Mutagenetix > Incidental Mutation

Incidental Mutation 'R1616:Hps1'

174316

Institutional Source

Beutler Lab

Gene Symbol

Hps1

Ensembl Gene

ENSMUSG00000025188

Gene Name

HPS1, biogenesis of lysosomal organelles complex 3 subunit 1

Synonyms

6030422N11Rik, Hermansky-Pudlak syndrome 1

MMRRC Submission

039653-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.214) question?

Stock #

R1616 (G1)

Quality Score

154

Status

Not validated

Chromosome

Chromosomal Location

42743544-42768417 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 42755624 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Tryptophan at position 201 (R201W)

Ref Sequence

ENSEMBL: ENSMUSP00000124209 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000026194] [ENSMUST00000069298] [ENSMUST00000160455] [ENSMUST00000162004] [ENSMUST00000162061]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000026194
AA Change: R201W

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000026194
Gene: ENSMUSG00000025188
AA Change: R201W

Domain	Start	End	E-Value	Type
coiled coil region	20	47	N/A	INTRINSIC
low complexity region	229	246	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000069298
AA Change: R201W

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000071069
Gene: ENSMUSG00000025188
AA Change: R201W

Domain	Start	End	E-Value	Type
coiled coil region	20	47	N/A	INTRINSIC
low complexity region	229	246	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000159974

Predicted Effect

probably damaging
Transcript: ENSMUST00000160455
AA Change: R201W

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000125662
Gene: ENSMUSG00000025188
AA Change: R201W

Domain	Start	End	E-Value	Type
coiled coil region	20	47	N/A	INTRINSIC
low complexity region	229	246	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000160621

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161761

Predicted Effect

probably damaging
Transcript: ENSMUST00000162004
AA Change: R201W

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000125226
Gene: ENSMUSG00000025188
AA Change: R201W

Domain	Start	End	E-Value	Type
coiled coil region	20	47	N/A	INTRINSIC
low complexity region	229	246	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000162061
AA Change: R201W

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000124209
Gene: ENSMUSG00000025188
AA Change: R201W

Domain	Start	End	E-Value	Type
coiled coil region	20	47	N/A	INTRINSIC
low complexity region	229	246	N/A	INTRINSIC

