Mutagenetix > Incidental Mutation

Incidental Mutation 'R0234:Hps1'

59082

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

038475-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.294) question?

Stock #

R0234 (G1)

Quality Score

141

Status

Not validated

Chromosome

Chromosomal Location

42743544-42768417 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 42750992 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 336 (E336G)

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: E336G

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

SMART Domains

Protein: ENSMUSP00000026194
Gene: ENSMUSG00000025188
AA Change: E336G

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: E344G

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

SMART Domains

Protein: ENSMUSP00000071069
Gene: ENSMUSG00000025188
AA Change: E344G

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: E344G

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

SMART Domains

Protein: ENSMUSP00000125662
Gene: ENSMUSG00000025188
AA Change: E344G

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

probably benign
Transcript: ENSMUST00000161252

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000161761

Predicted Effect

probably damaging
Transcript: ENSMUST00000162004
AA Change: E336G

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

SMART Domains

Protein: ENSMUSP00000125226
Gene: ENSMUSG00000025188
AA Change: E336G

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: E336G

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

SMART Domains

Protein: ENSMUSP00000124209
Gene: ENSMUSG00000025188
AA Change: E336G

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: 99.4%
3x: 98.9%
10x: 97.5%
20x: 95.1%

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: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A3galt2	A	G	4: 128,660,941 (GRCm39)	R197G	possibly damaging	Het
Acacb	A	T	5: 114,347,878 (GRCm39)	H983L	probably damaging	Het
Adal	T	A	2: 120,978,798 (GRCm39)	D139E	probably benign	Het
Adam6b	G	A	12: 113,454,230 (GRCm39)	R349H	probably damaging	Het
Agap1	A	G	1: 89,598,934 (GRCm39)	K331E	probably damaging	Het
Alyref	T	C	11: 120,489,133 (GRCm39)	D11G	probably damaging	Het
B3gat1	A	G	9: 26,667,377 (GRCm39)	E203G	probably damaging	Het
Bsn	T	C	9: 107,993,595 (GRCm39)	E719G	possibly damaging	Het
Cap2	G	C	13: 46,791,498 (GRCm39)		probably null	Het
Ccni	A	G	5: 93,350,186 (GRCm39)	V31A	probably benign	Het
Cdcp3	T	A	7: 130,796,032 (GRCm39)		probably null	Het
Cfap54	A	T	10: 92,735,022 (GRCm39)	L2343*	probably null	Het
Clns1a	T	A	7: 97,363,239 (GRCm39)	Y204N	possibly damaging	Het
Cox11	C	T	11: 90,535,326 (GRCm39)	T259I	probably damaging	Het
Dsp	A	G	13: 38,371,869 (GRCm39)	N940S	probably benign	Het
Erbb2	T	C	11: 98,327,265 (GRCm39)	V1181A	probably benign	Het
Exoc4	T	C	6: 33,839,022 (GRCm39)	V686A	possibly damaging	Het
F830045P16Rik	A	G	2: 129,305,384 (GRCm39)	V330A	possibly damaging	Het
Fbf1	A	C	11: 116,045,860 (GRCm39)	F245V	probably damaging	Het
Fut10	T	A	8: 31,726,225 (GRCm39)	F327I	probably damaging	Het
Galnt1	C	T	18: 24,387,690 (GRCm39)	P144S	probably damaging	Het
Garin4	T	C	1: 190,895,105 (GRCm39)	S513G	probably benign	Het
Ghrhr	A	T	6: 55,356,171 (GRCm39)	D88V	possibly damaging	Het
Greb1l	T	A	18: 10,560,331 (GRCm39)	C1864S	probably damaging	Het
H1f2	T	C	13: 23,923,106 (GRCm39)	I92T	probably benign	Het
Ibsp	GGAAGAAGAAGAAGAAGA	GGAAGAAGAAGAAGA	5: 104,457,935 (GRCm39)		probably benign	Het
Irgc	C	A	7: 24,132,753 (GRCm39)	E21D	possibly damaging	Het
