Mutagenetix > Incidental Mutation

Incidental Mutation 'R9688:Hps1'

729017

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

Accession Numbers

Essential gene?

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

Stock #

R9688 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

42743544-42768417 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 42755147 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Glycine at position 265 (V265G)

Ref Sequence

ENSEMBL: ENSMUSP00000125662 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000026194

SMART Domains

Protein: ENSMUSP00000026194
Gene: ENSMUSG00000025188

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 benign
Transcript: ENSMUST00000069298
AA Change: V265G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000071069
Gene: ENSMUSG00000025188
AA Change: V265G

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 benign
Transcript: ENSMUST00000160455
AA Change: V265G

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000125662
Gene: ENSMUSG00000025188
AA Change: V265G

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 benign
Transcript: ENSMUST00000162004

SMART Domains

Protein: ENSMUSP00000125226
Gene: ENSMUSG00000025188

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 benign
Transcript: ENSMUST00000162061

SMART Domains

Protein: ENSMUSP00000124209
Gene: ENSMUSG00000025188

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: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

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: 69 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700093K21Rik	A	G	11: 23,469,067 (GRCm39)		probably null	Het
Abca2	G	C	2: 25,324,459 (GRCm39)	A272P	possibly damaging	Het
Adarb1	T	A	10: 77,147,099 (GRCm39)	D479V	probably damaging	Het
Amz2	T	C	11: 109,320,765 (GRCm39)	F162S	probably damaging	Het
Ano4	A	T	10: 89,180,506 (GRCm39)	M1K	probably null	Het
Antxr1	G	A	6: 87,114,334 (GRCm39)	R478C	probably damaging	Het
Apobr	T	C	7: 126,186,663 (GRCm39)	S725P	probably benign	Het
Arap2	A	T	5: 62,872,109 (GRCm39)	D506E	probably damaging	Het
Ash1l	T	G	3: 88,892,024 (GRCm39)	I1301S	probably damaging	Het
Camk1g	T	A	1: 193,031,029 (GRCm39)	R305W	probably damaging	Het
Ces2g	A	T	8: 105,691,304 (GRCm39)	I147F	probably benign	Het
Cfap61	T	C	2: 145,878,758 (GRCm39)	F505L	probably damaging	Het
Cndp1	G	C	18: 84,655,982 (GRCm39)	N62K	probably benign	Het
Cog6	G	T	3: 52,916,528 (GRCm39)	Q214K	probably benign	Het
Depdc5	T	A	5: 33,055,276 (GRCm39)	Y226*	probably null	Het
Elp5	T	A	11: 69,861,425 (GRCm39)	I185F	probably damaging	Het
Ercc6	A	C	14: 32,297,755 (GRCm39)	H1334P	probably benign	Het
Ern1	T	C	11: 106,349,836 (GRCm39)	T27A	possibly damaging	Het
Esf1	A	T	2: 140,010,095 (GRCm39)	D80E	probably damaging	Het
Evpl	T	C	11: 116,124,986 (GRCm39)	K159E	probably damaging	Het
Gbx1	T	C	5: 24,731,510 (GRCm39)	Y102C	probably damaging	Het
Gjd2	A	G	2: 113,842,109 (GRCm39)	S123P	probably benign	Het
H2-M11	A	G	17: 36,859,054 (GRCm39)	Y198C	probably damaging	Het
Ifna16	C	A	4: 88,594,874 (GRCm39)	E74*	probably null	Het
