Mutagenetix > Incidental Mutation

Incidental Mutation 'R6318:Hps4'

510272

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

044473-MU

Accession Numbers

Essential gene?

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

Stock #

R6318 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

112490949-112526280 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 112494495 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glycine at position 26 (V26G)

Ref Sequence

ENSEMBL: ENSMUSP00000107978 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000031289] [ENSMUST00000035279] [ENSMUST00000112359] [ENSMUST00000146510]

AlphaFold

Q99KG7

Predicted Effect

probably benign
Transcript: ENSMUST00000031289

SMART Domains

Protein: ENSMUSP00000031289
Gene: ENSMUSG00000029346

Domain	Start	End	E-Value	Type
low complexity region	13	54	N/A	INTRINSIC
Pfam:SRR1	109	164	2.1e-25	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000035279
AA Change: V26G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000047920
Gene: ENSMUSG00000042328
AA Change: V26G

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 damaging
Transcript: ENSMUST00000112359
AA Change: V26G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000107978
Gene: ENSMUSG00000042328
AA Change: V26G

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

probably benign
Transcript: ENSMUST00000146510

SMART Domains

Protein: ENSMUSP00000119870
Gene: ENSMUSG00000029346

Domain	Start	End	E-Value	Type
low complexity region	12	53	N/A	INTRINSIC
Pfam:SRR1	109	162	1.8e-20	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000156083

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000175718

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000176737

Meta Mutation Damage Score

0.4607

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.1%
20x: 97.3%

Validation Efficiency

99% (74/75)

