Phenotypic Mutation '50-cal' (pdf version)
Allele50-cal
Mutation Type critical splice donor site (2 bp from exon)
Chromosome13
Coordinate13,882,797 bp (GRCm39)
Base Change T ⇒ A (forward strand)
Gene Lyst
Gene Name lysosomal trafficking regulator
Synonym(s) D13Sfk13
Chromosomal Location 13,764,982-13,953,388 bp (+) (GRCm39)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that regulates intracellular protein trafficking in endosomes, and may be involved in pigmentation. Mutations in this gene are associated with Chediak-Higashi syndrome, a lysosomal storage disorder. Alternative splicing results in multiple transcript variants, though the full-length nature of some of these variants has not been determined. [provided by RefSeq, Apr 2013]
PHENOTYPE: Homozygous mice have a phenotype similar to human Chediak-Higashi syndrome patients, exhibiting lysosomal dysfunction with resultant protein storage; diluted coat color; abnormal melanogenesis; immune cell dysfunction resulting in increased susceptibility to bacterial, viral, and parasitic infections and decreased cytotoxic activity against tumor cells. [provided by MGI curators]
Accession Number

NCBI RefSeq: NM_010748; MGI: 107448

MappedYes 
Amino Acid Change
Institutional SourceBeutler Lab
Gene Model predicted gene model for protein(s): [ENSMUSP00000106188 ]   † probably from a misspliced transcript
AlphaFold no structure available at present
SMART Domains Protein: ENSMUSP00000106188
Gene: ENSMUSG00000019726

DomainStartEndE-ValueType
low complexity region 26 36 N/A INTRINSIC
low complexity region 72 82 N/A INTRINSIC
low complexity region 399 412 N/A INTRINSIC
low complexity region 1333 1344 N/A INTRINSIC
low complexity region 2295 2307 N/A INTRINSIC
low complexity region 2427 2445 N/A INTRINSIC
low complexity region 2534 2546 N/A INTRINSIC
Pfam:PH_BEACH 3006 3101 5.8e-25 PFAM
Beach 3118 3408 1.25e-193 SMART
Blast:Beach 3441 3478 9e-13 BLAST
WD40 3539 3579 5.75e-1 SMART
WD40 3591 3630 2.89e-5 SMART
WD40 3633 3676 1.38e0 SMART
WD40 3724 3765 1.27e-1 SMART
Predicted Effect probably null
Meta Mutation Damage Score 0.9485 question?
Is this an essential gene? Possibly nonessential (E-score: 0.395) question?
Phenotypic Category Autosomal Recessive
Candidate Explorer Status loading ...
Single pedigree
Linkage Analysis Data
Penetrance  
Alleles Listed at MGI

All mutations/alleles(53) : Chemically induced (ENU)(6) Gene trapped(34) Radiation induced(1) Spontaneous(8) Targeted(4)