Inca1	C	T	11: 70,579,810 (GRCm39)		probably null	Het
Jag2	A	G	12: 112,872,564 (GRCm39)	V1230A	probably benign	Het
Jam3	G	A	9: 27,010,204 (GRCm39)	T260M	probably benign	Het
Klhl5	A	T	5: 65,321,930 (GRCm39)	D652V	probably damaging	Het
L3mbtl1	A	T	2: 162,790,697 (GRCm39)	I81L	possibly damaging	Het
Lgalsl	C	T	11: 20,779,442 (GRCm39)	A68T	probably benign	Het
Map3k14	T	A	11: 103,130,059 (GRCm39)	D286V	possibly damaging	Het
Mdn1	A	G	4: 32,745,590 (GRCm39)	I4083V	probably damaging	Het
Ms4a5	T	C	19: 11,254,058 (GRCm39)	I136M	possibly damaging	Het
Mtcl3	T	C	10: 29,072,691 (GRCm39)	V661A	possibly damaging	Het
Naa16	A	T	14: 79,573,309 (GRCm39)	Y820*	probably null	Het
Nbea	G	T	3: 55,557,165 (GRCm39)	N2537K	probably benign	Het
Ncapd3	A	G	9: 26,967,349 (GRCm39)	S562G	probably benign	Het
Or5t5	A	C	2: 86,617,005 (GRCm39)	K310N	probably damaging	Het
Or6c1b	C	A	10: 129,272,967 (GRCm39)	C95*	probably null	Het
Pcdhac2	A	G	18: 37,277,628 (GRCm39)	S203G	probably benign	Het
Pds5a	A	T	5: 65,812,196 (GRCm39)	F309I	probably benign	Het
Pdzd8	G	A	19: 59,333,683 (GRCm39)	L113F	probably benign	Het
Pex12	T	C	11: 83,189,257 (GRCm39)	Y4C	possibly damaging	Het
Ppfibp2	A	G	7: 107,318,448 (GRCm39)	D332G	probably benign	Het
Psg23	A	T	7: 18,344,547 (GRCm39)	W303R	probably damaging	Het
Pyy	T	A	11: 101,998,099 (GRCm39)	D27V	probably damaging	Het
Rc3h1	A	G	1: 160,770,234 (GRCm39)	Q302R	probably damaging	Het
Rhoh	A	G	5: 66,049,656 (GRCm39)		probably benign	Het
Samd9l	A	G	6: 3,377,087 (GRCm39)	M58T	probably damaging	Het
Scaf11	A	C	15: 96,313,808 (GRCm39)	H1324Q	probably damaging	Het
Serinc2	C	A	4: 130,158,133 (GRCm39)	A105S	probably damaging	Het
Setx	A	T	2: 29,036,328 (GRCm39)	S938C	probably damaging	Het
Sgo2a	A	T	1: 58,056,737 (GRCm39)	T974S	probably damaging	Het
Sh3rf1	T	C	8: 61,679,348 (GRCm39)	V130A	probably benign	Het
Slc43a2	T	C	11: 75,434,112 (GRCm39)	F97L	probably damaging	Het
Slc9a9	C	A	9: 95,111,107 (GRCm39)	Q642K	probably benign	Het
Sox6	G	T	7: 115,076,225 (GRCm39)	D804E	probably benign	Het
Tbx15	A	T	3: 99,233,708 (GRCm39)	R290S	possibly damaging	Het
Tent4a	A	G	13: 69,655,199 (GRCm39)	L425P	probably damaging	Het
Terf2	A	G	8: 107,821,543 (GRCm39)	S176P	probably damaging	Het
Ttc6	A	T	12: 57,720,602 (GRCm39)	H956L	possibly damaging	Het
Tti2	T	C	8: 31,644,279 (GRCm39)	V292A	probably damaging	Het
Vmn1r29	A	T	6: 58,284,739 (GRCm39)	E153V	probably benign	Het
Vmn1r55	G	T	7: 5,149,669 (GRCm39)	H251Q	probably benign	Het
Yeats4	T	C	10: 117,051,586 (GRCm39)	T224A	probably benign	Het
Yipf4	T	A	17: 74,806,078 (GRCm39)	F239Y	probably benign	Het
Zan	T	C	5: 137,466,717 (GRCm39)	D380G	probably damaging	Het
Zbtb9	T	C	17: 27,193,894 (GRCm39)	F433S	probably damaging	Het
Zic5	T	C	14: 122,701,435 (GRCm39)	K432R	unknown	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
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
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'- ATGATCCGCATGAGTGACCC -3'
(R):5'- GTTTTAGTTGCATGCTCACAGC -3'

Sequencing Primer
(F):5'- ATGAGTGACCCTGTCCCCAG -3'
(R):5'- TCATCCTTCTGGTGCAG -3'

Posted On

2022-10-06