Incidental Mutation 'R7332:Hps1'
ID 591019
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 045425-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.214) question?
Stock # R7332 (G1)
Quality Score 50.0072
Status Validated
Chromosome 19
Chromosomal Location 42743544-42768417 bp(-) (GRCm39)
Type of Mutation splice site (210 bp from exon)
DNA Base Change (assembly) T to C at 42766351 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000124209 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026194] [ENSMUST00000069298] [ENSMUST00000160455] [ENSMUST00000162004] [ENSMUST00000162061]
AlphaFold no structure available at present
Predicted Effect probably null
Transcript: ENSMUST00000026194
SMART Domains Protein: ENSMUSP00000026194
Gene: ENSMUSG00000025188

DomainStartEndE-ValueType
coiled coil region 20 47 N/A INTRINSIC
low complexity region 229 246 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000069298
SMART Domains Protein: ENSMUSP00000071069
Gene: ENSMUSG00000025188

DomainStartEndE-ValueType
coiled coil region 20 47 N/A INTRINSIC
low complexity region 229 246 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000160455
SMART Domains Protein: ENSMUSP00000125662
Gene: ENSMUSG00000025188

DomainStartEndE-ValueType
coiled coil region 20 47 N/A INTRINSIC
low complexity region 229 246 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000162004
SMART Domains Protein: ENSMUSP00000125226
Gene: ENSMUSG00000025188

DomainStartEndE-ValueType
coiled coil region 20 47 N/A INTRINSIC
low complexity region 229 246 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000162061
SMART Domains Protein: ENSMUSP00000124209
Gene: ENSMUSG00000025188

