Incidental Mutation 'R1860:Hps1'
ID 203857
Institutional Source Beutler Lab
Gene Symbol Hps1
Ensembl Gene ENSMUSG00000025188
Gene Name HPS1, biogenesis of lysosomal organelles complex 3 subunit 1
Synonyms 6030422N11Rik, Hermansky-Pudlak syndrome 1
MMRRC Submission 039883-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.214) question?
Stock # R1860 (G1)
Quality Score 225
Status Not validated
Chromosome 19
Chromosomal Location 42743544-42768417 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 42750888 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Tyrosine at position 371 (H371Y)
Ref Sequence ENSEMBL: ENSMUSP00000125226 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026194] [ENSMUST00000069298] [ENSMUST00000160455] [ENSMUST00000162004] [ENSMUST00000162061]
AlphaFold no structure available at present
Predicted Effect probably damaging
Transcript: ENSMUST00000026194
AA Change: H371Y

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000026194
Gene: ENSMUSG00000025188
AA Change: H371Y

DomainStartEndE-ValueType
coiled coil region 20 47 N/A INTRINSIC
low complexity region 229 246 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000069298
AA Change: H379Y

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000071069
Gene: ENSMUSG00000025188
AA Change: H379Y

DomainStartEndE-ValueType
coiled coil region 20 47 N/A INTRINSIC
low complexity region 229 246 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000159974
Predicted Effect possibly damaging
Transcript: ENSMUST00000160455
AA Change: H379Y

PolyPhen 2 Score 0.762 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000125662
Gene: ENSMUSG00000025188
AA Change: H379Y

DomainStartEndE-ValueType
coiled coil region 20 47 N/A INTRINSIC
low complexity region 229 246 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000160621
Predicted Effect probably benign
Transcript: ENSMUST00000161252
Predicted Effect probably damaging
Transcript: ENSMUST00000162004
AA Change: H371Y

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000125226
Gene: ENSMUSG00000025188
AA Change: H371Y

DomainStartEndE-ValueType
coiled coil region 20 47 N/A INTRINSIC
low complexity region 229 246 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000162061
AA Change: H371Y

PolyPhen 2 Score 0.964 (Sensitivity: 0.78; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000124209
Gene: ENSMUSG00000025188
AA Change: H371Y