Lab Alleles
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00156:Lyst APN 13 13823463 missense probably benign
IGL00474:Lyst APN 13 13818121 missense possibly damaging 0.48
IGL00484:Lyst APN 13 13884188 missense probably benign 0.02
IGL00492:Lyst APN 13 13852760 missense possibly damaging 0.54
IGL00807:Lyst APN 13 13825008 missense possibly damaging 0.91
IGL00949:Lyst APN 13 13810070 missense possibly damaging 0.87
IGL00952:Lyst APN 13 13852692 missense probably benign 0.05
IGL01305:Lyst APN 13 13852641 missense probably benign 0.01
IGL01317:Lyst APN 13 13845455 missense probably benign
IGL01419:Lyst APN 13 13810423 missense probably benign 0.00
IGL01445:Lyst APN 13 13826299 missense probably benign 0.00
IGL01690:Lyst APN 13 13917831 missense probably damaging 1.00
IGL01791:Lyst APN 13 13809887 missense probably damaging 1.00
IGL01809:Lyst APN 13 13812388 missense probably damaging 1.00
IGL01896:Lyst APN 13 13810162 missense probably benign 0.04
IGL01938:Lyst APN 13 13812009 missense possibly damaging 0.93
IGL01986:Lyst APN 13 13950212 critical splice donor site probably null
IGL02022:Lyst APN 13 13838629 nonsense probably null
IGL02044:Lyst APN 13 13887431 missense probably damaging 1.00
IGL02157:Lyst APN 13 13835541 missense probably benign
IGL02185:Lyst APN 13 13835678 nonsense probably null
IGL02215:Lyst APN 13 13835541 missense probably benign
IGL02245:Lyst APN 13 13835541 missense probably benign
IGL02246:Lyst APN 13 13835541 missense probably benign
IGL02247:Lyst APN 13 13835541 missense probably benign
IGL02297:Lyst APN 13 13812677 nonsense probably null
IGL02411:Lyst APN 13 13835541 missense probably benign
IGL02415:Lyst APN 13 13835541 missense probably benign
IGL02419:Lyst APN 13 13835541 missense probably benign
IGL02420:Lyst APN 13 13835541 missense probably benign
IGL02429:Lyst APN 13 13835541 missense probably benign
IGL02501:Lyst APN 13 13886230 missense probably benign 0.02
IGL02522:Lyst APN 13 13809290 missense possibly damaging 0.81
IGL02535:Lyst APN 13 13824927 missense probably benign 0.00
IGL02596:Lyst APN 13 13835541 missense probably benign
IGL02601:Lyst APN 13 13835541 missense probably benign
IGL02603:Lyst APN 13 13835541 missense probably benign
IGL02608:Lyst APN 13 13887339 missense probably damaging 0.98
IGL02622:Lyst APN 13 13855975 missense probably damaging 1.00
IGL02690:Lyst APN 13 13815710 missense possibly damaging 0.58
IGL02715:Lyst APN 13 13848905 splice site probably null
IGL02725:Lyst APN 13 13935412 missense probably damaging 1.00
IGL02729:Lyst APN 13 13921194 missense possibly damaging 0.95
IGL02729:Lyst APN 13 13848924 missense possibly damaging 0.81
IGL02820:Lyst APN 13 13812643 missense probably benign 0.03
IGL02945:Lyst APN 13 13935783 missense possibly damaging 0.48
IGL02981:Lyst APN 13 13809496 missense probably damaging 0.99
IGL03087:Lyst APN 13 13809641 missense probably damaging 1.00
IGL03149:Lyst APN 13 13856029 missense probably benign 0.14
IGL03158:Lyst APN 13 13826337 critical splice donor site probably null
IGL03226:Lyst APN 13 13884144 missense probably benign 0.01
IGL03242:Lyst APN 13 13831466 nonsense probably null
IGL03385:Lyst APN 13 13831565 nonsense probably null
charcoal UTSW 13 13871346 nonsense probably null
charlotte_gray UTSW 13 13602026 intron probably benign
charzard UTSW 13 13821668 nonsense probably null
grey_wolf UTSW 13 unclassified
lightspeed UTSW 13 13915121 missense possibly damaging 0.91
pardon UTSW 13 13852537 missense probably benign 0.00
robin UTSW 13 13823387 nonsense probably null
sooty UTSW 13 unclassified
souris UTSW 13 13857808 unclassified probably benign
Swallow UTSW 13 13932007 missense probably benign 0.00
vulpix UTSW 13 13871379 splice site probably null
ANU22:Lyst UTSW 13 13852641 missense probably benign 0.01
