Mutagenetix > Incidental Mutations

Incidental Mutation 'R4878:Hps4'

375056

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, C130020P05Rik

MMRRC Submission

042487-MU

Accession Numbers

Is this an essential gene?

Possibly non essential (E-score: 0.459) question?

Stock #

R4878 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

112343083-112378414 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 112375368 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 584 (V584A)

Ref Sequence

ENSEMBL: ENSMUSP00000107978 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000035279] [ENSMUST00000112359]

AlphaFold

Q99KG7

Predicted Effect

probably benign
Transcript: ENSMUST00000035279
AA Change: V584A

PolyPhen 2 Score 0.123 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000047920
Gene: ENSMUSG00000042328
AA Change: V584A

Domain	Start	End	E-Value	Type
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 benign
Transcript: ENSMUST00000112359
AA Change: V584A

PolyPhen 2 Score 0.123 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000107978
Gene: ENSMUSG00000042328
AA Change: V584A

Domain	Start	End	E-Value	Type
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: ENSMUST00000133708

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176660

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000177121

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000199500

Meta Mutation Damage Score

0.0672

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.8%
20x: 93.8%

Validation Efficiency

96% (70/73)

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: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aadacl4	C	A	4: 144,613,845	H47N	possibly damaging	Het
Adgrg3	A	T	8: 95,035,086	N159I	possibly damaging	Het
Agrn	A	T	4: 156,170,845	L1449Q	probably damaging	Het
Anks6	C	T	4: 47,030,795	G601S	probably damaging	Het
Atg2a	A	T	19: 6,250,244	E694V	probably damaging	Het
Ccndbp1	T	A	2: 121,014,691	L363*	probably null	Het
Cdh16	A	T	8: 104,618,064	D478E	probably damaging	Het
Cep295	A	T	9: 15,334,956	W735R	probably benign	Het
Cnnm2	C	T	19: 46,859,083	P682S	probably benign	Het
Daam2	C	A	17: 49,460,710	R951L	probably damaging	Het
Dmxl1	T	A	18: 49,851,476	F180I	probably damaging	Het
Dnajc6	T	C	4: 101,599,034		probably benign	Het
Efemp2	A	T	19: 5,480,761		probably benign	Het
Emilin1	A	G	5: 30,917,066	D217G	probably benign	Het
Enpep	A	T	3: 129,276,771	M829K	probably benign	Het
Epb41l4a	A	G	18: 33,798,572	V623A	probably damaging	Het
Erlin2	T	A	8: 27,027,166		probably null	Het
Fbln2	T	C	6: 91,256,995		probably null	Het
Gga3	A	T	11: 115,591,321	I157N	probably damaging	Het
Gm884	A	G	11: 103,617,891		probably benign	Het
Gtpbp6	C	T	5: 110,107,311		probably benign	Het
Ighv1-50	T	C	12: 115,119,947	Y51C	probably benign	Het
Kif13b	T	C	14: 64,806,154	L1801P	probably benign	Het
Kif16b	T	C	2: 142,848,003	I330V	probably damaging	Het
Klb	A	T	5: 65,348,490	R27W	probably damaging	Het
Lrif1	A	T	3: 106,735,640	K169M	probably damaging	Het
Met	A	G	6: 17,549,059	D970G	probably damaging	Het
Mical3	A	T	6: 120,969,387	M1051K	possibly damaging	Het
Mios	A	G	6: 8,215,094	N97D	probably benign	Het
Msh5	G	A	17: 35,038,456	R321C	probably damaging	Het
Mybpc1	T	C	10: 88,551,430	Q473R	possibly damaging	Het
Ncoa1	C	T	12: 4,275,004	G970D	probably damaging	Het
Neb	T	C	2: 52,219,394	Y232C	probably damaging	Het
Nefh	A	G	11: 4,941,333	S429P	probably damaging	Het
Notch3	C	T	17: 32,147,085	G1014D	probably damaging	Het
Nup107	A	T	10: 117,751,418	C859S	probably benign	Het
Olfr1033	A	G	2: 86,041,455	I47V	probably benign	Het
Olfr136	T	G	17: 38,335,627	F157V	probably benign	Het
Olfr412	T	C	11: 74,364,848	Y60H	probably damaging	Het
Otud7b	T	A	3: 96,136,510		probably benign	Het
Pde1a	A	T	2: 79,878,139	S312T	probably benign	Het
Piwil1	G	T	5: 128,740,981	R94L	probably damaging	Het
Pnma2	G	A	14: 66,917,054	W309*	probably null	Het
Ppef2	A	C	5: 92,228,740		probably null	Het
Rabac1	T	A	7: 24,969,967	Q212L	possibly damaging	Het
Rad51	T	C	2: 119,120,492		probably benign	Het
Rbm48	A	T	5: 3,591,853		probably benign	Het
Rft1	C	T	14: 30,677,804	S315L	probably benign	Het
Rgs13	C	T	1: 144,171,479	M1I	probably null	Het
Rhbg	A	C	3: 88,247,453	S215A	probably benign	Het
Rufy2	A	T	10: 63,002,211	N379I	probably damaging	Het
Slc17a1	T	C	13: 23,880,654	L367P	probably damaging	Het
Slc25a39	G	A	11: 102,403,675	R308C	probably benign	Het
Smo	A	G	6: 29,753,571	T149A	probably benign	Het
Sqle	A	G	15: 59,316,085	K81E	probably benign	Het
Tfpi	A	G	2: 84,452,555		probably null	Het
Tnk2	A	G	16: 32,679,630	D572G	probably damaging	Het
Ubr5	A	T	15: 38,006,564	M1149K	probably benign	Het
Utrn	T	A	10: 12,727,758	Q626L	probably damaging	Het
Virma	T	A	4: 11,544,971	H1643Q	probably damaging	Het
Wnt3	G	T	11: 103,808,205	G46C	possibly damaging	Het
Zkscan7	G	T	9: 122,890,800	G184*	probably null	Het