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: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700102P08Rik	A	G	9: 108,270,474 (GRCm39)	T13A	possibly damaging	Het
Abcg4	T	C	9: 44,186,645 (GRCm39)	T500A	probably benign	Het
Adcy4	T	A	14: 56,006,681 (GRCm39)	I1051F	probably damaging	Het
Adgrg6	A	T	10: 14,343,241 (GRCm39)	N235K	probably benign	Het
Aldh3a2	A	C	11: 61,153,245 (GRCm39)	Y160*	probably null	Het
Arhgef4	G	A	1: 34,762,558 (GRCm39)	A605T	unknown	Het
Armt1	T	C	10: 4,400,859 (GRCm39)	M202T	probably benign	Het
Brd2	C	A	17: 34,331,872 (GRCm39)	V349F	probably damaging	Het
Btnl10	A	T	11: 58,817,691 (GRCm39)		probably benign	Het
Ccdc178	A	G	18: 22,253,591 (GRCm39)	V216A	possibly damaging	Het
Ccdc85c	A	T	12: 108,240,968 (GRCm39)	L142Q	unknown	Het
Cdc27	A	T	11: 104,419,520 (GRCm39)	S172T	probably damaging	Het
Ceacam14	T	C	7: 17,548,237 (GRCm39)	I109T	probably damaging	Het
Ces5a	C	T	8: 94,261,211 (GRCm39)	G72E	probably damaging	Het
Cfb	A	G	17: 35,080,800 (GRCm39)	Y66H	possibly damaging	Het
Clec14a	G	A	12: 58,315,001 (GRCm39)	P207L	probably damaging	Het
Clec16a	G	A	16: 10,448,652 (GRCm39)	R599H	probably damaging	Het
Csmd1	A	T	8: 15,953,212 (GRCm39)	I3423N	probably damaging	Het
Cyp4a29	C	A	4: 115,107,396 (GRCm39)	N243K	probably benign	Het
Ddx59	T	C	1: 136,344,610 (GRCm39)	F94L	probably damaging	Het
Dusp3	A	C	11: 101,877,697 (GRCm39)	V19G	probably benign	Het
Fat3	T	C	9: 15,828,280 (GRCm39)		probably benign	Het
Fgfr4	T	A	13: 55,313,921 (GRCm39)	V545E	probably damaging	Het
Fxn	G	T	19: 24,257,790 (GRCm39)	A47D	probably damaging	Het
Gdpgp1	A	T	7: 79,888,898 (GRCm39)	I310F	possibly damaging	Het
Gm7210	A	T	7: 11,328,040 (GRCm39)		noncoding transcript	Het
Grm7	G	T	6: 111,335,836 (GRCm39)	C749F	probably damaging	Het
Igf1r	A	G	7: 67,814,981 (GRCm39)	D294G	probably benign	Het
Immp1l	T	C	2: 105,761,172 (GRCm39)	F27S	probably benign	Het
Kcnk3	T	A	5: 30,779,930 (GRCm39)	C327S	probably damaging	Het
Kif13a	T	A	13: 46,968,683 (GRCm39)		probably null	Het
Krtap5-4	T	C	7: 141,857,827 (GRCm39)	S166P	unknown	Het
Lyst	G	A	13: 13,917,896 (GRCm39)	D3319N	possibly damaging	Het
Malrd1	T	G	2: 16,047,078 (GRCm39)	S1735A	unknown	Het
Myh4	A	G	11: 67,134,268 (GRCm39)	T308A	probably benign	Het
Myh8	A	T	11: 67,190,167 (GRCm39)	Q1269L	probably benign	Het
Myo15b	G	A	11: 115,781,657 (GRCm39)	V1367I	probably damaging	Het
Nae1	T	C	8: 105,250,269 (GRCm39)	D208G	probably benign	Het
Nelfe	T	A	17: 35,073,432 (GRCm39)	V296D	probably damaging	Het
Nkapd1	T	C	9: 50,518,761 (GRCm39)	R284G	probably benign	Het
Npepps	A	T	11: 97,109,374 (GRCm39)	V734E	probably damaging	Het
Ogdh	A	G	11: 6,299,390 (GRCm39)	N752S	probably damaging	Het
Or11i1	T	C	3: 106,729,503 (GRCm39)	D124G	probably damaging	Het
Or3a1b	A	T	11: 74,012,547 (GRCm39)	Q144L	possibly damaging	Het
Or5t9	A	G	2: 86,659,998 (GRCm39)	I301V	possibly damaging	Het
Or8b1	T	C	9: 38,399,673 (GRCm39)	M116T	probably benign	Het
Otof	C	A	5: 30,571,888 (GRCm39)	G171V	probably damaging	Het
Phtf2	A	T	5: 21,006,939 (GRCm39)	V208D	probably damaging	Het
Pkn1	T	A	8: 84,410,220 (GRCm39)	T340S	probably damaging	Het
Plcd4	C	T	1: 74,602,753 (GRCm39)	L668F	possibly damaging	Het
Plch1	C	T	3: 63,688,811 (GRCm39)	W131*	probably null	Het
Prss50	A	T	9: 110,690,367 (GRCm39)	D170V	probably damaging	Het
Ptprg	T	C	14: 12,237,118 (GRCm38)	V604A	probably damaging	Het
Rab33b	T	C	3: 51,400,826 (GRCm39)	V100A	probably damaging	Het
Rbm26	T	A	14: 105,368,971 (GRCm39)	D736V	probably damaging	Het
Rela	C	A	19: 5,696,992 (GRCm39)	P400T	probably benign	Het
Rpusd4	T	C	9: 35,179,334 (GRCm39)	L50P	probably damaging	Het
Scn10a	A	C	9: 119,456,181 (GRCm39)	Y1214D	probably damaging	Het
Sema3c	A	G	5: 17,877,430 (GRCm39)	E179G	probably damaging	Het
Skint5	T	A	4: 113,374,330 (GRCm39)	D1253V	unknown	Het
Sp4	G	T	12: 118,201,913 (GRCm39)	P771H	probably damaging	Het
Sphkap	T	A	1: 83,256,099 (GRCm39)	Y263F	probably damaging	Het
Ssbp1	G	A	6: 40,453,687 (GRCm39)	V78I	probably benign	Het
St3gal6	A	G	16: 58,306,769 (GRCm39)	I87T	probably benign	Het
Tango6	T	A	8: 107,545,129 (GRCm39)	D997E	probably benign	Het
Tpr	C	T	1: 150,321,639 (GRCm39)	P2265S	possibly damaging	Het
Ttc7b	A	T	12: 100,291,936 (GRCm39)	F212Y	probably damaging	Het
Ubc	A	G	5: 125,465,324 (GRCm39)	M1T	probably null	Het
Vill	G	C	9: 118,892,716 (GRCm39)	Q376H	probably benign	Het
Yes1	T	C	5: 32,809,030 (GRCm39)	I132T	possibly damaging	Het
Ythdc2	A	G	18: 44,993,444 (GRCm39)	T830A	probably benign	Het
Zbtb41	T	A	1: 139,358,044 (GRCm39)	F451I	possibly damaging	Het
Zfp995	C	T	17: 22,099,493 (GRCm39)	C247Y	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
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
R9058: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'- TGATCTGGTTCCTGCAGGAG -3'
(R):5'- CTGAGAACTCTGAGAACCTGTC -3'

Sequencing Primer
(F):5'- ACAGCCTGTTGTGCTGC -3'
(R):5'- ACCTGTCTCAAAACTTCAAAGATAAG -3'

Posted On

2018-04-02