Incidental Mutation 'R9229:Hps4'
ID 700082
Institutional Source Beutler Lab
Gene Symbol Hps4
Ensembl Gene ENSMUSG00000042328
Gene Name HPS4, biogenesis of lysosomal organelles complex 3 subunit 2
Synonyms BLOC-3, 2010205O06Rik, Hermansky-Pudlak syndrome 4, C130020P05Rik
MMRRC Submission
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.292) question?
Stock # R9229 (G1)
Quality Score 225.009
Status Validated
Chromosome 5
Chromosomal Location 112490949-112526280 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to A at 112525905 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Asparagine at position 642 (S642N)
Ref Sequence ENSEMBL: ENSMUSP00000047920 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000035279] [ENSMUST00000112359]
AlphaFold Q99KG7
Predicted Effect possibly damaging
Transcript: ENSMUST00000035279
AA Change: S642N

PolyPhen 2 Score 0.810 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000047920
Gene: ENSMUSG00000042328
AA Change: S642N

DomainStartEndE-ValueType
low complexity region 171 180 N/A INTRINSIC
low complexity region 467 486 N/A INTRINSIC
low complexity region 514 529 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000112359
AA Change: S642N

PolyPhen 2 Score 0.810 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000107978
Gene: ENSMUSG00000042328
AA Change: S642N