IGL02835:Lyst UTSW 13 13835685 missense possibly damaging 0.82
P0031:Lyst UTSW 13 13838616 missense probably damaging 1.00
R0012:Lyst UTSW 13 13862279 missense probably benign 0.10
R0012:Lyst UTSW 13 13862279 missense probably benign 0.10
R0031:Lyst UTSW 13 13882741 missense probably benign 0.14
R0115:Lyst UTSW 13 13852537 missense probably benign 0.00
R0212:Lyst UTSW 13 13810570 missense possibly damaging 0.93
R0386:Lyst UTSW 13 13882799 splice site probably benign
R0393:Lyst UTSW 13 13821664 missense probably benign 0.01
R0415:Lyst UTSW 13 13886195 splice site probably benign
R0446:Lyst UTSW 13 13812633 missense probably benign 0.00
R0481:Lyst UTSW 13 13852537 missense probably benign 0.00
R0499:Lyst UTSW 13 13791298 missense probably damaging 1.00
R0506:Lyst UTSW 13 13812600 missense probably benign
R0530:Lyst UTSW 13 13931891 splice site probably benign
R0541:Lyst UTSW 13 13855878 missense probably benign 0.00
R0570:Lyst UTSW 13 13883971 missense probably benign 0.26
R0680:Lyst UTSW 13 13824926 missense probably benign 0.01
R0842:Lyst UTSW 13 13852826 nonsense probably null
R0848:Lyst UTSW 13 13809515 missense probably benign 0.00
R1014:Lyst UTSW 13 13808645 missense possibly damaging 0.49
R1205:Lyst UTSW 13 13854787 missense probably benign
R1251:Lyst UTSW 13 13809068 missense probably benign 0.00
R1304:Lyst UTSW 13 13926569 nonsense probably null
R1398:Lyst UTSW 13 13915121 missense possibly damaging 0.91
R1445:Lyst UTSW 13 13814639 missense possibly damaging 0.94
R1475:Lyst UTSW 13 13882797 critical splice donor site probably null
R1479:Lyst UTSW 13 13809067 missense probably benign 0.00
R1484:Lyst UTSW 13 13852775 missense probably benign 0.01
R1498:Lyst UTSW 13 13824960 missense possibly damaging 0.49
R1540:Lyst UTSW 13 13809686 missense possibly damaging 0.81
R1611:Lyst UTSW 13 13809482 missense probably damaging 0.97
R1653:Lyst UTSW 13 13809811 missense probably damaging 1.00
R1669:Lyst UTSW 13 13818672 missense possibly damaging 0.90
R1686:Lyst UTSW 13 13809290 missense possibly damaging 0.81
R1694:Lyst UTSW 13 13835746 missense probably damaging 0.98
R1747:Lyst UTSW 13 13932007 missense probably benign 0.00
R1793:Lyst UTSW 13 13821668 nonsense probably null
R1871:Lyst UTSW 13 13826297 missense probably benign 0.00
R1905:Lyst UTSW 13 13808719 missense probably benign
R1958:Lyst UTSW 13 13791203 missense probably damaging 1.00
R1969:Lyst UTSW 13 13904929 missense probably damaging 0.99
R2040:Lyst UTSW 13 13815807 missense probably benign 0.00
R2109:Lyst UTSW 13 13887405 missense possibly damaging 0.46
R2116:Lyst UTSW 13 13810286 missense probably damaging 0.99
R2121:Lyst UTSW 13 13835556 missense probably damaging 1.00
R2127:Lyst UTSW 13 13809847 missense probably damaging 1.00
R2187:Lyst UTSW 13 13883926 missense possibly damaging 0.61
R2238:Lyst UTSW 13 13917848 missense probably benign 0.41
R2258:Lyst UTSW 13 13812243 missense probably benign 0.00
R2292:Lyst UTSW 13 13915080 missense probably damaging 1.00
R2368:Lyst UTSW 13 13871248 missense probably damaging 0.96
R2908:Lyst UTSW 13 13844458 missense probably benign 0.03
R3001:Lyst UTSW 13 13871290 missense probably benign
R3002:Lyst UTSW 13 13871290 missense probably benign
R3024:Lyst UTSW 13 13833272 missense probably benign
R3113:Lyst UTSW 13 13844512 missense probably benign 0.12
R3406:Lyst UTSW 13 13809815 missense possibly damaging 0.56
R3972:Lyst UTSW 13 13881210 missense possibly damaging 0.67
R3978:Lyst UTSW 13 13808753 missense possibly damaging 0.82
R4032:Lyst UTSW 13 13791250 missense probably damaging 1.00
R4192:Lyst UTSW 13 13915098 missense probably damaging 1.00
R4206:Lyst UTSW 13 13810574 missense probably benign 0.03
R4298:Lyst UTSW 13 13809472 missense probably damaging 1.00
