Mutagenetix > Incidental Mutation

Incidental Mutation 'R7487:Hps1'

580297

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

045561-MU

Accession Numbers

Essential gene?

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

Stock #

R7487 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

42743544-42768417 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 42744700 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 658 (Y658C)

Ref Sequence

ENSEMBL: ENSMUSP00000125662 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000026194] [ENSMUST00000069298] [ENSMUST00000076505] [ENSMUST00000160455] [ENSMUST00000162004] [ENSMUST00000162061]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000026194
AA Change: Y650C

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

SMART Domains

Protein: ENSMUSP00000026194
Gene: ENSMUSG00000025188
AA Change: Y650C

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

SMART Domains

Protein: ENSMUSP00000071069
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: ENSMUST00000076505

SMART Domains

Protein: ENSMUSP00000075825
Gene: ENSMUSG00000060224

Domain	Start	End	E-Value	Type
Pfam:NAD_binding_8	39	97	3.5e-11	PFAM
Pfam:Amino_oxidase	46	423	2.7e-15	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000160455
AA Change: Y658C

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

SMART Domains

Protein: ENSMUSP00000125662
Gene: ENSMUSG00000025188
AA Change: Y658C

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: ENSMUST00000161252

Predicted Effect

probably damaging
Transcript: ENSMUST00000162004
AA Change: Y650C

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

SMART Domains

Protein: ENSMUSP00000125226
Gene: ENSMUSG00000025188
AA Change: Y650C

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

Meta Mutation Damage Score

0.7460

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.3%

Validation Efficiency

100% (89/89)