DomainStartEndE-ValueType
low complexity region 171 180 N/A INTRINSIC
low complexity region 467 486 N/A INTRINSIC
low complexity region 514 529 N/A INTRINSIC
Meta Mutation Damage Score 0.0638 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.9%
Validation Efficiency 97% (77/79)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein component of biogenesis of lysosome-related organelles complexes (BLOC). BLOC complexes are important for the formation of endosomal-lysosomal organelles such as melanosomes and platelet dense granules. Mutations in this gene result in subtype 4 of Hermansky-Pudlak syndrome, a form of albinism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]
PHENOTYPE: Homozygotes for a spontaneous null mutation exhibit hypopigmentation, prolonged bleeding associated with a platelet defect, reduced secretion of kidney lysosomal enzymes, and resistance to diet-induced atherosclerosis. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 83 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Actr10 A G 12: 70,990,259 (GRCm39) T104A probably damaging Het
Agbl1 G A 7: 76,774,270 (GRCm39) V1065I unknown Het
Agpat1 G T 17: 34,830,663 (GRCm39) V196L probably null Het
Agxt2 T A 15: 10,409,597 (GRCm39) V499E probably damaging Het
Amy2a1 T A 3: 113,325,955 (GRCm39) probably benign Het
Ankrd35 A G 3: 96,592,215 (GRCm39) T834A probably benign Het
Arhgef18 T A 8: 3,479,314 (GRCm39) S51T probably benign Het
Armc12 A C 17: 28,751,345 (GRCm39) D113A probably benign Het
Azin1 T A 15: 38,490,646 (GRCm39) I436F probably benign Het
B3galnt2 T C 13: 14,166,107 (GRCm39) V334A probably damaging Het
Ccdc68 C T 18: 70,080,203 (GRCm39) H183Y probably benign Het
Cd180 TA TAA 13: 102,841,514 (GRCm39) probably null Het
Cemip A T 7: 83,606,833 (GRCm39) W795R probably damaging Het
Cenpj C T 14: 56,802,176 (GRCm39) E130K possibly damaging Het
Ciao1 G C 2: 127,089,062 (GRCm39) C52W probably damaging Het
Cmya5 A G 13: 93,232,176 (GRCm39) S971P possibly damaging Het
Cnot2 A T 10: 116,384,960 (GRCm39) L9* probably null Het
Coro1c G T 5: 114,003,747 (GRCm39) H91N probably damaging Het
Crbn A T 6: 106,777,017 (GRCm39) M1K probably null Het
Ctsb T A 14: 63,373,112 (GRCm39) W90R probably damaging Het
Ctse A G 1: 131,595,862 (GRCm39) I185V probably damaging Het
Dennd1b G T 1: 138,981,100 (GRCm39) E105* probably null Het
Eif4a3l1 A G 6: 136,306,141 (GRCm39) I201V possibly damaging Het
Exoc5 G A 14: 49,251,710 (GRCm39) Q679* probably null Het
Firrm A T 1: 163,794,659 (GRCm39) W512R probably damaging Het
Gabrg3 G A 7: 56,374,268 (GRCm39) R433C probably damaging Het
Gria2 C A 3: 80,709,689 (GRCm39) M1I probably null Het
H1f6 T C 13: 23,880,029 (GRCm39) S61P probably damaging Het
Hoxb6 A T 11: 96,191,645 (GRCm39) Q189L probably damaging Het
Hoxd10 A G 2: 74,524,600 (GRCm39) N304S possibly damaging Het
Htra4 A T 8: 25,528,557 (GRCm39) C112S probably damaging Het
Ide T C 19: 37,261,598 (GRCm39) T715A Het
Ipo13 A T 4: 117,758,801 (GRCm39) I688N probably damaging Het
Irs2 A C 8: 11,057,400 (GRCm39) L344R probably damaging Het
Kat6a A G 8: 23,429,987 (GRCm39) T1781A unknown Het
Lin7a G T 10: 107,247,844 (GRCm39) V172L probably damaging Het
Lpcat1 G T 13: 73,653,650 (GRCm39) E282D probably damaging Het
Mcf2l A G 8: 13,063,584 (GRCm39) T963A probably benign Het
Mfsd14a G A 3: 116,439,118 (GRCm39) A128V probably benign Het
Mfsd6 C G 1: 52,747,903 (GRCm39) G321R probably damaging Het
Mill2 C T 7: 18,590,475 (GRCm39) T185I probably damaging Het
Mpped1 C T 15: 83,738,673 (GRCm39) T270I possibly damaging Het
Mrtfb G T 16: 13,230,185 (GRCm39) A957S possibly damaging Het
Myh9 T A 15: 77,675,017 (GRCm39) Y300F possibly damaging Het
Nlrp2 T A 7: 5,304,052 (GRCm39) T953S possibly damaging Het
Nlrp4e T A 7: 23,020,799 (GRCm39) S429T probably benign Het
Nphp3 T A 9: 103,913,376 (GRCm39) Y1003N probably damaging Het
Nrap T C 19: 56,310,339 (GRCm39) K1588R probably benign Het
Odad2 C A 18: 7,127,324 (GRCm39) R963L possibly damaging Het
Or10ag56 G A 2: 87,139,165 (GRCm39) V31I probably benign Het
Or5b124 T A 19: 13,611,414 (GRCm39) V313D probably damaging Het
Pam A G 1: 97,753,660 (GRCm39) V870A probably benign Het
Peg10 CCACATCAGGATCCACATCAGGATGCACATCAGCATCAGGATCCCCATCAGGATGCACATCAGGATCCACATCAGGATGCACATCAG CCACATCAGGATCCACATCAGGATGCACATCAG 6: 4,756,398 (GRCm39) probably benign Het
Pierce1 C A 2: 28,352,390 (GRCm39) M124I probably damaging Het
Plin3 A T 17: 56,591,315 (GRCm39) V155E probably damaging Het
Pmepa1 T C 2: 173,117,962 (GRCm39) T6A probably benign Het
