Mutagenetix > Incidental Mutation

Incidental Mutation 'R4739:Hps3'

359492

Institutional Source

Beutler Lab

Gene Symbol

Hps3

Ensembl Gene

ENSMUSG00000027615

Gene Name

HPS3, biogenesis of lysosomal organelles complex 2 subunit 1

Synonyms

Hermansky-Pudlak syndrome 3

MMRRC Submission

042025-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.076) question?

Stock #

R4739 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

20050109-20089478 bp(-) (GRCm39)

Type of Mutation

critical splice acceptor site

DNA Base Change (assembly)

C to T at 20084574 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000103957 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000012580] [ENSMUST00000108321]

AlphaFold

Q91VB4

Predicted Effect

probably damaging
Transcript: ENSMUST00000012580
AA Change: E205K

PolyPhen 2 Score 0.996 (Sensitivity: 0.55; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000012580
Gene: ENSMUSG00000027615
AA Change: E205K

Domain	Start	End	E-Value	Type
Pfam:HPS3_N	3	212	2.8e-74	PFAM
Pfam:HPS3_Mid	255	640	1.3e-167	PFAM
Pfam:HPS3_C	649	1000	1.8e-175	PFAM

Predicted Effect

probably null
Transcript: ENSMUST00000108321

SMART Domains

Protein: ENSMUSP00000103957
Gene: ENSMUSG00000027615

Domain	Start	End	E-Value	Type
Pfam:HPS3_N	3	87	5.6e-25	PFAM
Pfam:HPS3_Mid	121	508	4.2e-161	PFAM
Pfam:HPS3_C	517	870	9.2e-199	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124808