Itsn1	A	T	16: 91,625,168 (GRCm39)	R590*	probably null	Het
Katnip	T	C	7: 125,394,557 (GRCm39)	V211A	probably benign	Het
Lmln	T	C	16: 32,886,694 (GRCm39)	V67A	probably damaging	Het
Lsm14a	T	C	7: 34,065,042 (GRCm39)	Q179R	probably damaging	Het
Ltbr	A	C	6: 125,289,836 (GRCm39)	D119E	probably benign	Het
Mrc1	A	G	2: 14,284,705 (GRCm39)	T565A	possibly damaging	Het
Muc6	A	C	7: 141,235,939 (GRCm39)	N473K	possibly damaging	Het
Myocd	A	T	11: 65,078,066 (GRCm39)	D448E	probably benign	Het
Neil2	T	A	14: 63,420,975 (GRCm39)	I239F	probably damaging	Het
Npnt	A	G	3: 132,620,175 (GRCm39)	F123S	possibly damaging	Het
Or2g25	T	A	17: 37,970,997 (GRCm39)	I76F	probably damaging	Het
Or4f15	T	C	2: 111,813,645 (GRCm39)	Y258C	probably damaging	Het
Or52x1	C	A	7: 104,852,821 (GRCm39)	C243F	probably damaging	Het
Or56a5	T	C	7: 104,793,281 (GRCm39)	D73G	probably damaging	Het
Or5d37	T	A	2: 87,923,366 (GRCm39)	R305*	probably null	Het
Or8d1b	A	C	9: 38,887,547 (GRCm39)		probably null	Het
Or9i2	C	T	19: 13,815,902 (GRCm39)	V212M	possibly damaging	Het
Pcnx3	T	C	19: 5,722,646 (GRCm39)	T941A	probably benign	Het
Phldb3	G	A	7: 24,312,004 (GRCm39)	R106Q	probably benign	Het
Pitrm1	C	A	13: 6,625,115 (GRCm39)	Y864*	probably null	Het
Plcb4	T	C	2: 135,823,995 (GRCm39)	I844T	probably benign	Het
Plekhg5	T	C	4: 152,196,676 (GRCm39)	C695R	probably damaging	Het
Ppp1r3b	T	A	8: 35,851,655 (GRCm39)	F165I	probably damaging	Het
Prr5	T	A	15: 84,587,322 (GRCm39)	F357L	probably damaging	Het
Rasgrf1	A	T	9: 89,891,419 (GRCm39)	I1046F	probably damaging	Het
Rbm15b	T	C	9: 106,762,563 (GRCm39)	Y535C	probably damaging	Het
Rbp3	A	T	14: 33,677,858 (GRCm39)	E602V	probably damaging	Het
Rimklb	T	C	6: 122,433,292 (GRCm39)	N343S	probably benign	Het
Rrp12	A	G	19: 41,860,199 (GRCm39)	L1008P	probably damaging	Het
Sec63	C	T	10: 42,674,794 (GRCm39)	R226C	probably damaging	Het
Sirpa	T	C	2: 129,457,388 (GRCm39)	V154A	probably damaging	Het
Slc13a5	C	G	11: 72,141,626 (GRCm39)	V405L	probably damaging	Het
Slc17a3	C	T	13: 24,039,841 (GRCm39)	S293F	probably damaging	Het
Slc22a23	G	A	13: 34,367,244 (GRCm39)	T588I	probably damaging	Het
Slc22a27	C	A	19: 7,904,156 (GRCm39)		probably benign	Het
Slc4a4	A	C	5: 89,304,195 (GRCm39)	H502P	possibly damaging	Het
Slc5a5	A	T	8: 71,342,277 (GRCm39)	M258K	probably damaging	Het
Spry4	A	G	18: 38,723,142 (GRCm39)	I207T	possibly damaging	Het
Stk11ip	A	G	1: 75,505,711 (GRCm39)	D460G	possibly damaging	Het
Syn3	T	A	10: 86,284,750 (GRCm39)	I117F	possibly damaging	Het
Tead4	C	T	6: 128,220,365 (GRCm39)	A224T	probably damaging	Het
Tmtc3	A	T	10: 100,286,184 (GRCm39)	N546K	probably benign	Het
Tnn	T	A	1: 159,916,036 (GRCm39)	H1227L	probably damaging	Het
Tor2a	G	A	2: 32,648,716 (GRCm39)	G62D	probably damaging	Het
Trf	T	C	9: 103,104,078 (GRCm39)		probably null	Het
Ubr5	T	C	15: 37,968,737 (GRCm39)	T2727A	probably damaging	Het
Vmn2r27	T	A	6: 124,208,578 (GRCm39)	T56S	probably benign	Het
Wipf3	T	G	6: 54,473,486 (GRCm39)	L458R	probably damaging	Het
Zfp236	T	C	18: 82,648,119 (GRCm39)	K966R	probably damaging	Het
Zfp27	T	A	7: 29,593,532 (GRCm39)	H811L	possibly damaging	Het
Zfp366	A	G	13: 99,370,768 (GRCm39)	H496R	probably damaging	Het
Zfp467	A	T	6: 48,415,689 (GRCm39)	V321E	probably damaging	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
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
R1616:Hps1	UTSW	19	42,755,624 (GRCm39)	missense	probably damaging	1.00
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'- TCAGCAGCACCATGTTGATGCC -3'
(R):5'- ATTGGACAGAACAGCCCAGCAG -3'

Sequencing Primer
(F):5'- TGTTGGCATCCAGGAAGATC -3'
(R):5'- TGGCTATCTAAGCAAGCCTG -3'

Posted On

2013-07-11