Pnpla7 G A 2: 24,873,503 (GRCm39) V170I probably damaging Het
Pramel34 A T 5: 93,784,089 (GRCm39) C458* probably null Het
Ptprz1 A G 6: 22,986,283 (GRCm39) H361R probably null Het
Pvalb T A 15: 78,086,767 (GRCm39) I50F possibly damaging Het
Relch A T 1: 105,614,709 (GRCm39) I218F possibly damaging Het
Rhag G A 17: 41,142,081 (GRCm39) A175T probably damaging Het
Slc24a4 T C 12: 102,200,983 (GRCm39) V291A possibly damaging Het
Slc9b2 G A 3: 135,042,295 (GRCm39) E525K probably benign Het
Smg7 A G 1: 152,720,971 (GRCm39) F747S possibly damaging Het
Sorcs1 T G 19: 50,141,300 (GRCm39) I1144L probably benign Het
Sox1 A T 8: 12,447,390 (GRCm39) I344F possibly damaging Het
Speer4e2 A T 5: 15,027,718 (GRCm39) S53T probably benign Het
Spta1 A T 1: 174,067,750 (GRCm39) E2059V probably damaging Het
Sva T A 6: 42,017,050 (GRCm39) N52K possibly damaging Het
Sva T A 6: 42,017,052 (GRCm39) M53K probably benign Het
Thsd7b A G 1: 129,849,027 (GRCm39) Y913C probably damaging Het
Tiam1 A G 16: 89,634,719 (GRCm39) S864P possibly damaging Het
Tma16 A G 8: 66,936,779 (GRCm39) V16A probably benign Het
Tmco1 C T 1: 167,136,132 (GRCm39) probably benign Het
Treml1 A G 17: 48,673,774 (GRCm39) S262G probably benign Het
Ttn A T 2: 76,597,797 (GRCm39) D19705E probably benign Het
Utp20 A G 10: 88,594,239 (GRCm39) L2162P possibly damaging Het
Vmn2r60 A G 7: 41,791,723 (GRCm39) I549V possibly damaging Het
Xpo4 T C 14: 57,851,156 (GRCm39) N329S probably benign Het
Zfp879 T A 11: 50,723,886 (GRCm39) H390L probably damaging Het
Zranb1 C T 7: 132,583,117 (GRCm39) S512F probably damaging Het
Zswim8 A G 14: 20,766,393 (GRCm39) H847R probably benign Het
Other mutations in Hps4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01485:Hps4 APN 5 112,512,377 (GRCm39) splice site probably benign
IGL02331:Hps4 APN 5 112,517,402 (GRCm39) missense probably benign 0.03
IGL02410:Hps4 APN 5 112,518,093 (GRCm39) missense probably benign 0.07
IGL02821:Hps4 APN 5 112,523,307 (GRCm39) missense probably benign 0.02
R0748:Hps4 UTSW 5 112,522,780 (GRCm39) missense probably damaging 1.00
R1487:Hps4 UTSW 5 112,525,865 (GRCm39) nonsense probably null
R1891:Hps4 UTSW 5 112,517,422 (GRCm39) splice site probably null
R2010:Hps4 UTSW 5 112,517,342 (GRCm39) missense probably damaging 1.00
R2305:Hps4 UTSW 5 112,494,527 (GRCm39) missense probably damaging 0.99
R3196:Hps4 UTSW 5 112,512,429 (GRCm39) missense probably damaging 1.00
R4274:Hps4 UTSW 5 112,522,896 (GRCm39) intron probably benign
R4878:Hps4 UTSW 5 112,523,234 (GRCm39) missense probably benign 0.12
R4988:Hps4 UTSW 5 112,526,019 (GRCm39) utr 3 prime probably benign
R5843:Hps4 UTSW 5 112,497,296 (GRCm39) critical splice donor site probably null
R5896:Hps4 UTSW 5 112,517,351 (GRCm39) missense probably benign 0.02
R6318:Hps4 UTSW 5 112,494,495 (GRCm39) missense probably damaging 1.00
R7381:Hps4 UTSW 5 112,523,324 (GRCm39) missense possibly damaging 0.86
R7781:Hps4 UTSW 5 112,518,388 (GRCm39) missense probably benign 0.14
R8112:Hps4 UTSW 5 112,517,977 (GRCm39) missense probably benign 0.17
R8996:Hps4 UTSW 5 112,525,905 (GRCm39) missense possibly damaging 0.81
R9058:Hps4 UTSW 5 112,525,905 (GRCm39) missense possibly damaging 0.81
R9059:Hps4 UTSW 5 112,525,905 (GRCm39) missense possibly damaging 0.81
R9060:Hps4 UTSW 5 112,525,905 (GRCm39) missense possibly damaging 0.81
R9103:Hps4 UTSW 5 112,525,905 (GRCm39) missense possibly damaging 0.81
R9105:Hps4 UTSW 5 112,525,905 (GRCm39) missense possibly damaging 0.81
R9106:Hps4 UTSW 5 112,525,905 (GRCm39) missense possibly damaging 0.81
R9175:Hps4 UTSW 5 112,525,905 (GRCm39) missense possibly damaging 0.81
R9210:Hps4 UTSW 5 112,497,227 (GRCm39) missense possibly damaging 0.78
R9226:Hps4 UTSW 5 112,525,905 (GRCm39) missense possibly damaging 0.81
R9227:Hps4 UTSW 5 112,525,905 (GRCm39) missense possibly damaging 0.81
R9230:Hps4 UTSW 5 112,525,905 (GRCm39) missense possibly damaging 0.81
R9232:Hps4 UTSW 5 112,525,905 (GRCm39) missense possibly damaging 0.81
R9233:Hps4 UTSW 5 112,525,905 (GRCm39) missense possibly damaging 0.81
R9234:Hps4 UTSW 5 112,525,905 (GRCm39) missense possibly damaging 0.81
R9236:Hps4 UTSW 5 112,525,905 (GRCm39) missense possibly damaging 0.81
R9330:Hps4 UTSW 5 112,525,905 (GRCm39) missense possibly damaging 0.81
R9459:Hps4 UTSW 5 112,522,875 (GRCm39) missense probably benign 0.30
Z1177:Hps4 UTSW 5 112,518,243 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- AAGACAGGACAGTTGTTCCCTG -3'
(R):5'- CCACTCAGTTCTTGCAGCTG -3'

Sequencing Primer
(F):5'- CTGGGCCTGAAGTTCAAATCG -3'
(R):5'- GTTCTTGCAGCTGCCACTGAG -3'
Posted On 2022-02-07