DomainStartEndE-ValueType
coiled coil region 20 47 N/A INTRINSIC
low complexity region 229 246 N/A INTRINSIC
Meta Mutation Damage Score 0.9755 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.7%
  • 20x: 99.1%
Validation Efficiency 100% (68/68)
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: 67 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Afap1l2 A G 19: 56,906,553 (GRCm39) S449P probably damaging Het
Atp6v0c A C 17: 24,388,198 (GRCm39) S21A probably benign Het
Cacna1e T C 1: 154,601,547 (GRCm39) Y40C possibly damaging Het
Cdadc1 A G 14: 59,813,213 (GRCm39) I398T possibly damaging Het
Cfap44 T A 16: 44,250,191 (GRCm39) D756E probably damaging Het
Clcnkb A T 4: 141,141,243 (GRCm39) L104Q probably null Het
Clk1 G A 1: 58,451,853 (GRCm39) H421Y probably benign Het
Cmpk2 A T 12: 26,528,061 (GRCm39) D426V probably damaging Het
Cmya5 A G 13: 93,229,061 (GRCm39) L2009S possibly damaging Het
Col5a2 C G 1: 45,419,325 (GRCm39) D1252H probably damaging Het
Coro1b A G 19: 4,199,356 (GRCm39) K5R probably benign Het
Csmd2 A G 4: 128,313,360 (GRCm39) T1346A Het
Csrp1 G T 1: 135,667,149 (GRCm39) W4L probably benign Het
Cyp3a25 A G 5: 145,929,817 (GRCm39) I184T probably damaging Het
Egfl7 C A 2: 26,480,725 (GRCm39) R128S probably benign Het
Fggy A T 4: 95,511,719 (GRCm39) N157I probably damaging Het
Gldc A T 19: 30,093,926 (GRCm39) L697Q probably damaging Het
Gm4952 T A 19: 12,604,373 (GRCm39) Y262N probably damaging Het
Gsap T A 5: 21,495,119 (GRCm39) M821K probably benign Het
Hsbp1l1 T C 18: 80,280,038 (GRCm39) probably benign Het
Igfbp7 G A 5: 77,499,803 (GRCm39) T220I probably damaging Het
Ints3 T C 3: 90,322,819 (GRCm39) Q137R probably damaging Het
Kcna6 A G 6: 126,716,292 (GRCm39) F199S possibly damaging Het
Kirrel1 T C 3: 86,995,705 (GRCm39) I410V probably benign Het
Llgl2 T C 11: 115,739,125 (GRCm39) V332A probably damaging Het
Lrrc27 A G 7: 138,822,661 (GRCm39) I517M probably damaging Het
Mas1 T C 17: 13,061,106 (GRCm39) T106A probably benign Het
Mast4 T A 13: 102,887,932 (GRCm39) Y1159F possibly damaging Het
Mmp2 A G 8: 93,576,780 (GRCm39) D601G probably damaging Het
Mycbp2 T A 14: 103,434,793 (GRCm39) I2217F probably damaging Het
Mycbp2 A G 14: 103,393,889 (GRCm39) S2891P probably damaging Het
Naip6 A G 13: 100,437,209 (GRCm39) V438A possibly damaging Het
Or4g17 A G 2: 111,209,738 (GRCm39) H131R not run Het
Pdf T C 8: 107,775,173 (GRCm39) R20G probably benign Het
Pfdn2 T C 1: 171,184,162 (GRCm39) L47P probably damaging Het
Pik3c2g C A 6: 139,841,981 (GRCm39) N795K Het
Ppip5k1 A T 2: 121,142,450 (GRCm39) V1333D probably damaging Het
Pramel51 T C 12: 88,143,187 (GRCm39) T339A possibly damaging Het
Prss44 A T 9: 110,644,530 (GRCm39) I213F probably damaging Het
Rbm47 A G 5: 66,183,557 (GRCm39) Y349H probably damaging Het
Rcl1 A T 19: 29,108,096 (GRCm39) T253S probably benign Het
Rdh1 A G 10: 127,595,754 (GRCm39) probably benign Het
Scn7a C T 2: 66,522,898 (GRCm39) W935* probably null Het
Sec24b T C 3: 129,835,042 (GRCm39) N52S probably benign Het
Serpinb5 A T 1: 106,800,091 (GRCm39) I94L probably benign Het
Setx T C 2: 29,036,638 (GRCm39) V1041A probably benign Het
Slco3a1 G A 7: 73,968,232 (GRCm39) A496V possibly damaging Het
Spag5 T A 11: 78,204,205 (GRCm39) L486* probably null Het
Spink5 T C 18: 44,115,317 (GRCm39) I183T probably damaging Het
Srd5a1 T C 13: 69,759,173 (GRCm39) Y65C probably benign Het
Ssh2 T A 11: 77,344,349 (GRCm39) I778N possibly damaging Het
Sstr1 C T 12: 58,260,172 (GRCm39) S265L probably damaging Het
Syne2 T A 12: 76,014,529 (GRCm39) probably null Het
Tctn1 A T 5: 122,399,547 (GRCm39) D92E probably damaging Het
Tiam2 A G 17: 3,503,644 (GRCm39) I940M probably damaging Het
Tmeff2 T C 1: 51,018,599 (GRCm39) W194R unknown Het
Tomm20 T C 8: 127,663,903 (GRCm39) T94A probably benign Het
Ucn2 A G 9: 108,815,532 (GRCm39) N98S probably benign Het
V1rd19 A T 7: 23,702,743 (GRCm39) I70L probably benign Het
Vmn1r18 A G 6: 57,367,503 (GRCm39) L17P probably benign Het
Vmn2r61 A G 7: 41,909,534 (GRCm39) T20A probably benign Het
Wdr59 G A 8: 112,220,986 (GRCm39) T182I Het
Zfp40 A T 17: 23,395,155 (GRCm39) C477* probably null Het
Zfp68 A G 5: 138,604,830 (GRCm39) S498P possibly damaging Het
Zfp729b T C 13: 67,757,755 (GRCm39) probably null Het
Zfp846 T G 9: 20,505,521 (GRCm39) N460K probably benign Het
Zim1 T C 7: 6,680,352 (GRCm39) Y437C probably damaging 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
R1860:Hps1 UTSW 19 42,750,888 (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)
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'- GTGGCAGACAGTTCACTGAC -3'
(R):5'- GAGGTAATTACAGAACAGGCCGTC -3'

Sequencing Primer
(F):5'- TGGCAGACAGTTCACTGACTATGATG -3'
(R):5'- AGGCCGTCCTGGTGGAG -3'
Posted On 2019-11-08