Incidental Mutation 'R9303:Hps5'
ID 705058
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
Accession Numbers
Essential gene? Probably non essential (E-score: 0.104) question?
Stock # R9303 (G1)
Quality Score 225.009
Status Validated
Chromosome 7
Chromosomal Location 46409890-46445488 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 46438619 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Isoleucine at position 38 (T38I)
Ref Sequence ENSEMBL: ENSMUSP00000014562 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000014562] [ENSMUST00000107653] [ENSMUST00000107654] [ENSMUST00000123725] [ENSMUST00000142663] [ENSMUST00000152759] [ENSMUST00000211347]
AlphaFold P59438
Predicted Effect possibly damaging
Transcript: ENSMUST00000014562
AA Change: T38I

PolyPhen 2 Score 0.941 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000014562
Gene: ENSMUSG00000014418
AA Change: T38I

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 possibly damaging
Transcript: ENSMUST00000107653
AA Change: T38I

PolyPhen 2 Score 0.914 (Sensitivity: 0.81; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000103280
Gene: ENSMUSG00000014418
AA Change: T38I

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 possibly damaging
Transcript: ENSMUST00000107654
AA Change: T38I

PolyPhen 2 Score 0.941 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000103281
Gene: ENSMUSG00000014418
AA Change: T38I

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 possibly damaging
Transcript: ENSMUST00000123725
AA Change: T38I

PolyPhen 2 Score 0.941 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000116770
Gene: ENSMUSG00000014418
AA Change: T38I

DomainStartEndE-ValueType
SCOP:d1tbga_ 24 107 5e-4 SMART
Blast:WD40 63 103 1e-22 BLAST
Predicted Effect probably damaging
Transcript: ENSMUST00000142663
AA Change: T38I

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000122887
Gene: ENSMUSG00000014418
AA Change: T38I

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 possibly damaging
Transcript: ENSMUST00000152759
AA Change: T38I

PolyPhen 2 Score 0.941 (Sensitivity: 0.80; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000115786
Gene: ENSMUSG00000014418
AA Change: T38I

DomainStartEndE-ValueType
SCOP:d1jjub_ 44 192 2e-8 SMART
Blast:WD40 63 103 1e-21 BLAST
Blast:WD40 111 151 2e-20 BLAST
Predicted Effect possibly damaging
Transcript: ENSMUST00000211347
AA Change: T38I