Coding Region Coverage

1x: 98.8%
3x: 97.8%
10x: 94.3%
20x: 85.3%

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 that may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. The encoded protein is a component of three different protein complexes termed biogenesis of lysosome-related organelles complex (BLOC)-3, BLOC4, and BLOC5. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 1. Alternative splicing results in multiple transcript variants. A pseudogene related to this gene is located on chromosome 22. [provided by RefSeq, Aug 2015]
PHENOTYPE: Homozygotes for spontaneous mutations exhibit hypopigmentation and increased bleeding time. Impaired natural killer cell function, reduced secretion of kidney lysosomal enzymes,and abnormal retinofugal neuronal projections characterize some alleles. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933406P04Rik	T	C	10: 20,187,087 (GRCm39)		probably benign	Het
A1cf	A	G	19: 31,912,175 (GRCm39)	E430G	probably damaging	Het
Aacs	T	A	5: 125,561,590 (GRCm39)		probably null	Het
Acot12	G	A	13: 91,920,886 (GRCm39)	V331I	probably benign	Het
Acp7	A	G	7: 28,310,503 (GRCm39)	W445R	probably damaging	Het
Actl11	C	A	9: 107,809,135 (GRCm39)	Q1153K	probably benign	Het
Actr8	A	G	14: 29,704,601 (GRCm39)	T34A	possibly damaging	Het
Ahnak	A	G	19: 8,986,351 (GRCm39)	D2545G	possibly damaging	Het
Ap5z1	A	G	5: 142,457,991 (GRCm39)	Y388C	probably benign	Het
Apol7a	C	T	15: 77,273,806 (GRCm39)	G219S	probably damaging	Het
Arid1b	T	A	17: 5,389,569 (GRCm39)	I1705N	probably damaging	Het
Bod1l	T	C	5: 41,966,058 (GRCm39)	Q2669R	probably benign	Het
Braf	A	T	6: 39,620,067 (GRCm39)	S504T	probably benign	Het
Cbl	A	T	9: 44,064,197 (GRCm39)	Y780N	probably damaging	Het
Cd86	T	C	16: 36,449,338 (GRCm39)	I20V	probably benign	Het
Cep290	T	G	10: 100,404,698 (GRCm39)	D2353E	probably benign	Het
Ckmt2	G	A	13: 92,007,328 (GRCm39)	R289C	probably benign	Het
Col3a1	T	C	1: 45,367,648 (GRCm39)		probably null	Het
Cyp4f16	T	A	17: 32,761,942 (GRCm39)	Y163*	probably null	Het
Dimt1	T	C	13: 107,089,958 (GRCm39)	V227A	possibly damaging	Het
Dnah6	A	T	6: 73,077,095 (GRCm39)	M2338K	probably benign	Het
Dock4	T	G	12: 40,719,044 (GRCm39)	I274S	probably damaging	Het
Enthd1	T	C	15: 80,336,586 (GRCm39)	D616G	probably damaging	Het
Fignl2	T	C	15: 100,951,997 (GRCm39)	E95G	probably damaging	Het
Foxn1	A	G	11: 78,249,692 (GRCm39)	M611T	probably benign	Het
Foxs1	T	C	2: 152,774,559 (GRCm39)	S165G	probably benign	Het
Fzd3	G	T	14: 65,472,956 (GRCm39)	Q271K	probably benign	Het
Hadhb	A	T	5: 30,371,713 (GRCm39)	I55F	probably damaging	Het
Hipk3	G	A	2: 104,264,090 (GRCm39)	Q824*	probably null	Het
Kif21b	T	C	1: 136,099,423 (GRCm39)	S1477P	probably damaging	Het
Kif26a	A	T	12: 112,123,680 (GRCm39)		probably null	Het
Krt90	T	C	15: 101,469,026 (GRCm39)	E172G	possibly damaging	Het
Lama4	T	G	10: 38,951,446 (GRCm39)	F1064V	probably damaging	Het
Leng9	A	G	7: 4,151,902 (GRCm39)	V258A	probably benign	Het
Lgi2	A	C	5: 52,703,980 (GRCm39)	V217G	probably benign	Het
Lpgat1	T	C	1: 191,495,741 (GRCm39)	I310T	possibly damaging	Het
Ltbp3	A	G	19: 5,796,995 (GRCm39)	Y374C	probably damaging	Het
Magi2	C	A	5: 20,814,324 (GRCm39)	T1075K	probably damaging	Het
