Incidental Mutation 'R4912:Hps3'
ID 379602
Institutional Source Beutler Lab
Gene Symbol Hps3
Ensembl Gene ENSMUSG00000027615
Gene Name HPS3, biogenesis of lysosomal organelles complex 2 subunit 1
Synonyms Hermansky-Pudlak syndrome 3
MMRRC Submission 042514-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.076) question?
Stock # R4912 (G1)
Quality Score 225
Status Not validated
Chromosome 3
Chromosomal Location 20050109-20089478 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to A at 20068337 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Leucine to Phenylalanine at position 572 (L572F)
Ref Sequence ENSEMBL: ENSMUSP00000012580 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000012580] [ENSMUST00000108321]
AlphaFold Q91VB4
Predicted Effect probably damaging
Transcript: ENSMUST00000012580
AA Change: L572F

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000012580
Gene: ENSMUSG00000027615
AA Change: L572F

DomainStartEndE-ValueType
Pfam:HPS3_N 3 212 2.8e-74 PFAM
Pfam:HPS3_Mid 255 640 1.3e-167 PFAM
Pfam:HPS3_C 649 1000 1.8e-175 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000108321
AA Change: L440F

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000103957
Gene: ENSMUSG00000027615
AA Change: L440F

DomainStartEndE-ValueType
Pfam:HPS3_N 3 87 5.6e-25 PFAM
Pfam:HPS3_Mid 121 508 4.2e-161 PFAM
Pfam:HPS3_C 517 870 9.2e-199 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124808
Predicted Effect noncoding transcript
Transcript: ENSMUST00000126644
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130171
Predicted Effect noncoding transcript
Transcript: ENSMUST00000137408
Predicted Effect noncoding transcript
Transcript: ENSMUST00000151752
Predicted Effect noncoding transcript
Transcript: ENSMUST00000141308
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155121
Predicted Effect noncoding transcript
Transcript: ENSMUST00000139446
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.3%
  • 10x: 96.2%
  • 20x: 91.9%
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 containing a potential clathrin-binding motif, consensus dileucine signals, and tyrosine-based sorting signals for targeting to vesicles of lysosomal lineage. The encoded protein may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 3. [provided by RefSeq, Apr 2015]
PHENOTYPE: Homozygotes for spontaneous null mutations exhibit hypopigmentation and prolonged bleeding associated with a platelet defect. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 64 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700006A11Rik T C 3: 124,213,505 (GRCm39) D52G possibly damaging Het
Acaa1a C A 9: 119,171,827 (GRCm39) R102S probably damaging Het
Arhgef12 G A 9: 42,904,361 (GRCm39) R706* probably null Het
Best3 A G 10: 116,844,886 (GRCm39) Y347C probably damaging Het
Birc6 T A 17: 74,872,900 (GRCm39) D386E probably damaging Het
C130050O18Rik A T 5: 139,400,144 (GRCm39) T66S probably benign Het
Chd9 A T 8: 91,760,858 (GRCm39) D2201V possibly damaging Het
Csk A G 9: 57,538,063 (GRCm39) Y48H probably damaging Het
Dffb T A 4: 154,049,864 (GRCm39) probably benign Het
Diaph3 A C 14: 87,244,635 (GRCm39) C217W probably damaging Het
Eml2 T A 7: 18,927,924 (GRCm39) probably null Het
Ercc5 T C 1: 44,196,217 (GRCm39) I70T probably damaging Het
Fryl AGTGTGT AGTGT 5: 73,226,125 (GRCm39) probably null Het
Fsd1 C T 17: 56,298,241 (GRCm39) P189S possibly damaging Het
Gm42669 A G 5: 107,656,683 (GRCm39) K982R probably damaging Het
Gm5414 A G 15: 101,533,445 (GRCm39) I373T possibly damaging Het
