Mutagenetix > Incidental Mutation

Incidental Mutation 'R7452:Hps3'

577782

Institutional Source

Beutler Lab

Gene Symbol

Hps3

Ensembl Gene

ENSMUSG00000027615

Gene Name

HPS3, biogenesis of lysosomal organelles complex 2 subunit 1

Synonyms

coa, cocoa

MMRRC Submission

045526-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.079) question?

Stock #

R7452 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

19995945-20035315 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 20011428 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 749 (N749K)

Ref Sequence

ENSEMBL: ENSMUSP00000012580 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000003714] [ENSMUST00000012580] [ENSMUST00000108321] [ENSMUST00000108328] [ENSMUST00000108329]

AlphaFold

Q91VB4

Predicted Effect

probably benign
Transcript: ENSMUST00000003714

SMART Domains

Protein: ENSMUSP00000003714
Gene: ENSMUSG00000003617

Domain	Start	End	E-Value	Type
Pfam:Cu-oxidase_3	90	203	5.1e-8	PFAM
Pfam:Cu-oxidase	220	357	9.6e-11	PFAM
Pfam:Cu-oxidase_2	280	357	1.1e-7	PFAM
Pfam:Cu-oxidase_3	444	556	1.4e-7	PFAM
Blast:FA58C	598	673	3e-6	BLAST
Pfam:Cu-oxidase_3	789	897	2.3e-9	PFAM
Pfam:Cu-oxidase_2	927	1054	8.3e-18	PFAM
low complexity region	1067	1078	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000012580
AA Change: N749K

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

SMART Domains

Protein: ENSMUSP00000012580
Gene: ENSMUSG00000027615
AA Change: N749K

Domain	Start	End	E-Value	Type
Pfam:HPS3_N	3	212	2.8e-74	PFAM
Pfam:HPS3_Mid	255	640	1.3e-167	PFAM
Pfam:HPS3_C	649	1000	1.8e-175	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000108321
AA Change: N617K

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

SMART Domains

Protein: ENSMUSP00000103957
Gene: ENSMUSG00000027615
AA Change: N617K

Domain	Start	End	E-Value	Type
Pfam:HPS3_N	3	87	5.6e-25	PFAM
Pfam:HPS3_Mid	121	508	4.2e-161	PFAM
Pfam:HPS3_C	517	870	9.2e-199	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000108328

SMART Domains

Protein: ENSMUSP00000103964
Gene: ENSMUSG00000003617

Domain	Start	End	E-Value	Type
Pfam:Cu-oxidase_3	90	203	5.1e-8	PFAM
Pfam:Cu-oxidase	220	357	9.6e-11	PFAM
Pfam:Cu-oxidase_2	280	357	1.1e-7	PFAM
Pfam:Cu-oxidase_3	444	556	1.4e-7	PFAM
Blast:FA58C	598	673	3e-6	BLAST
Pfam:Cu-oxidase_3	789	897	2.3e-9	PFAM
Pfam:Cu-oxidase_2	927	1054	8.3e-18	PFAM
low complexity region	1067	1078	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000108329

SMART Domains

Protein: ENSMUSP00000103965
Gene: ENSMUSG00000003617

Domain	Start	End	E-Value	Type
Pfam:Cu-oxidase_3	89	203	8.7e-8	PFAM
Pfam:Cu-oxidase	220	357	7.8e-12	PFAM
Pfam:Cu-oxidase_2	242	356	2.1e-7	PFAM
Pfam:Cu-oxidase_3	445	555	4.4e-7	PFAM
Blast:FA58C	599	674	3e-6	BLAST
Pfam:Cu-oxidase_3	793	898	6.1e-9	PFAM
Pfam:Cu-oxidase_2	931	1055	5.2e-18	PFAM
low complexity region	1068	1079	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 98.8%