R4344:Lyst UTSW 13 13873051 missense probably benign 0.06
R4441:Lyst UTSW 13 13809968 missense probably damaging 1.00
R4445:Lyst UTSW 13 13884149 missense probably benign 0.42
R4477:Lyst UTSW 13 13809968 missense probably damaging 1.00
R4493:Lyst UTSW 13 13809968 missense probably damaging 1.00
R4494:Lyst UTSW 13 13809968 missense probably damaging 1.00
R4495:Lyst UTSW 13 13809968 missense probably damaging 1.00
R4622:Lyst UTSW 13 13848983 missense probably benign 0.01
R4638:Lyst UTSW 13 13871379 splice site probably null
R4658:Lyst UTSW 13 13809968 missense probably damaging 1.00
R4675:Lyst UTSW 13 13809968 missense probably damaging 1.00
R4719:Lyst UTSW 13 13824935 missense probably benign
R4729:Lyst UTSW 13 13812486 missense probably damaging 1.00
R4774:Lyst UTSW 13 13915182 missense probably damaging 1.00
R4811:Lyst UTSW 13 13951685 missense probably benign 0.33
R4877:Lyst UTSW 13 13857734 missense probably damaging 1.00
R4920:Lyst UTSW 13 13821645 missense possibly damaging 0.79
R4933:Lyst UTSW 13 13933963 missense probably benign 0.12
R4933:Lyst UTSW 13 13812349 missense probably damaging 0.98
R4958:Lyst UTSW 13 13810048 missense probably benign 0.00
R4982:Lyst UTSW 13 13900539 missense probably damaging 1.00
R4992:Lyst UTSW 13 13835748 missense probably damaging 1.00
R5024:Lyst UTSW 13 13808989 missense probably benign
R5049:Lyst UTSW 13 13810649 missense probably damaging 1.00
R5079:Lyst UTSW 13 13931938 missense probably benign 0.08
R5254:Lyst UTSW 13 13857655 missense probably benign 0.00
R5266:Lyst UTSW 13 13835555 missense probably damaging 1.00
R5279:Lyst UTSW 13 13823387 nonsense probably null
R5285:Lyst UTSW 13 13809011 missense probably benign 0.01
R5364:Lyst UTSW 13 13831439 missense probably benign 0.35
R5435:Lyst UTSW 13 13951649 missense possibly damaging 0.64
R5516:Lyst UTSW 13 13818707 missense probably benign 0.10
R5524:Lyst UTSW 13 13921364 missense probably benign 0.03
R5591:Lyst UTSW 13 13917918 missense probably damaging 0.99
R5592:Lyst UTSW 13 13917918 missense probably damaging 0.99
R5593:Lyst UTSW 13 13917918 missense probably damaging 0.99
R5594:Lyst UTSW 13 13917918 missense probably damaging 0.99
R5594:Lyst UTSW 13 13933982 missense probably benign 0.00
R5644:Lyst UTSW 13 13812081 missense possibly damaging 0.58
R5659:Lyst UTSW 13 13809212 missense possibly damaging 0.58
R5741:Lyst UTSW 13 13808615 missense probably benign 0.44
R5908:Lyst UTSW 13 13871346 nonsense probably null
R5969:Lyst UTSW 13 13862398 splice site probably null
R6128:Lyst UTSW 13 13933964 missense possibly damaging 0.67
R6271:Lyst UTSW 13 13833339 missense probably benign 0.30
R6315:Lyst UTSW 13 13818089 missense probably benign
R6318:Lyst UTSW 13 13917896 missense possibly damaging 0.88
R6555:Lyst UTSW 13 13823510 missense probably benign 0.01
R6663:Lyst UTSW 13 13838701 splice site probably null
R6701:Lyst UTSW 13 13856070 missense probably benign 0.06
R6711:Lyst UTSW 13 13809820 missense possibly damaging 0.80
R6909:Lyst UTSW 13 13917960 missense probably damaging 1.00
R6915:Lyst UTSW 13 13900629 missense probably benign 0.01
R6929:Lyst UTSW 13 13917909 missense probably damaging 1.00
R6960:Lyst UTSW 13 13808663 missense probably benign 0.12
R7018:Lyst UTSW 13 13918044 critical splice donor site probably null
R7037:Lyst UTSW 13 13791251 missense probably damaging 1.00
R7045:Lyst UTSW 13 13812293 missense probably damaging 1.00
R7045:Lyst UTSW 13 13809485 missense probably benign 0.34
R7070:Lyst UTSW 13 13932029 missense probably benign 0.23
R7188:Lyst UTSW 13 13926675 missense possibly damaging 0.66
R7201:Lyst UTSW 13 13883885 nonsense probably null
R7210:Lyst UTSW 13 13831568 missense probably damaging 1.00
R7229:Lyst UTSW 13 13818094 missense probably benign 0.00
R7293:Lyst UTSW 13 13854822 missense probably benign 0.01