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126644

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000130171

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000133094

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137408

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000151752

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000155121

Meta Mutation Damage Score

0.2757

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.9%
20x: 94.5%

Validation Efficiency

96% (102/106)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein containing a potential clathrin-binding motif, consensus dileucine signals, and tyrosine-based sorting signals for targeting to vesicles of lysosomal lineage. The encoded protein may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 3. [provided by RefSeq, Apr 2015]
PHENOTYPE: Homozygotes for spontaneous null mutations exhibit hypopigmentation and prolonged bleeding associated with a platelet defect. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 98 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1600012P17Rik	C	T	1: 158,796,904 (GRCm39)		noncoding transcript	Het
2300002M23Rik	A	G	17: 35,878,403 (GRCm39)		probably benign	Het
Aadat	T	C	8: 60,993,140 (GRCm39)	V360A	probably benign	Het
Abcc5	T	A	16: 20,218,376 (GRCm39)	D283V	probably damaging	Het
Abraxas1	T	A	5: 100,959,886 (GRCm39)	K155N	probably damaging	Het
Acot3	T	C	12: 84,105,364 (GRCm39)	I277T	probably benign	Het
Ankrd45	G	A	1: 160,982,960 (GRCm39)	C157Y	probably damaging	Het
Apol10a	C	T	15: 77,372,841 (GRCm39)	T159I	possibly damaging	Het
Arhgef11	G	A	3: 87,605,306 (GRCm39)	V214M	possibly damaging	Het
Ash1l	A	C	3: 88,890,152 (GRCm39)	N677T	probably benign	Het
Atg13	A	G	2: 91,515,040 (GRCm39)	S254P	probably damaging	Het
Atg16l2	A	G	7: 100,946,385 (GRCm39)	L129P	probably damaging	Het
Avl9	T	A	6: 56,703,294 (GRCm39)	V120D	probably damaging	Het
Castor1	A	G	11: 4,169,004 (GRCm39)	E57G	possibly damaging	Het
Cc2d1b	T	C	4: 108,485,239 (GRCm39)	V527A	probably benign	Het
Ccnl1	A	G	3: 65,854,092 (GRCm39)		probably benign	Het
Cenpl	T	A	1: 160,910,837 (GRCm39)	D261E	probably damaging	Het
Cep192	T	G	18: 67,984,803 (GRCm39)	I1604M	probably benign	Het
Cep95	A	G	11: 106,706,560 (GRCm39)	I573V	probably benign	Het
Cfap100	A	G	6: 90,389,825 (GRCm39)		probably null	Het
Ciao3	A	T	17: 26,000,283 (GRCm39)	H322L	probably damaging	Het
Cmc1	T	A	9: 117,904,245 (GRCm39)	M49L	probably benign	Het
Cyfip2	G	T	11: 46,170,820 (GRCm39)	N176K	probably damaging	Het
Cyp2w1	T	C	5: 139,342,430 (GRCm39)	F408L	probably damaging	Het
D630045J12Rik	G	A	6: 38,172,971 (GRCm39)	S399F	possibly damaging	Het
Dcbld2	T	A	16: 58,281,339 (GRCm39)	L528Q	probably damaging	Het
Dip2b	T	C	15: 100,105,658 (GRCm39)	V1138A	probably damaging	Het
Dip2c	T	A	13: 9,583,375 (GRCm39)	L119Q	probably damaging	Het
Dnah3	T	C	7: 119,677,169 (GRCm39)	D444G	possibly damaging	Het
Dsg1c	A	T	18: 20,408,246 (GRCm39)	N432Y	possibly damaging	Het
Dst	T	A	1: 34,230,228 (GRCm39)	I2785N	probably benign	Het
Dynap	A	T	18: 70,374,296 (GRCm39)	Y77N	possibly damaging	Het
Eif4g3	T	C	4: 137,910,510 (GRCm39)	L1330P	possibly damaging	Het
Eif4g3	T	A	4: 137,925,408 (GRCm39)	S1584T	probably benign	Het
Enpp1	A	T	10: 24,555,146 (GRCm39)	C67S	probably null	Het
Enpp5	C	T	17: 44,392,027 (GRCm39)	T152I	probably damaging	Het
Erbb4	T	C	1: 68,383,059 (GRCm39)	M313V	probably damaging	Het
Erc2	T	G	14: 27,498,838 (GRCm39)	L238R	probably damaging	Het
Eya3	T	A	4: 132,448,698 (GRCm39)		probably benign	Het
Farp1	T	C	14: 121,476,199 (GRCm39)	F339L	probably damaging	Het