Validation Efficiency

100% (75/75)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein containing a potential clathrin-binding motif, consensus dileucine signals, and tyrosine-based sorting signals for targeting to vesicles of lysosomal lineage. The encoded protein may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 3. [provided by RefSeq, Apr 2015]
PHENOTYPE: Homozygotes for spontaneous null mutations exhibit hypopigmentation and prolonged bleeding associated with a platelet defect. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4931406P16Rik	A	G	7: 34,245,671	S595P	probably benign	Het
A2m	C	A	6: 121,641,332	Q195K	probably damaging	Het
Abcg4	C	T	9: 44,279,600	G249R	probably damaging	Het
Actn1	T	C	12: 80,183,602	T293A	probably benign	Het
Adamts5	T	A	16: 85,877,981	T432S	probably benign	Het
Adh5	A	G	3: 138,454,745	T347A	probably benign	Het
Agbl5	A	G	5: 30,893,391	D432G	probably damaging	Het
Ank3	A	G	10: 69,899,051	T797A	possibly damaging	Het
Aoc1	T	G	6: 48,908,790	V743G	probably benign	Het
Arap2	A	T	5: 62,676,549	S858R	probably benign	Het
Arid1a	A	C	4: 133,753,127	V162G	possibly damaging	Het
Armc9	A	G	1: 86,213,092	D588G	possibly damaging	Het
Art3	A	G	5: 92,392,680	Y94C	probably damaging	Het
Btaf1	T	A	19: 36,969,127	D444E	probably damaging	Het
Cav2	A	G	6: 17,282,076	H111R	probably damaging	Het
Ccdc148	A	G	2: 58,827,584	L469P	probably damaging	Het
Celsr2	T	A	3: 108,413,090	E802V	possibly damaging	Het
Cfap57	T	C	4: 118,595,784	D574G	probably damaging	Het
Chd7	A	C	4: 8,854,731	D2024A	probably benign	Het
Corin	T	A	5: 72,435,247	D269V	possibly damaging	Het
Cyp4a12a	A	T	4: 115,327,598	I359F	probably damaging	Het
Defb6	T	C	8: 19,225,524	L7P	probably damaging	Het
Dnah7c	A	T	1: 46,647,036	M1817L	possibly damaging	Het
Dock3	A	G	9: 106,989,465	F682S	probably damaging	Het
Enpep	T	A	3: 129,271,403	Y879F	possibly damaging	Het
Enpp2	T	C	15: 54,866,736	N462S	probably damaging	Het
Ephb3	T	C	16: 21,217,357		probably null	Het
F7	C	T	8: 13,035,215	H414Y	probably benign	Het
Fbn1	T	C	2: 125,505,455	H50R	possibly damaging	Het
Fig4	T	C	10: 41,240,637	D586G	possibly damaging	Het
Fryl	A	G	5: 73,023,988	L2825P	probably damaging	Het
Gal3st2	T	A	1: 93,872,518	H30Q	possibly damaging	Het
Gm12886	G	A	4: 121,417,474	Q70*	probably null	Het
Gm8104	A	C	14: 43,110,044	T190P	probably benign	Het
Hr	A	G	14: 70,571,486	T1101A	probably damaging	Het
Htatip2	T	A	7: 49,773,326	S210T	probably benign	Het
Ift80	T	C	3: 68,994,282		probably null	Het
Iqgap1	A	G	7: 80,760,829	V212A	possibly damaging	Het
Itih5	A	G	2: 10,238,796	E448G	probably damaging	Het
Kdm5b	T	C	1: 134,624,948	C1221R	probably damaging	Het
Lrrc72	T	C	12: 36,212,693	Y52C	probably benign	Het
Map1b	C	T	13: 99,508,140	R85Q	probably damaging	Het
Mdn1	T	C	4: 32,739,030	I3617T	possibly damaging	Het
Mtpap	T	A	18: 4,379,705	H98Q	possibly damaging	Het
Nemf	A	T	12: 69,337,959		probably null	Het
Neto1	A	T	18: 86,498,931	I458L	probably benign	Het
Nfam1	T	A	15: 83,014,962	M128L	probably benign	Het
Olfr1279	A	G	2: 111,306,921	T239A	probably damaging	Het
Olfr1383	C	A	11: 49,524,381	H219Q	probably benign	Het
Olfr501-ps1	C	T	7: 108,508,593	T179I	unknown	Het
Olfr914	A	T	9: 38,607,088	I208F	probably benign	Het
P2ry14	C	T	3: 59,116,045	G7D	probably benign	Het
Pde11a	A	G	2: 76,136,414	Y564H	probably damaging	Het
Pex5l	C	T	3: 33,004,318	V262I	probably benign	Het
Poli	A	G	18: 70,508,978	V717A	possibly damaging	Het
Prdm14	A	T	1: 13,125,559	W93R	probably damaging	Het
Rbm46	T	C	3: 82,864,121	M396V	probably benign	Het
Rcor2	T	C	19: 7,271,222	V212A	probably benign	Het
Rcor3	C	A	1: 192,137,876	G8V	probably damaging	Het
Rhox4d	G	A	X: 37,518,992	G191E	unknown	Het
Rictor	C	T	15: 6,772,154	S441L	probably benign	Het
Skp2	T	A	15: 9,113,832	Q366L	probably damaging	Het
Slc13a3	A	T	2: 165,427,114	S312T	probably benign	Het
Sstr1	T	C	12: 58,213,356	L255P	probably damaging	Het
Steap3	T	C	1: 120,227,855	E458G	possibly damaging	Het
Sv2b	T	A	7: 75,147,713	D311V	probably damaging	Het
Tmem132b	A	G	5: 125,638,268	D347G	probably benign	Het
Tmem161a	A	G	8: 70,177,488	D108G	probably damaging	Het
Traf5	T	A	1: 191,999,831	I47F		Het
Trp53bp2	C	T	1: 182,446,568	Q95*	probably null	Het
Ttn	G	T	2: 76,877,143		probably null	Het
Usf3	T	C	16: 44,220,034	S1626P	probably benign	Het
Usp3	T	C	9: 66,566,898	R33G	probably benign	Het
Zbtb20	G	T	16: 43,610,676	A517S	probably damaging	Het

