K327N probably damaging Het
Dpy19l3 A G 7: 35,426,840 (GRCm39) probably benign Het
E2f8 T C 7: 48,516,899 (GRCm39) T827A probably benign Het
Edem3 T C 1: 151,668,136 (GRCm39) V305A possibly damaging Het
Fam170a T C 18: 50,414,845 (GRCm39) W164R probably benign Het
Fbxw14 T C 9: 109,103,640 (GRCm39) D24G possibly damaging Het
Gnmt T C 17: 47,037,606 (GRCm39) D124G probably benign Het
Gpx5 T C 13: 21,471,669 (GRCm39) D178G probably damaging Het
Gsdmd T A 15: 75,736,186 (GRCm39) I105N probably damaging Het
Hyal6 T C 6: 24,734,178 (GRCm39) F37S probably damaging Het
Il17c C T 8: 123,148,862 (GRCm39) T2I probably benign Het
Lyz1 A G 10: 117,127,093 (GRCm39) C48R probably damaging Het
Or52e18 T A 7: 104,609,946 (GRCm39) probably benign Het
Pafah1b3 G A 7: 24,994,570 (GRCm39) R215C possibly damaging Het
Psmb4 A T 3: 94,793,538 (GRCm39) probably null Het
Rnf213 T C 11: 119,373,944 (GRCm39) V5009A probably benign Het
Sema6a T C 18: 47,414,369 (GRCm39) K494E possibly damaging Het
Sfmbt1 T C 14: 30,491,777 (GRCm39) V17A probably benign Het
Speg T A 1: 75,387,920 (GRCm39) probably benign Het
Spint1 A G 2: 119,076,936 (GRCm39) D340G probably damaging Het
Tasor A G 14: 27,186,258 (GRCm39) E819G probably benign Het
Tctn3 T C 19: 40,596,081 (GRCm39) I309V probably benign Het
Tex19.1 T A 11: 121,038,072 (GRCm39) D143E probably damaging Het
Tktl2 A G 8: 66,965,548 (GRCm39) I369V probably benign Het
Tm2d2 A G 8: 25,510,573 (GRCm39) probably benign Het
Traf4 C A 11: 78,056,226 (GRCm39) R14L possibly damaging Het
Zfhx4 A G 3: 5,466,196 (GRCm39) Y2118C probably damaging Het
Zmynd15 C A 11: 70,354,416 (GRCm39) N425K 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
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
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 2013-10-07