Fsip2	A	C	2: 82,805,697 (GRCm39)	D672A	possibly damaging	Het
Gap43	G	T	16: 42,112,581 (GRCm39)	P60Q	probably benign	Het
Gpr37l1	T	A	1: 135,094,783 (GRCm39)	I154F	probably damaging	Het
Greb1	A	G	12: 16,746,329 (GRCm39)	S1314P	probably damaging	Het
Hectd4	A	T	5: 121,486,505 (GRCm39)	M3167L	probably benign	Het
Hps5	A	G	7: 46,436,013 (GRCm39)	C178R	probably benign	Het
Hspg2	T	A	4: 137,297,384 (GRCm39)		probably benign	Het
Impdh2-ps	A	G	8: 100,757,839 (GRCm39)		noncoding transcript	Het
Josd2	T	A	7: 44,120,678 (GRCm39)	N138K	probably damaging	Het
Mtmr6	T	G	14: 60,529,546 (GRCm39)	M315R	probably damaging	Het
Mtrf1	G	A	14: 79,650,520 (GRCm39)	V323M	probably damaging	Het
Myo16	G	T	8: 10,423,527 (GRCm39)	G288W	probably damaging	Het
Myo18a	T	C	11: 77,714,149 (GRCm39)	Y748H	probably damaging	Het
Nek1	A	T	8: 61,551,545 (GRCm39)	N853I	probably benign	Het
Npnt	T	G	3: 132,610,452 (GRCm39)	T272P	possibly damaging	Het
Obi1	C	T	14: 104,747,819 (GRCm39)	D43N	probably damaging	Het
Or2ag1b	C	A	7: 106,288,351 (GRCm39)	E196*	probably null	Het
Or2b6	T	A	13: 21,823,340 (GRCm39)	M118L	possibly damaging	Het
Or2y17	G	A	11: 49,232,148 (GRCm39)	G263D	probably benign	Het
Or51e1	T	A	7: 102,359,378 (GRCm39)	I304N	probably damaging	Het
Or52n2c	G	A	7: 104,574,017 (GRCm39)	T318I	possibly damaging	Het
Or5a1	A	G	19: 12,097,234 (GRCm39)	Y269H	possibly damaging	Het
Pappa2	T	C	1: 158,784,582 (GRCm39)	R143G	probably benign	Het
Pappa2	T	G	1: 158,784,572 (GRCm39)	D146A	probably damaging	Het
Pcsk9	C	T	4: 106,304,353 (GRCm39)	G496R	probably damaging	Het
Pes1	A	G	11: 3,914,058 (GRCm39)	K8E	probably damaging	Het
Phlpp2	G	A	8: 110,667,052 (GRCm39)	G1194S	probably damaging	Het
Pkn1	A	C	8: 84,398,378 (GRCm39)	V763G	probably damaging	Het
Pkp2	C	A	16: 16,048,588 (GRCm39)	A331E	probably damaging	Het
Plb1	T	A	5: 32,507,023 (GRCm39)		probably null	Het
Plxna1	A	T	6: 89,309,657 (GRCm39)		probably null	Het
Polq	C	T	16: 36,862,109 (GRCm39)	T264M	probably damaging	Het
Prkag3	T	C	1: 74,779,864 (GRCm39)	*490W	probably null	Het
Prl2c1	T	C	13: 28,041,661 (GRCm39)	C228R	probably damaging	Het
Pus7l	T	C	15: 94,438,591 (GRCm39)	S85G	probably benign	Het
Rfc3	A	C	5: 151,568,241 (GRCm39)		probably benign	Het
Riox2	A	G	16: 59,309,732 (GRCm39)	N362S	probably benign	Het
Scaper	A	T	9: 55,650,932 (GRCm39)	D904E	probably damaging	Het
Scn11a	T	C	9: 119,583,627 (GRCm39)	M1663V	probably benign	Het
Slc13a3	A	T	2: 165,272,209 (GRCm39)	I278N	possibly damaging	Het
Slc22a7	T	C	17: 46,745,923 (GRCm39)	E278G	probably damaging	Het
Snrnp48	T	A	13: 38,393,893 (GRCm39)	M66K	probably damaging	Het
Styk1	T	G	6: 131,277,429 (GRCm39)	E404A	probably damaging	Het
Synj1	T	A	16: 90,752,307 (GRCm39)	H1016L	probably benign	Het
Tbc1d8	G	A	1: 39,441,959 (GRCm39)	T211I	possibly damaging	Het
Tjp2	T	C	19: 24,097,475 (GRCm39)		probably null	Het
Tmem87a	A	G	2: 120,190,518 (GRCm39)		probably null	Het
Trappc9	T	G	15: 72,808,909 (GRCm39)	Y718S	probably damaging	Het
Ttn	A	T	2: 76,641,587 (GRCm39)	L5176Q	possibly damaging	Het
Ubqlnl	C	T	7: 103,798,925 (GRCm39)	V191M	probably benign	Het
Ugt2a3	C	T	5: 87,475,054 (GRCm39)	G397R	probably damaging	Het
Wdr33	T	A	18: 32,019,139 (GRCm39)	M454K	probably benign	Het
Wdtc1	G	T	4: 133,029,110 (GRCm39)	N325K	possibly damaging	Het
Whrn	T	C	4: 63,336,402 (GRCm39)	H720R	probably damaging	Het
Xirp2	A	T	2: 67,349,609 (GRCm39)	D3268V	probably damaging	Het
Zc3h7a	A	T	16: 10,959,573 (GRCm39)	H793Q	probably damaging	Het
Zfp518b	C	T	5: 38,831,841 (GRCm39)	A55T	possibly damaging	Het
Zmynd8	G	A	2: 165,647,249 (GRCm39)	T901M	probably damaging	Het

