Incidental Mutation 'R8243:Hps5'
ID 637650
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 067648-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.104) question?
Stock # R8243 (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 T at 46436066 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Glutamic Acid at position 160 (A160E)
Ref Sequence ENSEMBL: ENSMUSP00000014562 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000014562] [ENSMUST00000107653] [ENSMUST00000107654] [ENSMUST00000123725] [ENSMUST00000142663] [ENSMUST00000152759] [ENSMUST00000211347]
AlphaFold P59438
Predicted Effect probably damaging
Transcript: ENSMUST00000014562
AA Change: A160E

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000014562
Gene: ENSMUSG00000014418
AA Change: A160E

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: A160E

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000103280
Gene: ENSMUSG00000014418
AA Change: A160E

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: A160E

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000103281
Gene: ENSMUSG00000014418
AA Change: A160E

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: A160E

PolyPhen 2 Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000122887
Gene: ENSMUSG00000014418
AA Change: A160E

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 probably damaging
Transcript: ENSMUST00000152759
AA Change: A160E

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000115786
Gene: ENSMUSG00000014418
AA Change: A160E

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 probably damaging
Transcript: ENSMUST00000211347
AA Change: A160E

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
Predicted Effect probably benign
Transcript: ENSMUST00000211471
Coding Region Coverage
  • 1x: 99.8%
  • 3x: 99.5%
  • 10x: 98.7%
  • 20x: 96.0%
Validation Efficiency 100% (47/47)
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: 47 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam19 T A 11: 46,015,909 (GRCm39) H356Q probably damaging Het
BC030500 T C 8: 59,365,388 (GRCm39) I13T unknown Het
Bcl6 C T 16: 23,786,883 (GRCm39) C636Y probably damaging Het
Cabyr G T 18: 12,883,759 (GRCm39) C82F probably benign Het
Clec4a1 T C 6: 122,901,778 (GRCm39) V70A possibly damaging Het
Col11a1 C T 3: 113,855,141 (GRCm39) P134S unknown Het
Col27a1 A G 4: 63,144,120 (GRCm39) T603A probably damaging Het
Col6a6 T C 9: 105,576,468 (GRCm39) D1964G probably damaging Het
Dnajc8 A G 4: 132,278,775 (GRCm39) probably null Het
E330034G19Rik T C 14: 24,358,360 (GRCm39) Y318H Het
Efemp1 T A 11: 28,871,690 (GRCm39) S402T probably damaging Het
Emcn T C 3: 137,097,411 (GRCm39) V110A possibly damaging Het
Fgd5 C T 6: 91,966,004 (GRCm39) L746F possibly damaging Het
Gna13 A G 11: 109,287,239 (GRCm39) N354S probably damaging Het
Helq G T 5: 100,918,348 (GRCm39) S855R possibly damaging Het
Igfbp7 T A 5: 77,549,339 (GRCm39) E188V probably benign Het
Ivd A G 2: 118,702,018 (GRCm39) Y150C probably damaging Het
Jade2 T C 11: 51,708,045 (GRCm39) T723A probably benign Het
Kif1b T C 4: 149,288,724 (GRCm39) N1239S probably benign Het
Klb A G 5: 65,536,338 (GRCm39) N556S possibly damaging Het
Klhdc8a C T 1: 132,230,304 (GRCm39) R140C possibly damaging Het
Klhl2 T A 8: 65,202,084 (GRCm39) M531L probably benign Het
Mark3 T A 12: 111,613,956 (GRCm39) S546R possibly damaging Het
Mfsd8 G A 3: 40,789,628 (GRCm39) R140C probably damaging Het
Musk G A 4: 58,293,600 (GRCm39) R63K probably benign Het
Nacad C T 11: 6,552,643 (GRCm39) E183K probably damaging Het
Oasl1 T C 5: 115,066,220 (GRCm39) Y113H probably benign Het
Or10g9b A T 9: 39,917,484 (GRCm39) C254S probably benign Het
Or1x2 C T 11: 50,918,138 (GRCm39) T103M probably benign Het
Or4c111 T A 2: 88,844,051 (GRCm39) Y119F probably benign Het
Or51ab3 A T 7: 103,201,205 (GRCm39) D71V probably damaging Het
Or8b56 A G 9: 38,739,803 (GRCm39) E272G Het
P4hb T C 11: 120,454,206 (GRCm39) D296G probably benign Het
Plat G T 8: 23,262,248 (GRCm39) G91W probably damaging Het
Plekhh1 G A 12: 79,125,843 (GRCm39) R1293H probably benign Het
Prss21 A G 17: 24,088,376 (GRCm39) T114A probably damaging Het
Ptprn T C 1: 75,229,179 (GRCm39) D776G probably damaging Het
Rffl A G 11: 82,703,621 (GRCm39) C101R probably damaging Het
Rundc1 A G 11: 101,316,384 (GRCm39) D152G probably benign Het
Sema6c A G 3: 95,079,916 (GRCm39) T737A probably damaging Het
Sppl2c A G 11: 104,078,687 (GRCm39) T496A probably damaging Het
Supt7l T C 5: 31,673,013 (GRCm39) I412V probably benign Het
Trim38 T A 13: 23,975,378 (GRCm39) I439N probably damaging Het
Ugt1a1 CAGAGAGAGAGAGA CAGAGAGAGAGA 1: 88,139,706 (GRCm39) probably benign Het
Usp18 G A 6: 121,246,103 (GRCm39) R353H probably benign Het
Usp42 T C 5: 143,700,849 (GRCm39) K1058R probably benign Het
Utp25 T C 1: 192,796,937 (GRCm39) D598G 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
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
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'- GGAAGTCTACACAGCTAATGTCGT -3'
(R):5'- ACAAATTACATGGCTTATTTCACGT -3'

Sequencing Primer
(F):5'- CTACACAGCTAATGTCGTGGTCAG -3'
(R):5'- AGTACACGTGTGTGCTTC -3'
Posted On 2020-07-13