R7318:Lyst UTSW 13 13932028 missense probably benign 0.13
R7344:Lyst UTSW 13 13881140 missense probably benign
R7426:Lyst UTSW 13 13812109 missense probably benign
R7522:Lyst UTSW 13 13821668 nonsense probably null
R7583:Lyst UTSW 13 13810472 missense probably damaging 1.00
R7606:Lyst UTSW 13 13812060 missense probably damaging 1.00
R7636:Lyst UTSW 13 13791332 critical splice donor site probably null
R7658:Lyst UTSW 13 13905061 missense possibly damaging 0.63
R7685:Lyst UTSW 13 13844450 missense probably benign 0.00
R7689:Lyst UTSW 13 13857808 critical splice donor site probably null
R7765:Lyst UTSW 13 13884117 missense possibly damaging 0.75
R7779:Lyst UTSW 13 13809128 missense probably damaging 1.00
R7871:Lyst UTSW 13 13810637 nonsense probably null
R7872:Lyst UTSW 13 13810450 missense probably benign 0.14
R7884:Lyst UTSW 13 13882268 missense probably benign 0.09
R7890:Lyst UTSW 13 13915154 missense probably damaging 0.99
R7916:Lyst UTSW 13 13821657 missense possibly damaging 0.64
R7948:Lyst UTSW 13 13921174 missense possibly damaging 0.59
R7956:Lyst UTSW 13 13815788 missense possibly damaging 0.80
R8048:Lyst UTSW 13 13862230 missense probably benign 0.12
R8085:Lyst UTSW 13 13808894 missense probably damaging 0.98
R8165:Lyst UTSW 13 13872945 missense probably damaging 0.99
R8235:Lyst UTSW 13 13935323 missense possibly damaging 0.69
R8237:Lyst UTSW 13 13826317 missense probably benign 0.00
R8275:Lyst UTSW 13 13950667 missense probably benign 0.02
R8300:Lyst UTSW 13 13838643 missense possibly damaging 0.79
R8350:Lyst UTSW 13 13824973 nonsense probably null
R8526:Lyst UTSW 13 13935391 missense probably damaging 0.99
R8551:Lyst UTSW 13 13808645 missense possibly damaging 0.77
R8723:Lyst UTSW 13 13887342 missense possibly damaging 0.89
R8772:Lyst UTSW 13 13812077 nonsense probably null
R8778:Lyst UTSW 13 13903152 missense possibly damaging 0.89
R8778:Lyst UTSW 13 13810361 missense possibly damaging 0.89
R8801:Lyst UTSW 13 13835595 missense probably benign 0.10
R8837:Lyst UTSW 13 13852548 missense probably benign
R8874:Lyst UTSW 13 13812147 missense probably benign
R8878:Lyst UTSW 13 13815661 missense probably benign 0.00
R8891:Lyst UTSW 13 13887435 missense possibly damaging 0.67
R9077:Lyst UTSW 13 13857693 missense probably benign 0.02
R9127:Lyst UTSW 13 13808827 missense probably damaging 1.00
R9143:Lyst UTSW 13 13835750 missense probably damaging 0.98
R9216:Lyst UTSW 13 13823188 missense probably benign
R9217:Lyst UTSW 13 13871245 missense probably benign 0.01
R9291:Lyst UTSW 13 13883938 missense probably benign 0.01
R9302:Lyst UTSW 13 13904947 missense possibly damaging 0.46
R9370:Lyst UTSW 13 13935333 missense probably damaging 1.00
R9402:Lyst UTSW 13 13812463 missense probably benign
R9457:Lyst UTSW 13 13862330 missense possibly damaging 0.83
R9481:Lyst UTSW 13 13857653 missense possibly damaging 0.68
R9563:Lyst UTSW 13 13812408 missense probably benign 0.36
R9623:Lyst UTSW 13 13852587 missense probably benign
R9661:Lyst UTSW 13 13808779 missense probably benign 0.01
R9682:Lyst UTSW 13 13831526 missense probably benign 0.21
R9743:Lyst UTSW 13 13809323 missense possibly damaging 0.67
R9801:Lyst UTSW 13 13809290 missense probably damaging 0.97
RF001:Lyst UTSW 13 13810426 missense probably benign
RF002:Lyst UTSW 13 13808948 missense probably benign 0.05
X0024:Lyst UTSW 13 13809033 missense probably benign 0.00
X0026:Lyst UTSW 13 13926555 missense probably damaging 0.99
Z1088:Lyst UTSW 13 13918018 missense probably benign 0.09
Z1176:Lyst UTSW 13 13951664 missense probably benign 0.27
Z1176:Lyst UTSW 13 13814692 missense probably damaging 1.00
Z1177:Lyst UTSW 13 13854719 missense possibly damaging 0.73
Mode of Inheritance Autosomal Recessive
Local Stock
Repository