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: 87 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	A	T	3: 137,772,629 (GRCm39)	D606V	probably damaging	Het
1700009N14Rik	T	A	4: 39,450,929 (GRCm39)	V45E	probably damaging	Het
2510009E07Rik	C	T	16: 21,472,479 (GRCm39)	V74M	probably damaging	Het
Abca2	C	T	2: 25,327,915 (GRCm39)	T739M	probably benign	Het
Abra	T	C	15: 41,732,949 (GRCm39)	E39G	probably damaging	Het
Adam34	A	T	8: 44,104,191 (GRCm39)	C485S	probably damaging	Het
Add2	G	T	6: 86,070,432 (GRCm39)	V175F	possibly damaging	Het
Alk	T	A	17: 72,256,893 (GRCm39)	K655N	probably benign	Het
Ap3m1	A	G	14: 21,088,107 (GRCm39)	V317A	probably benign	Het
Astn1	A	G	1: 158,438,352 (GRCm39)		probably null	Het
Atm	A	T	9: 53,435,654 (GRCm39)	Y219N	probably benign	Het
Cep128	C	T	12: 90,966,404 (GRCm39)	A1068T	probably benign	Het
Cep20	T	C	16: 14,128,968 (GRCm39)	D85G	probably benign	Het
Cnksr3	T	C	10: 7,085,097 (GRCm39)	Q250R	probably benign	Het
Cst7	A	G	2: 150,419,624 (GRCm39)	T97A	probably benign	Het
Ctps1	G	A	4: 120,415,997 (GRCm39)	L209F	probably damaging	Het
Cyp2d10	A	T	15: 82,288,793 (GRCm39)	F230I	probably benign	Het
Daam2	T	C	17: 49,793,510 (GRCm39)	N336D	probably benign	Het
Dchs2	T	C	3: 83,263,613 (GRCm39)	S3294P	probably damaging	Het
Dhx36	G	T	3: 62,391,623 (GRCm39)	N574K	possibly damaging	Het
Dock10	G	T	1: 80,562,765 (GRCm39)	Q533K	probably benign	Het
Dync2h1	A	G	9: 7,132,041 (GRCm39)	S1589P	probably benign	Het
Enpp3	T	A	10: 24,681,821 (GRCm39)	Y295F	probably benign	Het
Esrrg	T	A	1: 187,878,620 (GRCm39)	Y234N	probably benign	Het
Fadd	A	C	7: 144,134,462 (GRCm39)	V141G	probably damaging	Het
Fam114a2	C	T	11: 57,404,515 (GRCm39)	G83D	probably damaging	Het
Fam170b	T	A	14: 32,557,776 (GRCm39)	C204S	probably damaging	Het
Fam186a	T	A	15: 99,840,017 (GRCm39)	I2076F	possibly damaging	Het
Fdxacb1	G	A	9: 50,681,519 (GRCm39)	V147I	possibly damaging	Het
Frem2	C	A	3: 53,561,970 (GRCm39)	V846F	probably benign	Het
Fry	G	A	5: 150,338,039 (GRCm39)	S1449N	possibly damaging	Het
Gucy1b2	A	G	14: 62,685,672 (GRCm39)	F98L	probably damaging	Het
Igkv3-9	T	A	6: 70,565,506 (GRCm39)	L35Q	probably damaging	Het
Irx2	A	G	13: 72,778,739 (GRCm39)	Y101C	probably damaging	Het
Kcnj11	G	T	7: 45,748,265 (GRCm39)	R353S	probably benign	Het
Kyat3	C	T	3: 142,431,955 (GRCm39)	Q228*	probably null	Het
Lama3	T	A	18: 12,552,294 (GRCm39)	D415E	probably benign	Het
Lcn3	G	A	2: 25,656,174 (GRCm39)		probably null	Het
Lin7b	T	C	7: 45,019,364 (GRCm39)	E68G	possibly damaging	Het
Lmbr1	T	A	5: 29,459,262 (GRCm39)	K379M	probably benign	Het
Lrig1	A	G	6: 94,583,099 (GRCm39)	S1006P	probably benign	Het
Lrrc37a	T	G	11: 103,389,045 (GRCm39)	T2127P	unknown	Het
Map4	A	G	9: 109,856,783 (GRCm39)	D151G	probably damaging	Het
Marchf1	A	T	8: 66,908,726 (GRCm39)	T149S	probably benign	Het
Msh4	A	T	3: 153,569,147 (GRCm39)	F809I	probably damaging	Het
Muc16	G	A	9: 18,496,095 (GRCm39)	P6699S	possibly damaging	Het
Mxi1	A	T	19: 53,360,088 (GRCm39)	D270V	probably damaging	Het
Myh6	A	T	14: 55,190,953 (GRCm39)	C907*	probably null	Het
Myo18b	T	C	5: 112,982,299 (GRCm39)	R1145G	possibly damaging	Het
Nkx2-6	A	C	14: 69,409,389 (GRCm39)	N47H	probably benign	Het
Nol7	G	A	13: 43,552,076 (GRCm39)	A66T	probably damaging	Het
Ntrk3	T	C	7: 77,900,461 (GRCm39)	N626S	probably damaging	Het
Nwd1	A	G	8: 73,393,266 (GRCm39)	Y77C	unknown	Het
Or12d17	G	T	17: 37,777,457 (GRCm39)	R120L	probably damaging	Het
Or12k5	A	C	2: 36,894,786 (GRCm39)	V280G	probably damaging	Het
Or8c14-ps1	A	G	9: 38,101,356 (GRCm39)	S112G	probably damaging	Het
Or8j3b	A	T	2: 86,205,475 (GRCm39)	Y94N	probably damaging	Het
Or9s23	G	A	1: 92,501,517 (GRCm39)	G208D	possibly damaging	Het
Otop3	A	G	11: 115,235,826 (GRCm39)	D486G	probably benign	Het
Pak1ip1	A	G	13: 41,162,731 (GRCm39)	K178R	probably benign	Het
Pcsk1	G	A	13: 75,259,002 (GRCm39)	G259S	probably benign	Het
Pde6a	A	G	18: 61,383,031 (GRCm39)	D338G	probably damaging	Het
Pias4	A	T	10: 80,999,806 (GRCm39)	D82E	probably benign	Het
Plekha5	C	A	6: 140,516,059 (GRCm39)	Q771K	probably benign	Het
Plekhh3	C	A	11: 101,056,405 (GRCm39)	A397S	possibly damaging	Het
Prg4	G	T	1: 150,331,656 (GRCm39)	T339N	unknown	Het
Prss22	A	T	17: 24,216,971 (GRCm39)	I3N	probably damaging	Het
Rasgrp1	T	C	2: 117,118,424 (GRCm39)	I522V	probably damaging	Het
Rspo2	T	C	15: 42,941,510 (GRCm39)	T138A	probably benign	Het
Rtcb	C	T	10: 85,789,333 (GRCm39)	G70S	probably benign	Het
Selenov	A	T	7: 27,989,803 (GRCm39)	S234T	probably damaging	Het
Shtn1	T	C	19: 58,992,292 (GRCm39)	T429A	probably damaging	Het
Slc4a3	G	T	1: 75,530,021 (GRCm39)	R622L	probably benign	Het
Smc2	T	C	4: 52,478,448 (GRCm39)	I1015T	probably damaging	Het
Spata9	G	T	13: 76,115,959 (GRCm39)	V3F	possibly damaging	Het
Tlr4	T	C	4: 66,842,659 (GRCm39)	I105T	probably benign	Het
Trav6d-4	A	T	14: 52,991,096 (GRCm39)	Y47F	possibly damaging	Het
Ttn	A	T	2: 76,657,377 (GRCm39)	I12450N	unknown	Het
Umad1	G	T	6: 8,270,560 (GRCm39)	A21S	probably damaging	Het
Unc5a	G	A	13: 55,144,362 (GRCm39)	R229H	probably benign	Het
Vmn1r216	A	T	13: 23,284,030 (GRCm39)	M238L	probably damaging	Het
Vps16	T	A	2: 130,280,977 (GRCm39)	C255*	probably null	Het
Wdr89	A	G	12: 75,679,388 (GRCm39)	F289L	probably benign	Het
Zfp180	A	T	7: 23,805,525 (GRCm39)	H648L	probably damaging	Het
Zfp735	A	G	11: 73,581,154 (GRCm39)	K64E	possibly damaging	Het
Zfp990	G	A	4: 145,264,157 (GRCm39)	C385Y	probably damaging	Het
Zswim3	G	T	2: 164,662,135 (GRCm39)	S205I	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
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
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'- AGCAGGGCGTGTTTCGAATG -3'
(R):5'- GGCCCCATTCCATTGTGTAAG -3'

Sequencing Primer
(F):5'- GCGTGTTTCGAATGCTTCTTC -3'
(R):5'- TCTCCTTCCCAGGCAAGG -3'

Posted On

2019-10-07