PolyPhen 2 Score 0.941 (Sensitivity: 0.80; Specificity: 0.94)
Predicted Effect probably benign
Transcript: ENSMUST00000211471
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.8%
Validation Efficiency 100% (57/57)
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: 56 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca16 A G 7: 120,126,989 (GRCm39) I1227V probably benign Het
Acte1 G T 7: 143,434,902 (GRCm39) probably null Het
Adamts17 T C 7: 66,489,645 (GRCm39) L21P probably damaging Het
Adcy1 T C 11: 7,094,766 (GRCm39) V564A probably damaging Het
Adgre1 A G 17: 57,748,275 (GRCm39) N492D probably benign Het
Aldh1b1 G A 4: 45,803,811 (GRCm39) V450M probably damaging Het
Arv1 T A 8: 125,457,685 (GRCm39) H196Q probably damaging Het
Atp9a A T 2: 168,517,163 (GRCm39) I390N probably benign Het
Bltp1 A G 3: 37,098,969 (GRCm39) I1277V Het
Capn10 T C 1: 92,871,665 (GRCm39) probably null Het
Casq2 A G 3: 102,052,700 (GRCm39) D404G unknown Het
Cenpf T C 1: 189,392,271 (GRCm39) probably null Het
Cep295nl G A 11: 118,224,766 (GRCm39) P26L possibly damaging Het
Chmp4c T G 3: 10,454,974 (GRCm39) S214A probably benign Het
Chrna5 T C 9: 54,912,156 (GRCm39) F319L probably benign Het
Csmd1 G T 8: 16,011,532 (GRCm39) T2507K probably benign Het
Ctnnd2 T C 15: 30,967,037 (GRCm39) M996T probably damaging Het
Dbf4 T C 5: 8,448,102 (GRCm39) T328A unknown Het
Ddc C T 11: 11,779,132 (GRCm39) V331I probably benign Het
Fads2b A T 2: 85,330,649 (GRCm39) C219* probably null Het
Fat1 T A 8: 45,463,498 (GRCm39) W1347R probably damaging Het
Fbxw21 A G 9: 108,986,727 (GRCm39) F51L probably benign Het
Gng2 G T 14: 19,925,961 (GRCm39) H44N probably damaging Het
Igf2 G A 7: 142,208,153 (GRCm39) R64C probably damaging Het
Inpp4b C T 8: 82,759,758 (GRCm39) A601V probably damaging Het
Kdm2a A G 19: 4,395,606 (GRCm39) Y342H probably benign Het
Kidins220 C A 12: 25,107,110 (GRCm39) T1430K probably benign Het
Knl1 T C 2: 118,898,829 (GRCm39) C177R possibly damaging Het
Krt32 T C 11: 99,972,029 (GRCm39) T440A probably benign Het
Kynu T A 2: 43,569,768 (GRCm39) F350Y probably damaging Het
Lama4 T C 10: 38,973,137 (GRCm39) L1568P probably damaging Het
Lrp1b A T 2: 41,618,574 (GRCm39) S281T Het
Or2y3 A T 17: 38,393,629 (GRCm39) V80D probably damaging Het
Or5h23 A G 16: 58,906,802 (GRCm39) S15P probably benign Het
Or8c19-ps1 C T 9: 38,220,463 (GRCm39) T124M probably benign Het
Orc3 G A 4: 34,607,181 (GRCm39) R50* probably null Het
Osbpl6 T A 2: 76,378,716 (GRCm39) D124E probably damaging Het
Parp4 TG T 14: 56,832,790 (GRCm39) probably null Het
Parp4 T C 14: 56,852,224 (GRCm39) probably null Het
Pcdhb18 A C 18: 37,625,004 (GRCm39) H778P probably benign Het
Polg A T 7: 79,105,860 (GRCm39) Y710N probably benign Het
Ppp2r2b C A 18: 42,779,025 (GRCm39) R370L possibly damaging Het
Raet1e C T 10: 22,057,872 (GRCm39) T213I possibly damaging Het
Reln T A 5: 22,193,705 (GRCm39) S1418C possibly damaging Het
Reln T C 5: 22,285,689 (GRCm39) S427G probably benign Het
Rhobtb2 G A 14: 70,025,376 (GRCm39) H633Y probably damaging Het
Serpina3i T C 12: 104,234,881 (GRCm39) V404A probably damaging Het
Serpinb8 T C 1: 107,526,769 (GRCm39) probably null Het
Sorl1 G T 9: 41,900,739 (GRCm39) Q1658K probably damaging Het
Tmem26 G A 10: 68,559,816 (GRCm39) W29* probably null Het
Togaram2 A G 17: 71,996,408 (GRCm39) E137G probably damaging Het
Ttc39b A G 4: 83,151,023 (GRCm39) L524S probably damaging Het
Usp43 T C 11: 67,767,345 (GRCm39) N675S probably damaging Het
Vmn2r104 A G 17: 20,268,439 (GRCm39) L10P possibly damaging Het
Zbtb1 G A 12: 76,432,773 (GRCm39) R253Q probably damaging Het
Zfp354b T A 11: 50,820,256 (GRCm39) R36S probably damaging 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
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
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'- TTGCCCCTTCCTAGAACATCAG -3'
(R):5'- TTACATTGTGTCCCGGGCAG -3'

Sequencing Primer
(F):5'- CTAGAACATCAGACAAGAATAGTTCG -3'
(R):5'- CCGGGCAGGGGAGAGAAG -3'
Posted On 2022-03-25