DomainStartEndE-ValueType
coiled coil region 20 47 N/A INTRINSIC
low complexity region 229 246 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000161761
Coding Region Coverage
  • 1x: 97.4%
  • 3x: 96.8%
  • 10x: 95.1%
  • 20x: 91.7%
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. The encoded protein is a component of three different protein complexes termed biogenesis of lysosome-related organelles complex (BLOC)-3, BLOC4, and BLOC5. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 1. Alternative splicing results in multiple transcript variants. A pseudogene related to this gene is located on chromosome 22. [provided by RefSeq, Aug 2015]
PHENOTYPE: Homozygotes for spontaneous mutations exhibit hypopigmentation and increased bleeding time. Impaired natural killer cell function, reduced secretion of kidney lysosomal enzymes,and abnormal retinofugal neuronal projections characterize some alleles. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 83 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930522L14Rik A G 5: 109,884,098 (GRCm39) C587R probably damaging Het
Abca16 T A 7: 120,133,986 (GRCm39) S1320T probably benign Het
Abra C A 15: 41,732,430 (GRCm39) R212L probably damaging Het
Acadsb T A 7: 131,045,958 (GRCm39) probably null Het
Adam26a A G 8: 44,022,578 (GRCm39) V304A possibly damaging Het
Adgre1 T C 17: 57,748,363 (GRCm39) V521A probably benign Het
Adh5 G A 3: 138,159,539 (GRCm39) V288I probably benign Het
Astn1 A C 1: 158,429,515 (GRCm39) N753T probably damaging Het
Atad2 A T 15: 57,960,114 (GRCm39) probably null Het
Best3 A G 10: 116,829,178 (GRCm39) T153A probably damaging Het
Ccdc122 G A 14: 77,348,847 (GRCm39) V226I probably damaging Het
Ccdc175 T C 12: 72,152,700 (GRCm39) Q735R probably benign Het
Cd19 T A 7: 126,008,813 (GRCm39) I499F probably damaging Het
Cftr T A 6: 18,268,288 (GRCm39) L749H probably benign Het
Clec2h G T 6: 128,652,790 (GRCm39) G186W probably damaging Het
Cpsf3 T A 12: 21,346,733 (GRCm39) I202N probably damaging Het
Crebbp G T 16: 3,905,600 (GRCm39) T1669N possibly damaging Het
Csmd3 A T 15: 47,522,588 (GRCm39) C2694S probably damaging Het
Cul4a G A 8: 13,173,565 (GRCm39) R204Q probably damaging Het
Derl2 A G 11: 70,909,169 (GRCm39) F43S probably damaging Het
Dnah14 T A 1: 181,591,525 (GRCm39) N3348K probably damaging Het
Dnhd1 T C 7: 105,353,412 (GRCm39) V2855A probably benign Het
Dpysl4 G T 7: 138,670,215 (GRCm39) C27F probably benign Het
Fam228b G A 12: 4,798,314 (GRCm39) A163V probably damaging Het
Fscn1 T C 5: 142,955,818 (GRCm39) probably null Het
Fzd5 C A 1: 64,774,153 (GRCm39) R536L probably damaging Het
Gm8180 T A 14: 44,021,196 (GRCm39) H4L probably benign Het
Gpr176 T A 2: 118,203,659 (GRCm39) N4Y probably damaging Het
Grin3a T C 4: 49,665,309 (GRCm39) I1109V possibly damaging Het
Hcar1 T A 5: 124,017,092 (GRCm39) I200F probably damaging Het
Heatr4 G A 12: 84,026,502 (GRCm39) Q252* probably null Het
Ikzf2 T C 1: 69,609,661 (GRCm39) T195A probably damaging Het
Kdm1b G A 13: 47,202,666 (GRCm39) A34T probably benign Het
Lef1 A G 3: 130,905,290 (GRCm39) N57S probably damaging Het
Ltn1 A T 16: 87,213,231 (GRCm39) D443E probably benign Het
Macroh2a1 A G 13: 56,231,017 (GRCm39) L287P probably damaging Het
Mamdc2 T C 19: 23,336,517 (GRCm39) T331A probably damaging Het
Marchf10 A T 11: 105,287,904 (GRCm39) S133T probably damaging Het
Mb A G 15: 76,901,784 (GRCm39) Y104H probably damaging Het
Mrc1 C A 2: 14,333,390 (GRCm39) P1357Q probably benign Het
Nfib C T 4: 82,241,917 (GRCm39) V425M probably damaging Het
Or12j2 G A 7: 139,916,132 (GRCm39) R119H possibly damaging Het
Or4a27 T G 2: 88,559,674 (GRCm39) I90L probably damaging Het
Or4b1b C A 2: 90,112,502 (GRCm39) C139F probably damaging Het
Or4c127 G A 2: 89,833,490 (GRCm39) V247I probably benign Het
Or4n4 A T 14: 50,518,848 (GRCm39) Y287* probably null Het
Or52u1 T C 7: 104,237,112 (GRCm39) S34P probably damaging Het
Or5b113 T A 19: 13,342,705 (GRCm39) S238T possibly damaging Het
Or5p53 A G 7: 107,533,597 (GRCm39) Y290C probably damaging Het
Or6c208 T C 10: 129,223,955 (GRCm39) F151S probably damaging Het
Or8b51 A T 9: 38,569,661 (GRCm39) V9E probably damaging Het
Phaf1 A G 8: 105,966,703 (GRCm39) E150G probably null Het
Piezo1 T C 8: 123,222,489 (GRCm39) N919S possibly damaging Het