None

Last Updated 2019-10-14 8:42 PM by Diantha La Vine
Record Created 2014-09-10 2:12 PM by Carlos Reyna
Record Posted 2015-02-05
Phenotypic Description
Figure 1. Hypopigmentation phenotype of the 50-cal mice (bottom). C57BL/6J mouse (top) is shown for reference.

Figure 2. 50-cal mice exhibited increased viral titers in the spleen after mouse cytomegalovirus (MCMV) infection. Normalized data are shown. Abbreviations: WT, wild-type; REF, homozygous reference mice; HET, heterozygous variant mice; VAR, homozygous variant mice. Mean (μ) and standard deviation (σ) are indicated.

Figure 3. 50-cal mice exhibited increased viral titers in the liver after mouse cytomegalovirus (MCMV) infection. Normalized data are shown. Abbreviations: WT, wild-type; REF, homozygous reference mice; HET, heterozygous variant mice; VAR, homozygous variant mice. Mean (μ) and standard deviation (σ) are indicated.

The 50-cal phenotype was identified among ENU-induced G3 mice of the pedigree R1475, some of which had a dark grey coat color (Figure 1). Some mice also showed increased mouse cytomegalovirus (MCMV) titers in the spleen (Figure 2) and liver (Figure 3) after MCMV infection.