Other mutations in Hps4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01485:Hps4	APN	5	112364511	splice site	probably benign
IGL02331:Hps4	APN	5	112369536	missense	probably benign	0.03
IGL02410:Hps4	APN	5	112370227	missense	probably benign	0.07
IGL02821:Hps4	APN	5	112375441	missense	probably benign	0.02
R0748:Hps4	UTSW	5	112374914	missense	probably damaging	1.00
R1487:Hps4	UTSW	5	112377999	nonsense	probably null
R1891:Hps4	UTSW	5	112369556	splice site	probably null
R2010:Hps4	UTSW	5	112369476	missense	probably damaging	1.00
R2305:Hps4	UTSW	5	112346661	missense	probably damaging	0.99
R3196:Hps4	UTSW	5	112364563	missense	probably damaging	1.00
R4274:Hps4	UTSW	5	112375030	intron	probably benign
R4988:Hps4	UTSW	5	112378153	utr 3 prime	probably benign
R5843:Hps4	UTSW	5	112349430	critical splice donor site	probably null
R5896:Hps4	UTSW	5	112369485	missense	probably benign	0.02
R6318:Hps4	UTSW	5	112346629	missense	probably damaging	1.00
R7381:Hps4	UTSW	5	112375458	missense	possibly damaging	0.86
R7781:Hps4	UTSW	5	112370522	missense	probably benign	0.14
R8112:Hps4	UTSW	5	112370111	missense	probably benign	0.17
R8996:Hps4	UTSW	5	112378039	missense	possibly damaging	0.81
R9058:Hps4	UTSW	5	112378039	missense	possibly damaging	0.81
R9059:Hps4	UTSW	5	112378039	missense	possibly damaging	0.81
R9060:Hps4	UTSW	5	112378039	missense	possibly damaging	0.81
R9103:Hps4	UTSW	5	112378039	missense	possibly damaging	0.81
R9105:Hps4	UTSW	5	112378039	missense	possibly damaging	0.81
R9106:Hps4	UTSW	5	112378039	missense	possibly damaging	0.81
R9175:Hps4	UTSW	5	112378039	missense	possibly damaging	0.81
R9210:Hps4	UTSW	5	112349361	missense	possibly damaging	0.78
R9226:Hps4	UTSW	5	112378039	missense	possibly damaging	0.81
R9227:Hps4	UTSW	5	112378039	missense	possibly damaging	0.81
R9229:Hps4	UTSW	5	112378039	missense	possibly damaging	0.81
R9230:Hps4	UTSW	5	112378039	missense	possibly damaging	0.81
R9232:Hps4	UTSW	5	112378039	missense	possibly damaging	0.81
R9233:Hps4	UTSW	5	112378039	missense	possibly damaging	0.81
R9234:Hps4	UTSW	5	112378039	missense	possibly damaging	0.81
R9236:Hps4	UTSW	5	112378039	missense	possibly damaging	0.81
R9330:Hps4	UTSW	5	112378039	missense	possibly damaging	0.81
Z1177:Hps4	UTSW	5	112370377	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- TTCCCGAGTTGGAACCTTTGG -3'
(R):5'- AGGCCTTCAAAGGGACCAAC -3'

Sequencing Primer
(F):5'- TTTGGTAAGGCGGGCCC -3'
(R):5'- TTCAAAGGGACCAACCACATTG -3'

Posted On

2016-03-17