Gm7356 A G 17: 14,221,498 (GRCm39) L177P possibly damaging Het
Grip1 G A 10: 119,767,153 (GRCm39) D93N probably damaging Het
Hbq1b T A 11: 32,237,014 (GRCm39) M1K probably null Het
Ighj2 T A 12: 113,393,100 (GRCm39) probably benign Het
Kcna3 T C 3: 106,945,207 (GRCm39) M490T probably benign Het
Krt76 T A 15: 101,796,597 (GRCm39) K404* probably null Het
Lgr4 A T 2: 109,836,847 (GRCm39) probably null Het
Ltbp4 G T 7: 27,005,541 (GRCm39) C1533* probably null Het
Mapre2 A G 18: 23,965,990 (GRCm39) N25S probably damaging Het
Mark3 T A 12: 111,559,087 (GRCm39) I43K probably benign Het
Mon1b T A 8: 114,368,585 (GRCm39) Y495* probably null Het
Mrfap1 A G 5: 36,954,089 (GRCm39) probably benign Het
Mxra8 A G 4: 155,925,361 (GRCm39) probably null Het
Myoz1 A T 14: 20,699,606 (GRCm39) L244Q probably damaging Het
Ndfip2 C T 14: 105,496,120 (GRCm39) R5W probably benign Het
Nek11 T C 9: 105,164,857 (GRCm39) D423G probably benign Het
Nin A T 12: 70,090,837 (GRCm39) D859E probably damaging Het
Nup210 G A 6: 90,994,511 (GRCm39) A1729V probably benign Het
Olfm3 A G 3: 114,895,589 (GRCm39) E157G probably damaging Het
Or1e1f A T 11: 73,856,166 (GRCm39) H244L probably damaging Het
Prickle1 A G 15: 93,398,429 (GRCm39) S800P probably benign Het
Reln A G 5: 22,130,191 (GRCm39) S2707P probably benign Het
Resf1 C G 6: 149,230,887 (GRCm39) S1311C probably damaging Het
Rexo4 G A 2: 26,852,404 (GRCm39) T200M possibly damaging Het
Saxo2 T A 7: 82,283,743 (GRCm39) I372L probably benign Het
Scgb2b2 T A 7: 31,003,056 (GRCm39) D50E probably benign Het
Sipa1l1 T C 12: 82,443,452 (GRCm39) L914P possibly damaging Het
Slf1 T A 13: 77,199,413 (GRCm39) D656V probably damaging Het
Sorbs1 T C 19: 40,300,171 (GRCm39) D1192G probably damaging Het
Tdrd6 A C 17: 43,935,218 (GRCm39) D1943E probably benign Het
Tmem163 G A 1: 127,419,362 (GRCm39) T281M probably damaging Het
Tmod3 A G 9: 75,439,730 (GRCm39) V35A probably damaging Het
Ttc39c A T 18: 12,867,951 (GRCm39) Q448L probably benign Het
Ulk1 A T 5: 110,935,455 (GRCm39) S937T probably damaging Het
Unc13c T A 9: 73,481,304 (GRCm39) D1711V probably damaging Het
Usp5 C G 6: 124,799,593 (GRCm39) K318N possibly damaging Het
Utp20 G T 10: 88,607,822 (GRCm39) Q1596K probably benign Het
Vmn1r28 A T 6: 58,242,525 (GRCm39) I123F possibly damaging Het
Vmn1r73 T A 7: 11,490,596 (GRCm39) V138E probably damaging Het
Vmn2r112 A G 17: 22,822,363 (GRCm39) D347G probably damaging Het
Vmn2r3 T G 3: 64,166,618 (GRCm39) T838P probably damaging Het
Vps13d A T 4: 144,882,427 (GRCm39) D1055E probably benign Het
Wdr17 T C 8: 55,082,896 (GRCm39) D1268G probably damaging Het
Zfp108 T A 7: 23,960,739 (GRCm39) H443Q probably damaging Het
Zfp608 A G 18: 55,079,663 (GRCm39) V374A probably damaging Het
Zfp831 G T 2: 174,486,417 (GRCm39) G364V probably damaging Het
Zfp94 A G 7: 24,003,166 (GRCm39) V86A probably benign Het
Zkscan16 A C 4: 58,946,506 (GRCm39) N127T possibly damaging Het
Other mutations in Hps3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00545:Hps3 APN 3 20,073,971 (GRCm39) missense possibly damaging 0.94
IGL00846:Hps3 APN 3 20,079,956 (GRCm39) missense probably benign 0.00
IGL01320:Hps3 APN 3 20,084,633 (GRCm39) missense probably benign 0.12
IGL01364:Hps3 APN 3 20,057,469 (GRCm39) missense possibly damaging 0.58
IGL01751:Hps3 APN 3 20,065,130 (GRCm39) missense probably damaging 1.00
IGL01843:Hps3 APN 3 20,083,165 (GRCm39) missense probably benign 0.05
IGL02294:Hps3 APN 3 20,068,212 (GRCm39) missense probably damaging 1.00
IGL02581:Hps3 APN 3 20,057,385 (GRCm39) intron probably benign