Nature of Mutation

Figure 4. Linkage mapping of the increased MCMV titer in the spleen after MCMV infection using a recessive model of inheritance. Manhattan plot shows -log10 P values (Y-axis) plotted against the chromosome positions of 54 mutations (X-axis) identified in the G1 male of pedigree R1475. Normalized phenotype data are shown for single locus linkage analysis with consideration of G2 dam identity.  Horizontal pink and red lines represent thresholds of P = 0.05, and the threshold for P = 0.05 after applying Bonferroni correction, respectively.

Whole exome HiSeq sequencing of the G1 grandsire identified 54 mutations. The increased susceptibility to MCMV infection phenotype was linked by continuous variable mapping to a mutation in Lyst. The Lyst mutation is a T to A transversion at base pair 13,708,212 (v38) on chromosome 13, or base pair 117,881 in the GenBank genomic region NC_000079 within the donor splice site of intron 34. The strongest association was found with a recessive model of linkage to the normalized MCMV titer in the spleen, wherein 1 variant homozygote departed phenotypically from 10 homozygous reference mice and 9 heterozygous mice with a P value of 5.221 x 10-50 (Figure 4).  The effect of the mutation at the cDNA and protein level have not examined, but the mutation is predicted to result in skipping of the 189-nucleotide exon 34 (out of 53 total exons), resulting in coding of one aberrant amino acid (S2857R); the rest of the protein product is unchanged.

              <--exon 33          <--exon 34 intron 34-->      exon 35-->

8735 ……AACAACAACCAGCAAAG ……CAGCTGACACATGACAG gtgtgcagtgggaac…… AGCAGTCTGGTATGAC……
2852 ……-N--N--N--Q--Q--S ……-Q--L--T--H--D--R                   --A--V--W--Y--D-……
           correct              deleted                              correct

The donor splice site of intron 34, which is destroyed by the 50-cal mutation, is indicated in blue lettering and the mutated nucleotide is indicated in red.  The highlighted amino acid (S2857) is aberrant as the result of the mutation.

Alternatively, the use of a cryptic site in exon 34 may be used resulting in deletion of 89 nucleotides in exon 34. The deletion would result in a frameshift, coding of four aberrant amino acids after amino acid 2890, and coding of a premature stop codon after amino acid 2894.

              <--exon 33                                <--exon 34 intron 34-->      exon 35-->
8735 ……AACAACAACCAGCAAAG ……AAGGAAGAAGGTGATCCAGC……CAGCTGACACATGACAG gtgtgcagtgggaac…… AGCAGTCTGGTATGA
2852 ……-N--N--N--Q--Q--S ……--R--K--K--V--I--Q--……-Q--L--T--H--D--R                   -S--S--L--V--*
           correct                          deleted                                     aberrant    

                                

The donor splice site of intron 34, which is destroyed by the 50-cal mutation, is indicated in blue lettering and the mutated nucleotide is indicated in red.  The putative cryptic splice donor site is highlighted.

Illustration of Mutations in
Gene & Protein
Protein Prediction

Figure 5. Domain structure of the Lyst protein. The Lyst protein is a 3788-amino acid protein whose biochemical functions remain unknown. The N-terminal portion of the protein contains approximately twenty repeats with homology to ARM  and HEAT repeat motifs and a perilipin domain (PD). The C-terminal portion of Lyst contains a BEACH  domain and seven WD40 motifs. The 50-cal mutation occurs in intron 34. This image is interactive. This image is interactive. Click on the mutations (red) for more specific information.

The Lyst gene encodes the protein Lyst (also CHS/Beige), a 3788-amino acid protein whose biochemical functions remain unknown (Figure 3). A large N-terminal portion of the protein (amino acids 1-3132) contains approximately twenty repeats with homology to ARM (Armadillo) and HEAT (huntingtin, elongation factor 3, A subunit of protein phosphatase A, target of rapamycin) repeat motifs (1;2). ARM and HEAT motifs are α-helical domains of about 50 amino acids that pack together to form elongated “solenoids” (3); evidence suggests they mediate protein associations at the membrane (4), and vesicle transport (5), respectively. The C-terminus of Lyst contains two distinct domains, a BEACH (beige and chediak) domain (amino acids 3132-3472) and seven WD40 motifs (1). The BEACH domain is a 345-amino acid region of unknown function (1), and WD40 motifs are protein interaction motifs that typically form β sheets arranged in a 7-bladed β propeller fold (6).The 50-cal mutation is predicted to affect the ARM/HEAT domain.