Man2c1	T	C	9: 57,042,793 (GRCm39)	I221T	probably benign	Het
Mydgf	A	G	17: 56,486,415 (GRCm39)	M72T	possibly damaging	Het
Myo1b	T	C	1: 51,815,474 (GRCm39)	N624S	probably damaging	Het
Myo5c	T	A	9: 75,203,299 (GRCm39)	M1465K	probably damaging	Het
Nek4	A	T	14: 30,709,094 (GRCm39)	D716V	probably damaging	Het
Nfxl1	T	A	5: 72,686,380 (GRCm39)	Q607L	probably benign	Het
Nlrp9c	A	T	7: 26,083,862 (GRCm39)	D572E	probably benign	Het
Nop14	G	T	5: 34,807,757 (GRCm39)	Q402K	possibly damaging	Het
Npy5r	C	G	8: 67,134,052 (GRCm39)	C247S	probably damaging	Het
Nrap	T	A	19: 56,378,255 (GRCm39)	I19F	probably damaging	Het
Or4c102	A	G	2: 88,422,352 (GRCm39)	D68G	probably damaging	Het
Or51t4	T	A	7: 102,597,721 (GRCm39)	N16K	probably damaging	Het
Or6z3	T	G	7: 6,463,744 (GRCm39)	S79A	probably damaging	Het
Pcdh9	A	T	14: 94,124,405 (GRCm39)	Y588*	probably null	Het
Ppp1r12a	A	G	10: 108,096,728 (GRCm39)	E183G	probably damaging	Het
Ppp2r2b	T	A	18: 42,821,375 (GRCm39)	H261L	probably benign	Het
Ptch1	G	T	13: 63,687,656 (GRCm39)	T374K	possibly damaging	Het
Ptpn13	A	T	5: 103,713,103 (GRCm39)	N1742I	possibly damaging	Het
Rab33a	C	T	X: 47,608,521 (GRCm39)	S15L	probably benign	Het
Ralb	T	C	1: 119,405,744 (GRCm39)	Y75C	probably damaging	Het
Rassf7	T	A	7: 140,796,645 (GRCm39)	V2D	probably damaging	Het
Rbm10	A	G	X: 20,512,230 (GRCm39)	N397S	probably benign	Het
Rbm15	T	C	3: 107,238,197 (GRCm39)	T734A	probably benign	Het
Rbm8a	G	T	3: 96,539,046 (GRCm39)		probably benign	Het
Rock2	T	C	12: 17,022,986 (GRCm39)	I1095T	probably benign	Het
Rxfp3	T	A	15: 11,036,389 (GRCm39)	T328S	probably damaging	Het
Sec31a	T	A	5: 100,534,054 (GRCm39)	K505N	possibly damaging	Het
Selenof	A	G	3: 144,302,642 (GRCm39)	*122W	probably null	Het
Sh3pxd2b	T	C	11: 32,331,441 (GRCm39)	M55T	possibly damaging	Het
Slc15a2	T	C	16: 36,574,843 (GRCm39)	D522G	probably benign	Het
Slc2a1	T	C	4: 118,993,503 (GRCm39)	F447L	probably damaging	Het
Slc45a2	T	A	15: 11,022,214 (GRCm39)	C319S	probably null	Het
Smad4	T	C	18: 73,773,333 (GRCm39)	D551G	probably benign	Het
Smarcc2	A	G	10: 128,318,662 (GRCm39)	Y648C	probably damaging	Het
Snrnp40	C	G	4: 130,271,836 (GRCm39)		probably null	Het
Stab2	A	T	10: 86,721,582 (GRCm39)		probably null	Het
Tanc1	A	G	2: 59,615,731 (GRCm39)	D246G	probably damaging	Het
Tekt3	T	G	11: 62,978,024 (GRCm39)		probably null	Het
Them5	G	A	3: 94,253,567 (GRCm39)		probably null	Het
Tlr4	T	A	4: 66,757,717 (GRCm39)	F170Y	probably damaging	Het
Tmem214	T	G	5: 31,028,907 (GRCm39)	Y165*	probably null	Het
Tmem94	T	C	11: 115,686,971 (GRCm39)		probably null	Het
Tom1l1	A	G	11: 90,547,177 (GRCm39)	L301S	possibly damaging	Het
Trpm3	A	G	19: 22,960,076 (GRCm39)	E1237G	probably damaging	Het
Ube2d1	C	A	10: 71,092,523 (GRCm39)	C107F	probably damaging	Het
Ugt3a1	C	T	15: 9,306,330 (GRCm39)	R160*	probably null	Het
Vcan	G	A	13: 89,853,782 (GRCm39)	P393S	probably damaging	Het
Virma	T	C	4: 11,544,954 (GRCm39)	F1638L	probably damaging	Het
Vmn1r31	G	A	6: 58,449,043 (GRCm39)	T274I	probably damaging	Het
Xylt2	C	T	11: 94,559,035 (GRCm39)	S445N	probably damaging	Het
Zfp457	A	G	13: 67,444,375 (GRCm39)	F43L	possibly damaging	Het
Zfp879	T	A	11: 50,723,473 (GRCm39)	M455L	probably benign	Het

