Mutagenetix > Incidental Mutation

Incidental Mutation 'R6807:Hps1'

533637

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

044920-MU

Accession Numbers

Essential gene?

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

Stock #

R6807 (G1)

Quality Score

219.009

Status

Validated

Chromosome

Chromosomal Location

42743544-42768417 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 42759217 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Alanine at position 125 (V125A)

Ref Sequence

ENSEMBL: ENSMUSP00000071069 (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
AA Change: V125A

PolyPhen 2 Score 0.186 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000026194
Gene: ENSMUSG00000025188
AA Change: V125A

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

Predicted Effect

possibly damaging
Transcript: ENSMUST00000069298
AA Change: V125A

PolyPhen 2 Score 0.601 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000071069
Gene: ENSMUSG00000025188
AA Change: V125A

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: V125A

PolyPhen 2 Score 0.092 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000125662
Gene: ENSMUSG00000025188
AA Change: V125A

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
AA Change: V125A

PolyPhen 2 Score 0.186 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000125226
Gene: ENSMUSG00000025188
AA Change: V125A

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
AA Change: V125A

PolyPhen 2 Score 0.401 (Sensitivity: 0.89; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000124209
Gene: ENSMUSG00000025188
AA Change: V125A

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

0.1065

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.7%
20x: 96.9%

Validation Efficiency

100% (72/72)

