Mutagenetix > Incidental Mutation

Incidental Mutation 'R7823:Hps1'

602042

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

045877-MU

Accession Numbers

Essential gene?

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

Stock #

R7823 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

42743544-42768417 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 42744146 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Methionine at position 681 (T681M)

Ref Sequence

ENSEMBL: ENSMUSP00000125226 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

possibly damaging
Transcript: ENSMUST00000026194
AA Change: T681M

PolyPhen 2 Score 0.580 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000026194
Gene: ENSMUSG00000025188
AA Change: T681M

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 benign
Transcript: ENSMUST00000160455
AA Change: T689M

PolyPhen 2 Score 0.251 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000125662
Gene: ENSMUSG00000025188
AA Change: T689M

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

possibly damaging
Transcript: ENSMUST00000162004
AA Change: T681M

PolyPhen 2 Score 0.580 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000125226
Gene: ENSMUSG00000025188
AA Change: T681M

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: 99.9%
10x: 99.6%
20x: 98.8%

Validation Efficiency

99% (68/69)

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: 73 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc4	A	G	14: 118,771,484 (GRCm39)	V869A	probably benign	Het
Alox15	C	A	11: 70,235,494 (GRCm39)	V623L	possibly damaging	Het
Angpt4	T	G	2: 151,753,286 (GRCm39)	L12R	unknown	Het
Cdh24	C	T	14: 54,874,875 (GRCm39)	A42T	probably damaging	Het
Cep250	T	A	2: 155,807,336 (GRCm39)	S234T	possibly damaging	Het
Clnk	T	A	5: 38,907,694 (GRCm39)	Y188F	probably benign	Het
Csmd2	A	T	4: 128,103,698 (GRCm39)	T306S		Het
Cyp2f2	G	A	7: 26,828,678 (GRCm39)	V183I	probably benign	Het
Dgka	T	A	10: 128,572,135 (GRCm39)	Y50F	probably benign	Het
Dgkh	C	T	14: 78,841,921 (GRCm39)	V434I	probably benign	Het
Epb41	A	G	4: 131,701,993 (GRCm39)		probably null	Het
Fam220a	A	G	5: 143,549,011 (GRCm39)	D141G	probably damaging	Het
Fbxo11	A	G	17: 88,300,610 (GRCm39)	L807S	probably damaging	Het
G530012D18Rik	G	C	1: 85,504,923 (GRCm39)		probably benign	Het
Ggt1	G	A	10: 75,410,175 (GRCm39)	V36M	possibly damaging	Het
Gjb2	T	C	14: 57,337,963 (GRCm39)	I82V	probably benign	Het
Gm7579	T	A	7: 141,766,307 (GRCm39)	C238S	unknown	Het
Iqck	T	C	7: 118,472,046 (GRCm39)	Y64H	probably damaging	Het
Ldlr	G	A	9: 21,653,602 (GRCm39)		probably null	Het
Macc1	A	C	12: 119,410,800 (GRCm39)	K523Q	probably damaging	Het
Mon2	A	T	10: 122,868,559 (GRCm39)	I498N	probably damaging	Het
Mphosph9	T	C	5: 124,442,319 (GRCm39)	E373G	probably damaging	Het
Mthfr	T	C	4: 148,135,944 (GRCm39)	I314T	probably benign	Het
Mtmr4	T	G	11: 87,503,015 (GRCm39)	I1023S	probably damaging	Het
Myo9a	T	A	9: 59,719,233 (GRCm39)	F507I	probably damaging	Het
Nlrp10	T	A	7: 108,523,468 (GRCm39)	M671L	probably benign	Het
Nt5c1a	T	C	4: 123,102,365 (GRCm39)	V97A	probably damaging	Het