Blue UTSW 3 20,084,960 (GRCm39) missense probably damaging 1.00
earl_grey UTSW 3 20,017,173 (GRCm38) intron probably benign
gandalf UTSW 3 20,066,960 (GRCm39) nonsense probably null
pam_gray UTSW 3 20,017,173 (GRCm38) intron probably benign
R0107:Hps3 UTSW 3 20,084,960 (GRCm39) missense probably damaging 1.00
R0245:Hps3 UTSW 3 20,066,960 (GRCm39) nonsense probably null
R0421:Hps3 UTSW 3 20,083,480 (GRCm39) missense probably benign 0.00
R0524:Hps3 UTSW 3 20,066,940 (GRCm39) missense probably damaging 1.00
R0763:Hps3 UTSW 3 20,057,443 (GRCm39) missense probably damaging 1.00
R1795:Hps3 UTSW 3 20,066,859 (GRCm39) critical splice donor site probably null
R1864:Hps3 UTSW 3 20,074,123 (GRCm39) critical splice acceptor site probably null
R2029:Hps3 UTSW 3 20,084,691 (GRCm39) missense probably benign 0.01
R2101:Hps3 UTSW 3 20,066,947 (GRCm39) missense possibly damaging 0.95
R2221:Hps3 UTSW 3 20,056,527 (GRCm39) missense probably benign
R2268:Hps3 UTSW 3 20,067,099 (GRCm39) splice site probably benign
R2520:Hps3 UTSW 3 20,083,194 (GRCm39) missense probably damaging 1.00
R3809:Hps3 UTSW 3 20,072,976 (GRCm39) missense probably damaging 1.00
R3888:Hps3 UTSW 3 20,057,387 (GRCm39) critical splice donor site probably null
R3942:Hps3 UTSW 3 20,051,103 (GRCm39) missense probably damaging 1.00
R4022:Hps3 UTSW 3 20,089,425 (GRCm39) missense possibly damaging 0.69
R4156:Hps3 UTSW 3 20,083,393 (GRCm39) missense probably damaging 1.00
R4739:Hps3 UTSW 3 20,084,574 (GRCm39) critical splice acceptor site probably null
R4823:Hps3 UTSW 3 20,066,890 (GRCm39) missense probably benign 0.03
R5307:Hps3 UTSW 3 20,066,865 (GRCm39) missense possibly damaging 0.89
R5859:Hps3 UTSW 3 20,063,034 (GRCm39) missense probably benign 0.02
R6140:Hps3 UTSW 3 20,051,151 (GRCm39) missense probably damaging 1.00
R6183:Hps3 UTSW 3 20,063,032 (GRCm39) missense probably benign 0.04
R6971:Hps3 UTSW 3 20,065,699 (GRCm39) missense probably damaging 1.00
R6981:Hps3 UTSW 3 20,076,984 (GRCm39) missense probably damaging 1.00
R7120:Hps3 UTSW 3 20,065,705 (GRCm39) missense probably damaging 1.00
R7146:Hps3 UTSW 3 20,063,050 (GRCm39) missense probably damaging 1.00
R7223:Hps3 UTSW 3 20,084,583 (GRCm39) missense probably benign 0.05
R7448:Hps3 UTSW 3 20,089,329 (GRCm39) missense probably damaging 0.99
R7452:Hps3 UTSW 3 20,065,592 (GRCm39) missense probably damaging 1.00
R7560:Hps3 UTSW 3 20,084,616 (GRCm39) missense probably benign 0.29
R7659:Hps3 UTSW 3 20,076,978 (GRCm39) nonsense probably null
R7769:Hps3 UTSW 3 20,072,972 (GRCm39) splice site probably null
R8050:Hps3 UTSW 3 20,057,492 (GRCm39) missense probably benign
R8242:Hps3 UTSW 3 20,068,290 (GRCm39) missense possibly damaging 0.59
R8802:Hps3 UTSW 3 20,074,070 (GRCm39) missense probably damaging 1.00
R8822:Hps3 UTSW 3 20,057,391 (GRCm39) missense probably benign
R8945:Hps3 UTSW 3 20,068,224 (GRCm39) missense probably damaging 0.99
R9111:Hps3 UTSW 3 20,084,575 (GRCm39) critical splice acceptor site probably null
R9131:Hps3 UTSW 3 20,083,350 (GRCm39) missense probably damaging 0.98
R9645:Hps3 UTSW 3 20,084,831 (GRCm39) missense probably benign 0.01
R9728:Hps3 UTSW 3 20,065,128 (GRCm39) missense probably benign 0.06
X0021:Hps3 UTSW 3 20,084,913 (GRCm39) missense probably benign 0.14
X0066:Hps3 UTSW 3 20,070,152 (GRCm39) missense probably damaging 1.00
Z1177:Hps3 UTSW 3 20,063,065 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CCACAATAGCCTCCATGCTG -3'
(R):5'- ATTGTCGATGACTGAGATGAGG -3'

Sequencing Primer
(F):5'- TAGCCTCCATGCTGAATACTAAGG -3'
(R):5'- ATGCTCAGGAAAAATGCTACTG -3'
Posted On 2016-04-15