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: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acaca	A	G	11: 84,282,356 (GRCm39)	T2158A	probably benign	Het
Apeh	G	A	9: 107,969,878 (GRCm39)	H186Y	probably damaging	Het
Apol7a	T	C	15: 77,277,520 (GRCm39)		probably null	Het
Bicdl1	C	T	5: 115,810,202 (GRCm39)		probably null	Het
Bop1	T	A	15: 76,339,183 (GRCm39)	Q362L	probably damaging	Het
C4b	T	C	17: 34,949,930 (GRCm39)	D1418G	probably benign	Het
Cdh23	A	G	10: 60,214,650 (GRCm39)	V1455A	possibly damaging	Het
Cecr2	T	G	6: 120,711,503 (GRCm39)		probably null	Het
Cer1	T	C	4: 82,801,052 (GRCm39)	S204G	probably benign	Het
Cers3	G	C	7: 66,413,968 (GRCm39)	W15C	probably damaging	Het
Csn1s2a	A	T	5: 87,929,731 (GRCm39)	H110L	probably benign	Het
Dnah10	T	G	5: 124,867,064 (GRCm39)		probably null	Het
Dync2h1	T	C	9: 7,041,718 (GRCm39)	N3315S	probably benign	Het
Dynlrb2	T	C	8: 117,234,299 (GRCm39)	M21T	probably benign	Het
Emilin1	T	A	5: 31,072,871 (GRCm39)	F103I	probably benign	Het
Esrra	T	A	19: 6,889,142 (GRCm39)	M416L	probably benign	Het
Etaa1	C	A	11: 17,902,680 (GRCm39)	V86L	probably benign	Het
Extl3	A	G	14: 65,314,211 (GRCm39)	S324P	probably damaging	Het
Fam90a1a	T	C	8: 22,453,368 (GRCm39)	V241A	probably benign	Het
Fat4	C	A	3: 39,036,589 (GRCm39)	Q3414K	probably benign	Het
Gpr162	C	T	6: 124,838,164 (GRCm39)	R162H	probably damaging	Het
Gpr21	T	A	2: 37,407,974 (GRCm39)	Y173*	probably null	Het
Gprc6a	G	A	10: 51,502,841 (GRCm39)	Q341*	probably null	Het
Herc2	T	A	7: 55,814,670 (GRCm39)	S2674R	probably damaging	Het
Hnrnpdl	A	T	5: 100,186,995 (GRCm39)	H9Q	probably null	Het
Iba57	G	T	11: 59,049,440 (GRCm39)	P243H	probably damaging	Het
Incenp	G	T	19: 9,855,120 (GRCm39)	A597E	unknown	Het
Kat6a	T	A	8: 23,430,384 (GRCm39)	M1913K	unknown	Het
Klb	G	A	5: 65,536,877 (GRCm39)	V736M	probably damaging	Het
Krt33a	T	A	11: 99,903,209 (GRCm39)	T278S	possibly damaging	Het
Krt73	T	G	15: 101,704,842 (GRCm39)	E348A	probably damaging	Het
Lig3	T	A	11: 82,674,577 (GRCm39)	D134E	probably benign	Het
Limd2	T	C	11: 106,049,771 (GRCm39)	T73A	probably benign	Het
Lrpprc	A	G	17: 85,056,531 (GRCm39)	S787P	possibly damaging	Het
Macf1	A	G	4: 123,268,208 (GRCm39)	M6735T	probably damaging	Het
Mapkbp1	C	A	2: 119,851,640 (GRCm39)	Q861K	probably damaging	Het
Mc4r	T	A	18: 66,992,927 (GRCm39)	N62I	probably damaging	Het
Metap1d	G	A	2: 71,341,858 (GRCm39)	V151I	probably damaging	Het
Nek2	T	C	1: 191,554,729 (GRCm39)	V147A	probably damaging	Het
Nlrp1b	A	T	11: 71,108,530 (GRCm39)	W324R	probably damaging	Het
Nol4l	G	T	2: 153,325,746 (GRCm39)	S113*	probably null	Het
Oc90	T	A	15: 65,761,463 (GRCm39)	D185V	probably damaging	Het
Or2a52	T	C	6: 43,144,172 (GRCm39)	F60S	probably damaging	Het
Or2v1	G	A	11: 49,025,805 (GRCm39)	R262K	probably damaging	Het
Or4a71	G	A	2: 89,357,932 (GRCm39)	T274M	probably damaging	Het
Or5m13	A	T	2: 85,748,382 (GRCm39)	T38S	possibly damaging	Het
Or5p51	T	A	7: 107,444,797 (GRCm39)	T48S	possibly damaging	Het
Or8g50	A	T	9: 39,648,914 (GRCm39)	K268*	probably null	Het
Pcdha8	A	G	18: 37,127,401 (GRCm39)	T628A	probably damaging	Het
Pcsk5	A	T	19: 17,549,986 (GRCm39)		probably null	Het
Pdgfrb	T	C	18: 61,211,721 (GRCm39)		probably null	Het
Pgm3	A	T	9: 86,438,555 (GRCm39)		probably null	Het
Pin1rt1	T	A	2: 104,545,063 (GRCm39)	Y23F	probably benign	Het
Poli	T	A	18: 70,663,222 (GRCm39)		probably null	Het
Pom121	C	A	5: 135,409,978 (GRCm39)		probably benign	Het
Ppp2r5c	A	G	12: 110,535,456 (GRCm39)	D407G	possibly damaging	Het
Pramel28	A	G	4: 143,691,581 (GRCm39)	S381P	probably damaging	Het
Rgs12	A	G	5: 35,180,515 (GRCm39)	D116G	probably null	Het
Serpina3b	A	T	12: 104,099,251 (GRCm39)	E255D	probably benign	Het
Sft2d1rt	T	C	11: 45,942,859 (GRCm39)	Q88R	probably damaging	Het
Slc46a1	A	G	11: 78,357,790 (GRCm39)	H281R	probably damaging	Het
Spata6	T	C	4: 111,642,012 (GRCm39)	I294T	probably benign	Het
Srgap1	T	A	10: 121,664,631 (GRCm39)		probably null	Het
Stag1	C	T	9: 100,826,903 (GRCm39)	R957C	probably damaging	Het
Stk35	G	A	2: 129,643,573 (GRCm39)	E186K	probably damaging	Het
Tenm4	G	A	7: 96,202,703 (GRCm39)	R106H	probably benign	Het
Tenm4	G	A	7: 96,544,478 (GRCm39)	V2165I	probably damaging	Het
Tmem53	T	C	4: 117,125,528 (GRCm39)	S207P	probably benign	Het
Ugt2a3	A	G	5: 87,484,617 (GRCm39)	F136L	probably benign	Het
Unc13d	T	C	11: 115,957,577 (GRCm39)	K795E	probably damaging	Het
Zbtb11	C	A	16: 55,810,865 (GRCm39)	T341K	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
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
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'- TACACAGCTGGGTGCACTAG -3'
(R):5'- CAGAAACTGCAGTGTATCAGAGTC -3'

Sequencing Primer
(F):5'- CACTAGGGAGGGTGCCTAAGTTC -3'
(R):5'- CTTACTCTCTGAGACCTGGAAGG -3'

Posted On

2018-09-12