Please see the record for souris for information about Lyst.

Putative Mechanism

In humans, mutations in the LYST gene cause Chediak-Higashi Syndrome (CHS, OMIM #214500), a rare autosomal recessive disorder characterized by oculocutaneous albinism, severe immune deficiency, bleeding tendency, recurrent pyogenic infection, progressive neurologic defects and a lymphoproliferative syndrome [(7;8); reviewed in (2)]. These defects are caused by the aberrant formation of giant granules within a variety of cell types, and disrupted intracellular protein trafficking (2;9;10). The enlarged granules consist of organelles such as lysosomes, melanosomes, cytolytic granules and platelet dense bodies, and it is thought that the increased size of these organelles inhibits their migration and fusion at the cell surface and/or organelle-organelle fusion. There is no clear understanding of the molecular mechanisms of Lyst protein function, or how its loss leads to the formation of enlarged lysosomes and lysosome-related organelles. In mice, mutations in Lyst cause the beige phenotype (7;8). As in humans, beige mice exhibit hypopigmentation, bleeding tendency, and defective immune cell function resulting from the formation of giant granules in melanosomes, lymphocytes, neutrophils, and other cell types (10-12). Beige mice have defective NK cell (13) and cytotoxic T lymphocyte function (14), and increased susceptibility to infections including MCMV (15;16). However, beige mice do not develop lymphoproliferative disorder, even after challenge with infection (15). The 50-cal hypopigmentation and MCMV susceptibility phenotype mimics other known alleles of Lyst (see MGI for a list of Lyst alleles as well as the Beutler alleles souris and charlotte_gray) indicating that there is loss of function in the Lyst50-cal protein.

Primers PCR Primer
50-cal_pcr_F: GTATGCTGGAGACGGTACTCAGG
50-cal_pcr_R: ACCCTCTCCTCTCCAGGTATGTC

Sequencing Primer
50-cal_seq_F: GGTTCTCCAGCATGCTAGTC
50-cal_seq_R: GTCTGAGGACAGTTACAGTG
Genotyping

PCR program

1) 94°C 2:00
2) 94°C 0:30
3) 55°C 0:30
4) 72°C 1:00
5) repeat steps (2-4) 40x
6) 72°C 10:00
7) 4°C hold


The following sequence of 494 nucleotides is amplified (chromosome 13, + strand):


1   gtatgctgga gacggtactc aggttctcca gcatgctagt caaatgctat accactgagc
61  tgtatcccag cctgaggtgt actgttcaga tacttaatgt ttagtgaata cttaactttg
121 gaacaatctt gttggtttag tctcttccag aggctcgatt tcaaatccaa ggatatatct
181 aaaatcgctg cagacatcac ccaggctgta tcactctccc aaggcattga aaggaagaag
241 gtgatccagc acatcagagg gatgtacaaa gttgacctga gtgccagcag gcactggcag
301 gaatgcatcc agcagctgac acatgacagg tgtgcagtgg gaacacgtgg ctgagcacag
361 cttctatatg tgatgtgtaa tagtgttttc attccagtac tcacatttat acaattattt
421 ttttaaaaga tttatttatt gttatatgta agtacactgt aactgtcctc agacatacct
481 ggagaggaga gggt


Primer binding sites are underlined and the sequencing primers are highlighted; the mutated nucleotide is shown in red.

References
  11. Kelly, E. M. (1957) Beige, Bg. Mouse News Lett. 16, 36-36.
Science Writers Anne Murray
Illustrators Katherine Timer
AuthorsTao Yue, Duanwu Zhang, Carlos Reyna, Tiana Purrington, Bruce Beutler