Incidental Mutation 'R6275:Hps1'
ID 507612
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 044445-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.214) question?
Stock # R6275 (G1)
Quality Score 225.009
Status Validated
Chromosome 19
Chromosomal Location 42743544-42768417 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 42758046 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamic Acid to Glycine at position 169 (E169G)
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
AA Change: E169G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000026194
Gene: ENSMUSG00000025188
AA Change: E169G

DomainStartEndE-ValueType
coiled coil region 20 47 N/A INTRINSIC
low complexity region 229 246 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000069298
AA Change: E169G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000071069
Gene: ENSMUSG00000025188
AA Change: E169G

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 probably null
Transcript: ENSMUST00000160455
AA Change: E169G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000125662
Gene: ENSMUSG00000025188
AA Change: E169G

DomainStartEndE-ValueType
coiled coil region 20 47 N/A INTRINSIC
low complexity region 229 246 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000161761
Predicted Effect probably null
Transcript: ENSMUST00000162004
AA Change: E169G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000125226
Gene: ENSMUSG00000025188
AA Change: E169G

DomainStartEndE-ValueType
coiled coil region 20 47 N/A INTRINSIC
low complexity region 229 246 N/A INTRINSIC
Predicted Effect probably null
Transcript: ENSMUST00000162061
AA Change: E169G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000124209
Gene: ENSMUSG00000025188
AA Change: E169G

DomainStartEndE-ValueType
coiled coil region 20 47 N/A INTRINSIC
low complexity region 229 246 N/A INTRINSIC
Meta Mutation Damage Score 0.7001 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.3%
  • 20x: 95.4%
Validation Efficiency 98% (56/57)
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. 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: 57 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca7 T A 10: 79,833,625 (GRCm39) L30H probably damaging Het
Abcb6 T C 1: 75,149,195 (GRCm39) probably null Het
Acsbg1 T A 9: 54,517,056 (GRCm39) M586L probably benign Het
Ano6 A T 15: 95,811,314 (GRCm39) Y159F probably damaging Het
C1ql1 A G 11: 102,830,575 (GRCm39) I254T probably damaging Het
Ccdc81 T C 7: 89,531,519 (GRCm39) D318G possibly damaging Het
Ccr7 C T 11: 99,036,489 (GRCm39) M144I probably damaging Het
Cdca3 C T 6: 124,809,627 (GRCm39) probably null Het
Ces1h A T 8: 94,099,274 (GRCm39) L93I probably benign Het
Cntfr T C 4: 41,663,216 (GRCm39) D197G possibly damaging Het
Cyp2d12 C A 15: 82,440,859 (GRCm39) P126T probably benign Het
Dnah10 A G 5: 124,862,248 (GRCm39) T2225A probably damaging Het
Edrf1 A T 7: 133,269,311 (GRCm39) N1147Y possibly damaging Het
Eif1ad15 T C 12: 88,287,995 (GRCm39) D86G possibly damaging Het
Eif1ad16 T C 12: 87,985,255 (GRCm39) N96S probably benign Het
Ermap C T 4: 119,035,747 (GRCm39) V414M probably damaging Het
Fam13a A G 6: 58,931,242 (GRCm39) I446T probably damaging Het
Fgfbp3 T C 19: 36,896,153 (GRCm39) H155R possibly damaging Het
Folr1 T A 7: 101,508,742 (GRCm39) N61I probably damaging Het
Fsip1 T C 2: 118,035,583 (GRCm39) I431V probably benign Het
Gm5493 A T 17: 22,969,043 (GRCm39) E74D probably benign Het
H2-Oa A G 17: 34,313,540 (GRCm39) D197G probably benign Het
Il17rc A T 6: 113,457,308 (GRCm39) M372L probably benign Het
Itga10 A G 3: 96,565,501 (GRCm39) S1042G probably benign Het
Jchain A T 5: 88,669,212 (GRCm39) V147E probably damaging Het
Laptm4b A G 15: 34,283,473 (GRCm39) T211A probably benign Het
Mal2 T C 15: 54,435,035 (GRCm39) probably null Het
Mov10l1 T A 15: 88,910,823 (GRCm39) I1071N probably damaging Het
Mpp2 T A 11: 101,951,795 (GRCm39) Y401F probably damaging Het
Myh15 A G 16: 48,965,610 (GRCm39) T1172A probably benign Het
Or51q1 T A 7: 103,629,181 (GRCm39) S261T probably damaging Het
Pcnx1 G T 12: 81,965,381 (GRCm39) S516I probably benign Het
Pidd1 C T 7: 141,019,708 (GRCm39) A685T probably damaging Het
Psg28 A C 7: 18,164,365 (GRCm39) Y116D probably damaging Het
Psmd11 T C 11: 80,329,458 (GRCm39) probably benign Het
Rapgefl1 T A 11: 98,741,946 (GRCm39) Y637N probably damaging Het
Rbm25 T A 12: 83,691,206 (GRCm39) M66K probably damaging Het
Rnf38 T A 4: 44,152,408 (GRCm39) H52L probably benign Het
Rsf1 CGGCGGCGG CGGCGGCGGTGGCGGCGG 7: 97,229,130 (GRCm39) probably benign Het
Sec62 A G 3: 30,863,985 (GRCm39) Q89R probably damaging Het
Serpina6 T A 12: 103,614,979 (GRCm39) Q289L probably benign Het
Sf3b2 A C 19: 5,333,678 (GRCm39) I640S probably damaging Het
Slc13a2 CGTTATCTGT CGT 11: 78,294,306 (GRCm39) probably benign Het
Slc26a11 T C 11: 119,250,125 (GRCm39) F127L probably benign Het
Spata31h1 T C 10: 82,121,202 (GRCm39) D3936G probably damaging Het
Stac3 T A 10: 127,343,615 (GRCm39) Y252* probably null Het
Stoml3 G A 3: 53,414,927 (GRCm39) A240T probably damaging Het
Tanc1 A T 2: 59,673,854 (GRCm39) H1653L probably benign Het
Tll1 A T 8: 64,504,401 (GRCm39) L665* probably null Het
Tnr A C 1: 159,688,840 (GRCm39) Q434P probably damaging Het
Tpgs1 C A 10: 79,511,354 (GRCm39) D165E probably benign Het
Tsc2 A G 17: 24,819,394 (GRCm39) V1185A probably benign Het
Tulp4 A G 17: 6,249,011 (GRCm39) H203R probably damaging Het
Txnl4a T A 18: 80,261,980 (GRCm39) M72K possibly damaging Het
Usp42 G A 5: 143,700,727 (GRCm39) R1099W probably damaging Het
Zfp292 G A 4: 34,808,883 (GRCm39) A1387V possibly damaging Het
Zfp994 A T 17: 22,418,972 (GRCm39) L659* probably null 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
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'- TGAAACTCTCACCCGGAATTCAG -3'
(R):5'- GACAGGAACCTTGGATTGGG -3'

Sequencing Primer
(F):5'- GGAATTCAGTTGCTCACCATGGAAC -3'
(R):5'- GGCCGGACAAGACCAACTTTC -3'
Posted On 2018-03-15