Mutagenetix > Incidental Mutation

Incidental Mutation 'R9459:Hps4'

714754

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

Accession Numbers

Essential gene?

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

Stock #

R9459 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

112343083-112378414 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 112375009 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 578 (S578P)

Ref Sequence

ENSEMBL: ENSMUSP00000047920 (fasta)

Gene Model

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

AlphaFold

Q99KG7

Predicted Effect

probably benign
Transcript: ENSMUST00000035279
AA Change: S578P

PolyPhen 2 Score 0.300 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000047920
Gene: ENSMUSG00000042328
AA Change: S578P

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: S578P

PolyPhen 2 Score 0.300 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000107978
Gene: ENSMUSG00000042328
AA Change: S578P

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

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: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700020D05Rik	T	A	19: 5,503,729	H8L	probably benign	Het
Abcb1a	T	A	5: 8,685,414		probably null	Het
Alms1	T	A	6: 85,627,964	C2199S	probably damaging	Het
Aox3	A	G	1: 58,150,309	I390V	probably benign	Het
Ap3b2	T	C	7: 81,473,903	N400S	probably benign	Het
Baalc	A	T	15: 38,934,024	N70I	probably benign	Het
Brca2	T	A	5: 150,540,629	V1286D	probably damaging	Het
Ccdc30	T	C	4: 119,377,273	R81G	possibly damaging	Het
Cd209g	T	C	8: 4,135,610	S15P	probably benign	Het
Chrnb3	G	A	8: 27,393,856	W207*	probably null	Het
Cmpk2	C	T	12: 26,478,023	T413M	probably damaging	Het
Coq4	T	A	2: 29,788,550	Y63N	probably damaging	Het
Depdc5	T	A	5: 32,990,773	S1478T	probably damaging	Het
Etf1	A	G	18: 34,906,081	F378L	probably benign	Het
Exoc6	T	C	19: 37,585,893	V324A	probably benign	Het
Frem2	A	G	3: 53,653,486	L1200P	probably benign	Het
Gadl1	T	C	9: 115,965,611	W285R	probably damaging	Het
Gbp3	A	G	3: 142,564,946		probably null	Het
Gm14295	C	T	2: 176,807,372	T5I	possibly damaging	Het
Kctd13	T	A	7: 126,945,082	D317E	probably damaging	Het
Kdm4b	T	A	17: 56,399,509	D881E	probably benign	Het
Klf10	G	A	15: 38,295,927	P473L	probably damaging	Het
Lrch3	A	T	16: 32,979,405	D371V	probably damaging	Het
Msh2	T	C	17: 87,678,330	S112P	possibly damaging	Het
Msh3	A	G	13: 92,215,539	V1036A	possibly damaging	Het
Mybl1	A	G	1: 9,676,259	V392A	possibly damaging	Het
Myo7a	T	C	7: 98,073,173	I1182V	possibly damaging	Het
Nectin1	A	C	9: 43,803,793	E442A	probably benign	Het
Obsl1	G	T	1: 75,498,240	H839N	probably benign	Het
Olfr1202	T	C	2: 88,817,623	F151L	probably benign	Het
Olfr1505	T	C	19: 13,919,310	C97R	possibly damaging	Het
Pacs1	C	T	19: 5,145,070		probably null	Het
Pcdh17	G	T	14: 84,448,623	E843D	probably benign	Het
Pcnt	A	G	10: 76,392,738	L1531P	probably damaging	Het
Pdgfra	A	G	5: 75,192,468	D973G	probably damaging	Het
Pkd2	A	G	5: 104,466,934	Y214C	probably damaging	Het
Plcb1	T	C	2: 135,322,638	Y427H	probably benign	Het
Ppm1h	A	G	10: 122,907,577	N402S	possibly damaging	Het
Rassf4	T	A	6: 116,641,788		probably null	Het
Ryr1	G	A	7: 29,068,643	T2856I	probably damaging	Het
Serpinb8	A	T	1: 107,605,790	K192*	probably null	Het
Slfn14	T	G	11: 83,279,372	Q482P	possibly damaging	Het
Spata2	A	G	2: 167,485,285	V64A	probably benign	Het
Tax1bp1	T	G	6: 52,729,329	V105G	probably damaging	Het
Tbc1d22a	T	G	15: 86,235,820	S142A	possibly damaging	Het
Tdrd9	T	C	12: 112,025,573	F594S	probably damaging	Het
Uba3	T	C	6: 97,189,598	I281V	probably benign	Het
Uggt2	T	C	14: 119,049,183	E723G	probably benign	Het
Usp20	C	T	2: 31,011,012	S391F	probably damaging	Het
Usp24	T	A	4: 106,342,358	D166E	probably damaging	Het
Vmn1r1	A	G	1: 182,157,938	V54A	probably benign	Het
Zfp442	T	A	2: 150,408,748	E411D	unknown	Het
Zfp804a	T	C	2: 82,259,409	I1194T	probably damaging	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
R4878:Hps4	UTSW	5	112375368	missense	probably benign	0.12
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'- TGGTGCTTTAGGAGACACCG -3'
(R):5'- TGCCTCTGGGAGAAAGCAAG -3'

Sequencing Primer
(F):5'- GGTACTTACCTTTCAACTAAGTGTGC -3'
(R):5'- TGCAAGCCACACCAGCC -3'

Posted On

2022-06-15