Mutagenetix > Phenotypic Mutation

Phenotypic Mutation 'sooty' (pdf version)

Allele

sooty

Mutation Type

Chromosome

Coordinate

Base Change

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

Mapped

Yes

Amino Acid Change

Institutional Source

Beutler Lab

Ref Sequences

Ensembl: ENSMUSP00000106188 (fasta)

Gene Model

not available

AlphaFold

no structure available at present

SMART Domains

Domain	Start	End	E-Value	Type
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
Beach	3118	3408	1.25e-193	SMART
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

Meta Mutation Damage Score

Not available question?

Is this an essential gene?

Possibly nonessential (E-score: 0.414) question?

Phenotypic Category

Autosomal Recessive

Candidate Explorer Status

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Single pedigree
Linkage Analysis Data

Penetrance

100%

Alleles Listed at MGI

All alleles(45) : Gene trapped(30) Spontaneous(8) Chemically induced(6) Radiation induced(1)

Lab Alleles

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
50-cal	UTSW	13	13882797	critical splice donor site	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
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

Lost

Repository

none

Last Updated

2016-05-13 3:09 PM by Eva Marie Y. Moresco

Record Created

unknown

Record Posted

2007-10-10

Phenotypic Description

Sooty mice have a subtle gray coat color. They have no discernable ocular albinism. Sooty mice are highly susceptible to infection by mouse cytomegalovirus (MCMV) (MCMV Susceptibility and Resistance Screen), and sooty NK cells fail to degranulate after antibody stimulation of NKp46 or Ly49H receptors, or after exposure to YAC-1 cells or PMA/ionomycin. The strain was lost prior to the availability of germline preservation methods.

Nature of Mutation

The sooty mutation was mapped to Chromosome 13 between the centromere and the distal marker d13mit14. The region contains the Lyst locus, mutated in beige mice (1;2). Sooty was found to be allelic with beige.

Please see the record for souris for information about Lyst.

Illustration of Mutations in
Gene & Protein

Primers

Primers cannot be located by automatic search.

References

1. Barbosa, M. D., Nguyen, Q. A., Tchernev, V. T., Ashley, J. A., Detter, J. C., Blaydes, S. M., Brandt, S. J., Chotai, D., Hodgman, C., Solari, R. C., Lovett, M., and Kingsmore, S. F. (1996) Identification of the homologous beige and Chediak-Higashi syndrome genes, Nature 382, 262-265.

2. Perou, C. M., Moore, K. J., Nagle, D. L., Misumi, D. J., Woolf, E. A., McGrail, S. H., Holmgren, L., Brody, T. H., Dussault, B. J., Jr., Monroe, C. A., Duyk, G. M., Pryor, R. J., Li, L., Justice, M. J., and Kaplan, J. (1996) Identification of the murine beige gene by YAC complementation and positional cloning, Nat. Genet. 13, 303-308.

Science Writers

Eva Marie Y. Moresco

Authors

Jason Goode, Bruce Beutler