Other mutations in Hps1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02116:Hps1	APN	19	42,759,568 (GRCm39)	nonsense	probably null
IGL02327:Hps1	APN	19	42,744,784 (GRCm39)	unclassified	probably benign
IGL02488:Hps1	APN	19	42,746,227 (GRCm39)	unclassified	probably benign
IGL03161:Hps1	APN	19	42,755,710 (GRCm39)	missense	probably damaging	1.00
R0127:Hps1	UTSW	19	42,759,550 (GRCm39)	splice site	probably benign
R0134:Hps1	UTSW	19	42,754,619 (GRCm39)	missense	probably damaging	0.98
R0234:Hps1	UTSW	19	42,750,992 (GRCm39)	missense	probably damaging	1.00
R0234:Hps1	UTSW	19	42,750,992 (GRCm39)	missense	probably damaging	1.00
R0394:Hps1	UTSW	19	42,759,338 (GRCm39)	splice site	probably null
R1435:Hps1	UTSW	19	42,750,714 (GRCm39)	missense	probably benign	0.04
R1537:Hps1	UTSW	19	42,748,143 (GRCm39)	critical splice donor site	probably null
R1860:Hps1	UTSW	19	42,750,888 (GRCm39)	missense	probably damaging	1.00
R2014:Hps1	UTSW	19	42,750,951 (GRCm39)	missense	probably benign	0.00
R3424:Hps1	UTSW	19	42,748,952 (GRCm39)	missense	possibly damaging	0.75
R4472:Hps1	UTSW	19	42,750,935 (GRCm39)	missense	probably damaging	1.00
R5476:Hps1	UTSW	19	42,758,041 (GRCm39)	splice site	probably null
R6054:Hps1	UTSW	19	42,759,217 (GRCm39)	missense	probably damaging	0.96
R6275:Hps1	UTSW	19	42,758,046 (GRCm39)	missense	probably null	1.00
R6807:Hps1	UTSW	19	42,759,217 (GRCm39)	missense	possibly damaging	0.60
R6916:Hps1	UTSW	19	42,755,164 (GRCm39)
R7332:Hps1	UTSW	19	42,766,351 (GRCm39)	splice site	probably null
R7487:Hps1	UTSW	19	42,744,700 (GRCm39)	missense	probably damaging	1.00
R7504:Hps1	UTSW	19	42,755,159 (GRCm39)	missense	probably benign	0.00
R7823:Hps1	UTSW	19	42,744,146 (GRCm39)	missense	possibly damaging	0.58
R7955:Hps1	UTSW	19	42,759,221 (GRCm39)	missense	probably damaging	0.99
R8198:Hps1	UTSW	19	42,755,659 (GRCm39)	missense	probably benign	0.05
R8819:Hps1	UTSW	19	42,759,648 (GRCm39)	missense	probably benign	0.06
R9688:Hps1	UTSW	19	42,755,147 (GRCm39)	missense	probably benign
Z1176:Hps1	UTSW	19	42,755,125 (GRCm39)	missense	probably null	0.00
Z1177:Hps1	UTSW	19	42,754,657 (GRCm39)	critical splice acceptor site	probably null
Z1177:Hps1	UTSW	19	42,748,270 (GRCm39)	missense	probably damaging	1.00
Z1177:Hps1	UTSW	19	42,744,135 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- TATCATTAGGAAGGCTCCAGCGGC -3'
(R):5'- TGTTCCTGCTTGGCACATACTACAG -3'

Sequencing Primer
(F):5'- GACTCCAAGTGTTGGTTAGAAC -3'
(R):5'- GGCACATACTACAGTTGATTTTTCC -3'

Posted On

2014-04-24