Nxpe5	A	G	5: 138,237,844 (GRCm39)	R123G	possibly damaging	Het
Obscn	T	C	11: 58,998,766 (GRCm39)	S1369G	probably damaging	Het
Oga	A	G	19: 45,765,354 (GRCm39)	V151A	possibly damaging	Het
Or4a75	A	G	2: 89,447,613 (GRCm39)	*308Q	probably null	Het
Or52m2	A	G	7: 102,264,164 (GRCm39)	S11P	probably benign	Het
Or5b99	A	T	19: 12,976,781 (GRCm39)	I144F	probably damaging	Het
Or6c33	T	A	10: 129,854,136 (GRCm39)	M302K	probably benign	Het
Or6k2	A	G	1: 173,987,254 (GRCm39)	K305R	probably benign	Het
Or8b57	A	T	9: 40,003,644 (GRCm39)	V202E	probably damaging	Het
Pak6	G	A	2: 118,525,793 (GRCm39)	A618T	probably benign	Het
Pax7	T	A	4: 139,468,150 (GRCm39)	E489V	probably benign	Het
Phactr4	G	A	4: 132,088,930 (GRCm39)	R651*	probably null	Het
Pik3c2b	C	T	1: 133,030,043 (GRCm39)	R1435C	probably damaging	Het
Pla2g4c	A	T	7: 13,063,944 (GRCm39)	I68F	probably damaging	Het
Plppr1	A	G	4: 49,325,703 (GRCm39)	M300V	probably benign	Het
Ptgfrn	C	T	3: 100,950,725 (GRCm39)	V863I	probably damaging	Het
Rabep2	T	C	7: 126,037,893 (GRCm39)	S222P	probably damaging	Het
Ramacl	A	G	13: 67,055,351 (GRCm39)		probably benign	Het
Rbm20	A	T	19: 53,831,785 (GRCm39)	D673V	probably benign	Het
Rsf1	GCG	GCGACGGCGACG	7: 97,229,114 (GRCm39)		probably benign	Het
Scn4a	C	A	11: 106,233,334 (GRCm39)	A413S	probably damaging	Het
Scn9a	A	T	2: 66,314,135 (GRCm39)	M1850K	probably damaging	Het
Sh3tc2	T	A	18: 62,086,188 (GRCm39)	M1K	probably null	Het
Slc22a28	G	A	19: 8,041,890 (GRCm39)	T439I	probably benign	Het
Slc25a36	A	G	9: 96,966,444 (GRCm39)		probably null	Het
Smpd3	A	C	8: 106,982,254 (GRCm39)	C617G	probably benign	Het
Spata3	T	C	1: 85,949,781 (GRCm39)		probably benign	Het
Srp68	C	T	11: 116,156,265 (GRCm39)	R159Q	probably damaging	Het
Ssbp2	C	A	13: 91,790,448 (GRCm39)	L104I	possibly damaging	Het
St8sia3	T	A	18: 64,400,027 (GRCm39)	F7L	probably benign	Het
Stard9	T	C	2: 120,532,587 (GRCm39)	V2948A	probably damaging	Het
Syne4	A	G	7: 30,018,280 (GRCm39)	T341A	probably benign	Het
Tcf7l2	T	A	19: 55,731,521 (GRCm39)	D91E	possibly damaging	Het
Tekt5	T	A	16: 10,203,943 (GRCm39)	I236F	probably damaging	Het
Tlk2	T	C	11: 105,144,133 (GRCm39)	Y316H	probably damaging	Het
Tmem184b	C	T	15: 79,249,491 (GRCm39)	A326T	probably benign	Het
Tnks2	G	A	19: 36,829,954 (GRCm39)		probably null	Het
Trpc4	C	A	3: 54,209,640 (GRCm39)	Y668*	probably null	Het
Ttc9c	A	T	19: 8,793,286 (GRCm39)	F118Y	probably benign	Het
Ulk1	C	T	5: 110,946,780 (GRCm39)	C95Y	probably damaging	Het
Vars2	A	C	17: 35,970,028 (GRCm39)	L787R	probably damaging	Het
Vwa3a	T	C	7: 120,372,185 (GRCm39)	S254P	probably damaging	Het
Wdr81	T	C	11: 75,340,627 (GRCm39)	Y1250C	probably damaging	Het
Xirp2	A	T	2: 67,342,118 (GRCm39)	D1453V	probably damaging	Het
Zbtb38	A	T	9: 96,568,029 (GRCm39)	C1018*	probably null	Het
Zfp622	C	T	15: 25,984,709 (GRCm39)	T25M	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
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
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'- GGCCACAGAATCATGGCATC -3'
(R):5'- GGGACATTAGGTAGTGCCAC -3'

Sequencing Primer
(F):5'- TCCCTGCCCTTCAGAGAAG -3'
(R):5'- ATTAGGTAGTGCCACACCCTG -3'

Posted On

2019-12-03