Other mutations in Hps3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00545:Hps3	APN	3	20019807	missense	possibly damaging	0.94
IGL00846:Hps3	APN	3	20025792	missense	probably benign	0.00
IGL01320:Hps3	APN	3	20030469	missense	probably benign	0.12
IGL01364:Hps3	APN	3	20003305	missense	possibly damaging	0.58
IGL01751:Hps3	APN	3	20010966	missense	probably damaging	1.00
IGL01843:Hps3	APN	3	20029001	missense	probably benign	0.05
IGL02294:Hps3	APN	3	20014048	missense	probably damaging	1.00
IGL02581:Hps3	APN	3	20003221	intron	probably benign
Blue	UTSW	3	20030796	missense	probably damaging	1.00
earl_grey	UTSW	3	20017173	intron	probably benign
gandalf	UTSW	3	20012796	nonsense	probably null
pam_gray	UTSW	3	20017173	intron	probably benign
R0107:Hps3	UTSW	3	20030796	missense	probably damaging	1.00
R0245:Hps3	UTSW	3	20012796	nonsense	probably null
R0421:Hps3	UTSW	3	20029316	missense	probably benign	0.00
R0524:Hps3	UTSW	3	20012776	missense	probably damaging	1.00
R0763:Hps3	UTSW	3	20003279	missense	probably damaging	1.00
R1795:Hps3	UTSW	3	20012695	critical splice donor site	probably null
R1864:Hps3	UTSW	3	20019959	critical splice acceptor site	probably null
R2029:Hps3	UTSW	3	20030527	missense	probably benign	0.01
R2101:Hps3	UTSW	3	20012783	missense	possibly damaging	0.95
R2221:Hps3	UTSW	3	20002363	missense	probably benign
R2268:Hps3	UTSW	3	20012935	splice site	probably benign
R2520:Hps3	UTSW	3	20029030	missense	probably damaging	1.00
R3809:Hps3	UTSW	3	20018812	missense	probably damaging	1.00
R3888:Hps3	UTSW	3	20003223	critical splice donor site	probably null
R3942:Hps3	UTSW	3	19996939	missense	probably damaging	1.00
R4022:Hps3	UTSW	3	20035261	missense	possibly damaging	0.69
R4156:Hps3	UTSW	3	20029229	missense	probably damaging	1.00
R4739:Hps3	UTSW	3	20030410	critical splice acceptor site	probably null
R4823:Hps3	UTSW	3	20012726	missense	probably benign	0.03
R4912:Hps3	UTSW	3	20014173	missense	probably damaging	1.00
R5307:Hps3	UTSW	3	20012701	missense	possibly damaging	0.89
R5859:Hps3	UTSW	3	20008870	missense	probably benign	0.02
R6140:Hps3	UTSW	3	19996987	missense	probably damaging	1.00
R6183:Hps3	UTSW	3	20008868	missense	probably benign	0.04
R6971:Hps3	UTSW	3	20011535	missense	probably damaging	1.00
R6981:Hps3	UTSW	3	20022820	missense	probably damaging	1.00
R7120:Hps3	UTSW	3	20011541	missense	probably damaging	1.00
R7146:Hps3	UTSW	3	20008886	missense	probably damaging	1.00
R7223:Hps3	UTSW	3	20030419	missense	probably benign	0.05
R7448:Hps3	UTSW	3	20035165	missense	probably damaging	0.99
R7560:Hps3	UTSW	3	20030452	missense	probably benign	0.29
R7659:Hps3	UTSW	3	20022814	nonsense	probably null
R7769:Hps3	UTSW	3	20018808	splice site	probably null
R8050:Hps3	UTSW	3	20003328	missense	probably benign
R8242:Hps3	UTSW	3	20014126	missense	possibly damaging	0.59
R8802:Hps3	UTSW	3	20019906	missense	probably damaging	1.00
R8822:Hps3	UTSW	3	20003227	missense	probably benign
R8945:Hps3	UTSW	3	20014060	missense	probably damaging	0.99
R9111:Hps3	UTSW	3	20030411	critical splice acceptor site	probably null
R9131:Hps3	UTSW	3	20029186	missense	probably damaging	0.98
R9645:Hps3	UTSW	3	20030667	missense	probably benign	0.01
R9728:Hps3	UTSW	3	20010964	missense	probably benign	0.06
X0021:Hps3	UTSW	3	20030749	missense	probably benign	0.14
X0066:Hps3	UTSW	3	20015988	missense	probably damaging	1.00
Z1177:Hps3	UTSW	3	20008901	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GGCATGTATGGAATTTCTGCAGAAAG -3'
(R):5'- TGGCCCCTAAATCATGAAGAC -3'

Sequencing Primer
(F):5'- ACAGAAGTCTGTCTTTTCAG -3'
(R):5'- TGGCCCCTAAATCATGAAGACACTAG -3'

Posted On

2019-10-07