Mutagenetix > Incidental Mutation

Incidental Mutation 'R9058:Hps4'

688806

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

068884-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.272) question?

Stock #

R9058 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

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

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

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

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

Meta Mutation Damage Score

0.0638

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.2%

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: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acox1	T	C	11: 116,080,268 (GRCm39)	T135A	possibly damaging	Het
Adrm1b	A	T	3: 92,335,559 (GRCm39)	M283K	probably benign	Het
Aldh8a1	T	C	10: 21,258,344 (GRCm39)	I147T	possibly damaging	Het
Alkbh5	T	C	11: 60,444,548 (GRCm39)	L288S	probably benign	Het
Bpifb5	A	G	2: 154,080,817 (GRCm39)	D478G	possibly damaging	Het
Cacna1s	A	T	1: 135,998,436 (GRCm39)	K155*	probably null	Het
Ccser1	T	C	6: 61,350,976 (GRCm39)	L511P	probably damaging	Het
Cebpz	A	T	17: 79,243,227 (GRCm39)	N142K	probably benign	Het
Cfap299	A	T	5: 98,932,400 (GRCm39)	D200V	probably damaging	Het
Clip1	G	T	5: 123,752,645 (GRCm39)	R379S		Het
Cpne8	T	A	15: 90,381,276 (GRCm39)	I513F	probably damaging	Het
Ctnnb1	T	A	9: 120,780,476 (GRCm39)	C213*	probably null	Het
Dnah7b	A	G	1: 46,282,575 (GRCm39)	K2903E	probably damaging	Het
Dnah7c	G	T	1: 46,805,816 (GRCm39)	G3422W	probably damaging	Het
Dnhd1	T	A	7: 105,333,270 (GRCm39)	H247Q	probably benign	Het
Efna2	A	G	10: 80,022,720 (GRCm39)	Y88C	probably damaging	Het
Eppk1	C	T	15: 75,992,265 (GRCm39)	G1539R	probably benign	Het
Exoc3l2	A	T	7: 19,203,821 (GRCm39)	K138*	probably null	Het
Fam47e	A	G	5: 92,719,367 (GRCm39)		probably benign	Het
Frmpd1	T	A	4: 45,283,948 (GRCm39)	M923K	probably damaging	Het
Gbe1	A	G	16: 70,324,059 (GRCm39)	E558G	possibly damaging	Het
Gm5431	T	C	11: 48,786,049 (GRCm39)	T109A	probably benign	Het
Gm9508	G	A	10: 77,532,620 (GRCm39)	P150S	unknown	Het
Grep1	T	C	17: 23,935,016 (GRCm39)	N63S	probably benign	Het
Hrob	T	C	11: 102,146,386 (GRCm39)	S221P	probably benign	Het
Hsfy2	A	T	1: 56,676,504 (GRCm39)	V11D	probably benign	Het
Kif13a	T	C	13: 46,944,941 (GRCm39)	N887D	probably damaging	Het
Kirrel1	A	G	3: 86,992,442 (GRCm39)	V541A	probably benign	Het
Klk15	C	T	7: 43,587,790 (GRCm39)	H73Y	possibly damaging	Het
Lamc3	G	A	2: 31,798,653 (GRCm39)	R453H	probably benign	Het
Mideas	A	G	12: 84,220,642 (GRCm39)	M104T	probably damaging	Het
Muc6	G	C	7: 141,218,154 (GRCm39)	T2173S	possibly damaging	Het
Neb	T	C	2: 52,075,341 (GRCm39)	N208S	probably benign	Het
Nlrc5	A	T	8: 95,238,938 (GRCm39)	T1459S	possibly damaging	Het
Npy1r	T	C	8: 67,156,600 (GRCm39)	S7P	probably benign	Het
Nr4a2	T	C	2: 57,002,255 (GRCm39)	N66S	probably benign	Het
Nr5a1	T	C	2: 38,584,034 (GRCm39)	T462A	probably damaging	Het
Ntng2	A	G	2: 29,094,202 (GRCm39)	C390R	probably benign	Het
Or4p23	A	C	2: 88,577,030 (GRCm39)	D67E		Het
Or5b119	G	A	19: 13,456,956 (GRCm39)	T202I	possibly damaging	Het
Or7g12	T	A	9: 18,900,222 (GRCm39)	*313R	probably null	Het
Pecam1	G	T	11: 106,590,675 (GRCm39)	P33Q	probably damaging	Het
Phc2	T	A	4: 128,616,769 (GRCm39)	F347L	probably benign	Het
Phldb2	T	A	16: 45,592,604 (GRCm39)	H938L	possibly damaging	Het
Pkd1l3	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	8: 110,350,827 (GRCm39)		probably benign	Het
Prkch	G	T	12: 73,822,308 (GRCm39)		probably null	Het
Prr5	A	G	15: 84,641,241 (GRCm39)	N169S	probably benign	Het
Puf60	C	T	15: 75,942,425 (GRCm39)	D483N	probably benign	Het
Puf60	C	T	15: 75,944,382 (GRCm39)	M133I	probably benign	Het
Rmnd1	T	C	10: 4,363,398 (GRCm39)	H284R	probably benign	Het
Scaper	T	C	9: 55,722,762 (GRCm39)	E682G	probably damaging	Het
Sds	A	G	5: 120,618,779 (GRCm39)	E111G	possibly damaging	Het
Sec23b	T	A	2: 144,424,010 (GRCm39)	I553N	probably damaging	Het
Serpina1a	A	T	12: 103,820,001 (GRCm39)	I415K	possibly damaging	Het
Slc14a1	T	A	18: 78,145,785 (GRCm39)		probably null	Het
Socs1	G	A	16: 10,602,692 (GRCm39)	P15L	probably benign	Het
Sv2b	A	T	7: 74,789,822 (GRCm39)		probably null	Het
Sync	T	C	4: 129,187,217 (GRCm39)	I83T	probably damaging	Het
Syt16	T	A	12: 74,282,019 (GRCm39)	L381Q	probably damaging	Het
Tbx20	T	C	9: 24,681,019 (GRCm39)	R158G	probably damaging	Het
Tmco1	C	T	1: 167,136,132 (GRCm39)		probably benign	Het
Tmem19	C	A	10: 115,198,031 (GRCm39)		probably benign	Het
Trpa1	A	C	1: 14,959,618 (GRCm39)	N689K	probably damaging	Het
Ube3b	C	A	5: 114,553,300 (GRCm39)	H891N	probably benign	Het
Vmn2r19	T	A	6: 123,313,021 (GRCm39)	M697K	possibly damaging	Het
Zfp142	A	T	1: 74,608,955 (GRCm39)	C1613*	probably null	Het
Zfp7	T	A	15: 76,764,981 (GRCm39)	M1K	probably null	Het
Zfp936	A	T	7: 42,839,196 (GRCm39)	Q221L	probably benign	Het

Other mutations in Hps4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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'- GCTGAAAAGACAGGACAGTTGTTC -3'
(R):5'- AGTTCTTGCAGCTGCCACTG -3'

Sequencing Primer
(F):5'- CTGGGCCTGAAGTTCAAATCG -3'
(R):5'- TTGCAGCTGCCACTGAGGAG -3'

Posted On

2021-11-19