Prkaca T C 8: 84,707,852 (GRCm39) S46P probably benign Het
Prkcb T G 7: 122,167,424 (GRCm39) V378G probably damaging Het
Ptprf A T 4: 118,081,129 (GRCm39) L576Q probably damaging Het
Rapgef4 T C 2: 72,065,064 (GRCm39) V687A probably benign Het
Rsad2 C T 12: 26,500,616 (GRCm39) V224I probably damaging Het
Ryr1 A T 7: 28,708,977 (GRCm39) D4796E unknown Het
Scn1a C T 2: 66,148,326 (GRCm39) S1073N probably damaging Het
Slc26a3 A G 12: 31,515,845 (GRCm39) M582V probably benign Het
Tbc1d32 A T 10: 55,999,633 (GRCm39) Y846* probably null Het
Tbk1 A T 10: 121,383,076 (GRCm39) M719K probably benign Het
Timeless A G 10: 128,081,983 (GRCm39) K536R probably benign Het
Tle6 G T 10: 81,430,163 (GRCm39) Q330K probably damaging Het
Tmem208 A G 8: 106,061,438 (GRCm39) K155E possibly damaging Het
Toe1 T C 4: 116,662,426 (GRCm39) Y273C probably damaging Het
Tppp2 A C 14: 52,158,062 (GRCm39) N169T probably benign Het
Ttll6 T A 11: 96,029,700 (GRCm39) Y204* probably null Het
Ubxn11 G A 4: 133,852,149 (GRCm39) S32N probably damaging Het
Usp8 G A 2: 126,597,960 (GRCm39) C961Y probably damaging Het
Vdac3 A T 8: 23,070,515 (GRCm39) I132K possibly damaging Het
Vmn2r124 G T 17: 18,269,759 (GRCm39) W5L probably benign Het
Vmn2r71 A T 7: 85,264,782 (GRCm39) D38V probably damaging Het
Vmn2r87 C T 10: 130,315,755 (GRCm39) V104I probably benign Het
Vmn2r97 C T 17: 19,167,648 (GRCm39) T634I probably benign Het
Vps50 T C 6: 3,520,279 (GRCm39) probably null Het
Wwc2 T C 8: 48,443,137 (GRCm39) N32S possibly damaging Het
Ythdc2 T A 18: 45,006,023 (GRCm39) I1172K possibly damaging Het
Zfp14 C T 7: 29,738,116 (GRCm39) V290M probably damaging Het
Zfp317 G A 9: 19,553,280 (GRCm39) A18T possibly damaging Het
Zfp354b A T 11: 50,814,369 (GRCm39) N185K probably benign Het
Zscan21 T A 5: 138,124,892 (GRCm39) D269E probably benign Het
Other mutations in Hps1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02116:Hps1 APN 19 42,759,568 (GRCm39) nonsense probably null
IGL02327:Hps1 APN 19 42,744,784 (GRCm39) unclassified probably benign
IGL02488:Hps1 APN 19 42,746,227 (GRCm39) unclassified probably benign
IGL03161:Hps1 APN 19 42,755,710 (GRCm39) missense probably damaging 1.00
R0127:Hps1 UTSW 19 42,759,550 (GRCm39) splice site probably benign
R0134:Hps1 UTSW 19 42,754,619 (GRCm39) missense probably damaging 0.98
R0234:Hps1 UTSW 19 42,750,992 (GRCm39) missense probably damaging 1.00
R0234:Hps1 UTSW 19 42,750,992 (GRCm39) missense probably damaging 1.00
R0394:Hps1 UTSW 19 42,759,338 (GRCm39) splice site probably null
R1435:Hps1 UTSW 19 42,750,714 (GRCm39) missense probably benign 0.04
R1537:Hps1 UTSW 19 42,748,143 (GRCm39) critical splice donor site probably null
R1616:Hps1 UTSW 19 42,755,624 (GRCm39) missense probably damaging 1.00
R2014:Hps1 UTSW 19 42,750,951 (GRCm39) missense probably benign 0.00
R3424:Hps1 UTSW 19 42,748,952 (GRCm39) missense possibly damaging 0.75
R4472:Hps1 UTSW 19 42,750,935 (GRCm39) missense probably damaging 1.00
R5476:Hps1 UTSW 19 42,758,041 (GRCm39) splice site probably null
R6054:Hps1 UTSW 19 42,759,217 (GRCm39) missense probably damaging 0.96
R6275:Hps1 UTSW 19 42,758,046 (GRCm39) missense probably null 1.00
R6807:Hps1 UTSW 19 42,759,217 (GRCm39) missense possibly damaging 0.60
R6916:Hps1 UTSW 19 42,755,164 (GRCm39)
R7332:Hps1 UTSW 19 42,766,351 (GRCm39) splice site probably null
R7487:Hps1 UTSW 19 42,744,700 (GRCm39) missense probably damaging 1.00
R7504:Hps1 UTSW 19 42,755,159 (GRCm39) missense probably benign 0.00
R7823:Hps1 UTSW 19 42,744,146 (GRCm39) missense possibly damaging 0.58
R7955:Hps1 UTSW 19 42,759,221 (GRCm39) missense probably damaging 0.99
R8198:Hps1 UTSW 19 42,755,659 (GRCm39) missense probably benign 0.05
R8819:Hps1 UTSW 19 42,759,648 (GRCm39) missense probably benign 0.06
R9688:Hps1 UTSW 19 42,755,147 (GRCm39) missense probably benign
Z1176:Hps1 UTSW 19 42,755,125 (GRCm39) missense probably null 0.00
Z1177:Hps1 UTSW 19 42,754,657 (GRCm39) critical splice acceptor site probably null
Z1177:Hps1 UTSW 19 42,748,270 (GRCm39) missense probably damaging 1.00
Z1177:Hps1 UTSW 19 42,744,135 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- CCAGCAGTTGGTACAGGATCAG -3'
(R):5'- TCAAGTTGTGGATGAGCCTG -3'

Sequencing Primer
(F):5'- TTGGTACAGGATCAGGGCCAG -3'
(R):5'- TGGATGAGCCTGGACCTTC -3'
Posted On 2014-06-23