Incidental Mutation 'R3196:Hps4'
ID 267638
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 040617-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.292) question?
Stock # R3196 (G1)
Quality Score 189
Status Not validated
Chromosome 5
Chromosomal Location 112490949-112526280 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 112512429 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 182 (T182A)
Ref Sequence ENSEMBL: ENSMUSP00000107978 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000035279] [ENSMUST00000112359]
AlphaFold Q99KG7
Predicted Effect probably damaging
Transcript: ENSMUST00000035279
AA Change: T182A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000047920
Gene: ENSMUSG00000042328
AA Change: T182A

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 probably damaging
Transcript: ENSMUST00000112359
AA Change: T182A

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000107978
Gene: ENSMUSG00000042328
AA Change: T182A

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 noncoding transcript
Transcript: ENSMUST00000129839
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133708
Predicted Effect noncoding transcript
Transcript: ENSMUST00000196925
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.1%
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 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: 67 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
9130401M01Rik A T 15: 57,892,132 (GRCm39) N158K probably benign Het
Acnat1 G C 4: 49,447,457 (GRCm39) P357A probably damaging Het
Akap6 T A 12: 53,119,240 (GRCm39) C1102* probably null Het
Amelx T C X: 167,964,826 (GRCm39) probably benign Het
Brap G A 5: 121,803,259 (GRCm39) V136I possibly damaging Het
Crygs C T 16: 22,624,301 (GRCm39) G102D possibly damaging Het
Csgalnact1 TGG TG 8: 68,913,737 (GRCm39) probably null Het
Csk A T 9: 57,537,556 (GRCm39) C119* probably null Het
Dcbld1 T C 10: 52,195,587 (GRCm39) L265P probably damaging Het
Desi1 T A 15: 81,887,976 (GRCm39) K31N probably damaging Het
Dpy19l2 C A 9: 24,607,285 (GRCm39) G59C probably damaging Het
Eif2b5 T C 16: 20,324,272 (GRCm39) V498A probably benign Het
Epdr1 A T 13: 19,778,815 (GRCm39) Y94N probably damaging Het
Fat1 T C 8: 45,404,905 (GRCm39) V552A probably benign Het
Focad A G 4: 88,325,588 (GRCm39) E151G possibly damaging Het
Frem1 A G 4: 82,932,351 (GRCm39) F117L probably damaging Het
Frem2 A T 3: 53,444,752 (GRCm39) Y2460N probably damaging Het
Gm3604 A T 13: 62,517,868 (GRCm39) C163* probably null Het
Gpalpp1 A C 14: 76,336,063 (GRCm39) probably null Het
Grid2ip A G 5: 143,373,933 (GRCm39) I858V probably damaging Het
Grin2b ATTGTTGT ATTGT 6: 135,709,453 (GRCm39) probably benign Het
Impa1 A T 3: 10,394,075 (GRCm39) probably null Het
Kcnh3 T C 15: 99,131,862 (GRCm39) S606P probably damaging Het
Kif23 T A 9: 61,839,193 (GRCm39) R301* probably null Het
Kirrel1 C T 3: 86,996,458 (GRCm39) M380I probably null Het
Lcp2 G T 11: 34,040,670 (GRCm39) A529S probably benign Het
Lhx8 G A 3: 154,035,925 (GRCm39) A22V probably benign Het
Lin28a A T 4: 133,735,235 (GRCm39) S134T possibly damaging Het
Med27 T A 2: 29,236,882 (GRCm39) V9E possibly damaging Het
Mmp7 C A 9: 7,692,219 (GRCm39) S31R probably benign Het
Mtcl1 T G 17: 66,650,829 (GRCm39) E1545D probably benign Het
Muc16 A G 9: 18,409,126 (GRCm39) Y187H probably damaging Het
Myo3a G T 2: 22,404,679 (GRCm39) K678N possibly damaging Het
Nsmce1 T C 7: 125,085,645 (GRCm39) M15V probably benign Het
Nxpe3 A T 16: 55,670,078 (GRCm39) N342K probably damaging Het
Or7g25 A G 9: 19,160,495 (GRCm39) S67P probably damaging Het
Or8g2 T A 9: 39,821,756 (GRCm39) I219N probably damaging Het
Pcdhb9 A G 18: 37,534,663 (GRCm39) N219S probably benign Het
Pck2 T A 14: 55,781,449 (GRCm39) V190E probably damaging Het
Pde4b G A 4: 102,456,840 (GRCm39) A429T probably damaging Het
Phf1 T C 17: 27,153,429 (GRCm39) V54A probably damaging Het
Pla2r1 T C 2: 60,353,127 (GRCm39) E278G probably damaging Het
Ptges3 G T 10: 127,908,016 (GRCm39) R122L probably benign Het
Rnpepl1 C T 1: 92,844,881 (GRCm39) T391I probably damaging Het
Rps6kb1 G A 11: 86,397,633 (GRCm39) A404V probably benign Het
Rrm2b T C 15: 37,945,391 (GRCm39) probably null Het
Sh3rf1 C T 8: 61,679,321 (GRCm39) P121L probably benign Het
Skint9 T G 4: 112,248,148 (GRCm39) I199L probably benign Het
Slc9b2 G T 3: 135,042,290 (GRCm39) R523L probably benign Het
Slco1c1 T A 6: 141,477,174 (GRCm39) probably null Het
Stox2 T C 8: 47,645,865 (GRCm39) T532A probably damaging Het
Tbcel A G 9: 42,327,248 (GRCm39) L385P probably damaging Het
Tle5 A G 10: 81,401,474 (GRCm39) N181D probably benign Het
Tmem268 G A 4: 63,496,149 (GRCm39) probably null Het
Tns2 C T 15: 102,017,369 (GRCm39) R281C probably damaging Het
Top3a G A 11: 60,650,182 (GRCm39) T122M probably damaging Het
Trav7n-4 G A 14: 53,329,088 (GRCm39) V33I probably benign Het
Ttn T G 2: 76,539,551 (GRCm39) E26151D possibly damaging Het
Ttn C T 2: 76,687,228 (GRCm39) probably benign Het
Tyk2 A G 9: 21,035,328 (GRCm39) C195R possibly damaging Het
Ugt2b38 T C 5: 87,558,078 (GRCm39) K528E probably damaging Het
Usp28 T A 9: 48,937,125 (GRCm39) D483E probably benign Het
Vldlr A G 19: 27,220,554 (GRCm39) D598G probably damaging Het
Vmn1r51 T G 6: 90,106,498 (GRCm39) I138S probably damaging Het
Vps13b G A 15: 35,869,541 (GRCm39) A2682T probably damaging Het
Wac T A 18: 7,917,568 (GRCm39) V346E probably damaging Het
Zdbf2 T C 1: 63,347,579 (GRCm39) V1986A possibly damaging 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
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
R9229: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'- GCTCATGTGATCTTCCTGGC -3'
(R):5'- TGAACATCTCTAAGTGCATCCAG -3'

Sequencing Primer
(F):5'- GCTGGGCAGTTAATTCCTTACAAG -3'
(R):5'- ATCCAGTTGATGCACACCCTGG -3'
Posted On 2015-02-18