Other mutations in Hps3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00545:Hps3	APN	3	20,073,971 (GRCm39)	missense	possibly damaging	0.94
IGL00846:Hps3	APN	3	20,079,956 (GRCm39)	missense	probably benign	0.00
IGL01320:Hps3	APN	3	20,084,633 (GRCm39)	missense	probably benign	0.12
IGL01364:Hps3	APN	3	20,057,469 (GRCm39)	missense	possibly damaging	0.58
IGL01751:Hps3	APN	3	20,065,130 (GRCm39)	missense	probably damaging	1.00
IGL01843:Hps3	APN	3	20,083,165 (GRCm39)	missense	probably benign	0.05
IGL02294:Hps3	APN	3	20,068,212 (GRCm39)	missense	probably damaging	1.00
IGL02581:Hps3	APN	3	20,057,385 (GRCm39)	intron	probably benign
Blue	UTSW	3	20,084,960 (GRCm39)	missense	probably damaging	1.00
earl_grey	UTSW	3	20,017,173 (GRCm38)	intron	probably benign
gandalf	UTSW	3	20,066,960 (GRCm39)	nonsense	probably null
pam_gray	UTSW	3	20,017,173 (GRCm38)	intron	probably benign
R0107:Hps3	UTSW	3	20,084,960 (GRCm39)	missense	probably damaging	1.00
R0245:Hps3	UTSW	3	20,066,960 (GRCm39)	nonsense	probably null
R0421:Hps3	UTSW	3	20,083,480 (GRCm39)	missense	probably benign	0.00
R0524:Hps3	UTSW	3	20,066,940 (GRCm39)	missense	probably damaging	1.00
R0763:Hps3	UTSW	3	20,057,443 (GRCm39)	missense	probably damaging	1.00
R1795:Hps3	UTSW	3	20,066,859 (GRCm39)	critical splice donor site	probably null
R1864:Hps3	UTSW	3	20,074,123 (GRCm39)	critical splice acceptor site	probably null
R2029:Hps3	UTSW	3	20,084,691 (GRCm39)	missense	probably benign	0.01
R2101:Hps3	UTSW	3	20,066,947 (GRCm39)	missense	possibly damaging	0.95
R2221:Hps3	UTSW	3	20,056,527 (GRCm39)	missense	probably benign
R2268:Hps3	UTSW	3	20,067,099 (GRCm39)	splice site	probably benign
R2520:Hps3	UTSW	3	20,083,194 (GRCm39)	missense	probably damaging	1.00
R3809:Hps3	UTSW	3	20,072,976 (GRCm39)	missense	probably damaging	1.00
R3888:Hps3	UTSW	3	20,057,387 (GRCm39)	critical splice donor site	probably null
R3942:Hps3	UTSW	3	20,051,103 (GRCm39)	missense	probably damaging	1.00
R4022:Hps3	UTSW	3	20,089,425 (GRCm39)	missense	possibly damaging	0.69
R4156:Hps3	UTSW	3	20,083,393 (GRCm39)	missense	probably damaging	1.00
R4823:Hps3	UTSW	3	20,066,890 (GRCm39)	missense	probably benign	0.03
R4912:Hps3	UTSW	3	20,068,337 (GRCm39)	missense	probably damaging	1.00
R5307:Hps3	UTSW	3	20,066,865 (GRCm39)	missense	possibly damaging	0.89
R5859:Hps3	UTSW	3	20,063,034 (GRCm39)	missense	probably benign	0.02
R6140:Hps3	UTSW	3	20,051,151 (GRCm39)	missense	probably damaging	1.00
R6183:Hps3	UTSW	3	20,063,032 (GRCm39)	missense	probably benign	0.04
R6971:Hps3	UTSW	3	20,065,699 (GRCm39)	missense	probably damaging	1.00
R6981:Hps3	UTSW	3	20,076,984 (GRCm39)	missense	probably damaging	1.00
R7120:Hps3	UTSW	3	20,065,705 (GRCm39)	missense	probably damaging	1.00
R7146:Hps3	UTSW	3	20,063,050 (GRCm39)	missense	probably damaging	1.00
R7223:Hps3	UTSW	3	20,084,583 (GRCm39)	missense	probably benign	0.05
R7448:Hps3	UTSW	3	20,089,329 (GRCm39)	missense	probably damaging	0.99
R7452:Hps3	UTSW	3	20,065,592 (GRCm39)	missense	probably damaging	1.00
R7560:Hps3	UTSW	3	20,084,616 (GRCm39)	missense	probably benign	0.29
R7659:Hps3	UTSW	3	20,076,978 (GRCm39)	nonsense	probably null
R7769:Hps3	UTSW	3	20,072,972 (GRCm39)	splice site	probably null
R8050:Hps3	UTSW	3	20,057,492 (GRCm39)	missense	probably benign
R8242:Hps3	UTSW	3	20,068,290 (GRCm39)	missense	possibly damaging	0.59
R8802:Hps3	UTSW	3	20,074,070 (GRCm39)	missense	probably damaging	1.00
R8822:Hps3	UTSW	3	20,057,391 (GRCm39)	missense	probably benign
R8945:Hps3	UTSW	3	20,068,224 (GRCm39)	missense	probably damaging	0.99
R9111:Hps3	UTSW	3	20,084,575 (GRCm39)	critical splice acceptor site	probably null
R9131:Hps3	UTSW	3	20,083,350 (GRCm39)	missense	probably damaging	0.98
R9645:Hps3	UTSW	3	20,084,831 (GRCm39)	missense	probably benign	0.01
R9728:Hps3	UTSW	3	20,065,128 (GRCm39)	missense	probably benign	0.06
X0021:Hps3	UTSW	3	20,084,913 (GRCm39)	missense	probably benign	0.14
X0066:Hps3	UTSW	3	20,070,152 (GRCm39)	missense	probably damaging	1.00
Z1177:Hps3	UTSW	3	20,063,065 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GGCATGCCACTATAGATACCAGG -3'
(R):5'- CAATGTCTGAGGCCCCTTTG -3'

Sequencing Primer
(F):5'- TCCGCCTCTTTCAATGGA -3'
(R):5'- GAGGCCCCTTTGTGCTTTTCG -3'

Posted On

2015-11-11