Mutagenetix > Incidental Mutation

Incidental Mutation 'R7223:Hps3'

561926

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

045295-MU

Accession Numbers

Essential gene?

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

Stock #

R7223 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

19995945-20035315 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 20030419 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 202 (S202T)

Ref Sequence

ENSEMBL: ENSMUSP00000012580 (fasta)

Gene Model

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

AlphaFold

Q91VB4

Predicted Effect

probably benign
Transcript: ENSMUST00000012580
AA Change: S202T

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000012580
Gene: ENSMUSG00000027615
AA Change: S202T

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 null
Transcript: ENSMUST00000108321

SMART Domains

Protein: ENSMUSP00000103957
Gene: ENSMUSG00000027615

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.8%

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 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: 82 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb11	A	T	2: 69,274,143 (GRCm38)	V733E	probably benign	Het
Adam34	A	T	8: 43,652,004 (GRCm38)	N201K	probably benign	Het
Aldh3b2	A	C	19: 3,979,592 (GRCm38)	S322R	probably damaging	Het
Anpep	A	T	7: 79,825,310 (GRCm38)	L914Q	probably damaging	Het
Arhgap30	T	C	1: 171,407,571 (GRCm38)	F535S	probably damaging	Het
Baiap3	G	A	17: 25,243,840 (GRCm38)	R1075C	probably benign	Het
Baz2a	G	T	10: 128,112,606 (GRCm38)	G252V	probably damaging	Het
Brinp3	T	A	1: 146,901,074 (GRCm38)	S420T	possibly damaging	Het
Carmil3	T	C	14: 55,496,238 (GRCm38)	F359S	possibly damaging	Het
Ccdc124	A	T	8: 70,868,526 (GRCm38)	L190Q	probably damaging	Het
Ccr6	T	C	17: 8,256,140 (GRCm38)	V59A	probably damaging	Het
Ccr8	T	A	9: 120,094,617 (GRCm38)	I266N	probably damaging	Het
Cdh23	T	A	10: 60,331,817 (GRCm38)	E1798V	probably damaging	Het
Cdk5rap2	T	C	4: 70,235,447 (GRCm38)	N1713S	probably benign	Het
Cep19	T	A	16: 32,104,015 (GRCm38)	I33N	probably damaging	Het
Cers3	A	T	7: 66,783,415 (GRCm38)	Y196F	probably damaging	Het
Cidea	T	C	18: 67,366,421 (GRCm38)	I126T	probably damaging	Het
Copg2	A	T	6: 30,812,754 (GRCm38)	Y546*	probably null	Het
Cul3	A	T	1: 80,287,000 (GRCm38)	V261E	probably benign	Het
Cyp2g1	A	T	7: 26,814,632 (GRCm38)	D221V	probably damaging	Het
Cyp8b1	G	A	9: 121,915,097 (GRCm38)	H390Y	probably damaging	Het
Daam1	T	C	12: 71,988,943 (GRCm38)	F971L	probably damaging	Het
Dnajc24	G	A	2: 106,001,966 (GRCm38)	S24L	possibly damaging	Het
Dpysl3	T	C	18: 43,438,042 (GRCm38)	S56G	probably benign	Het
Esp1	A	G	17: 40,731,081 (GRCm38)	D88G	probably benign	Het
Fam171b	A	G	2: 83,878,230 (GRCm38)	T359A	probably damaging	Het
Fam186b	T	C	15: 99,279,837 (GRCm38)	E536G	possibly damaging	Het
Fbxo3	T	C	2: 104,043,012 (GRCm38)	V156A	possibly damaging	Het
Gls2	C	A	10: 128,199,194 (GRCm38)	H65Q	probably benign	Het
Gp2	A	G	7: 119,451,498 (GRCm38)		probably null	Het
Gpcpd1	T	A	2: 132,534,056 (GRCm38)	K435I	probably benign	Het
Gpx6	T	A	13: 21,317,670 (GRCm38)		probably null	Het
Htr1d	T	A	4: 136,443,501 (GRCm38)	L347H	probably damaging	Het
Igfals	T	C	17: 24,881,234 (GRCm38)	L433P	probably damaging	Het
Ilvbl	C	T	10: 78,583,696 (GRCm38)	H537Y	probably benign	Het
Iqgap2	A	T	13: 95,628,972 (GRCm38)	M1530K	probably damaging	Het
Jarid2	A	G	13: 44,896,322 (GRCm38)	T247A	possibly damaging	Het
L3hypdh	C	T	12: 72,074,009 (GRCm38)	V323I	possibly damaging	Het
Lama3	C	T	18: 12,582,608 (GRCm38)	T1707I	possibly damaging	Het
Map6	G	T	7: 99,268,025 (GRCm38)	A2S	probably damaging	Het
Mfap3	T	A	11: 57,530,240 (GRCm38)	I349K	probably benign	Het
Mybl2	A	G	2: 163,072,705 (GRCm38)	T248A	probably benign	Het
N6amt1	A	G	16: 87,362,660 (GRCm38)	*151W	probably null	Het
Nhlrc1	A	G	13: 47,014,208 (GRCm38)	V191A	probably benign	Het
Nkx2-5	T	C	17: 26,839,620 (GRCm38)	E120G	possibly damaging	Het
Or2y10	T	A	11: 49,564,098 (GRCm38)	M59K	probably damaging	Het
Or52r1b	C	A	7: 103,041,632 (GRCm38)	T46N	possibly damaging	Het
Or8b41	T	C	9: 38,143,753 (GRCm38)	V201A	probably benign	Het
Or8k28	T	A	2: 86,455,867 (GRCm38)	I135F	possibly damaging	Het
Pcdha8	T	G	18: 36,993,148 (GRCm38)	L228V	probably benign	Het
Pcsk2	A	G	2: 143,690,333 (GRCm38)	T134A	possibly damaging	Het
Phldb3	G	A	7: 24,624,653 (GRCm38)	R484Q	probably benign	Het
Pipox	A	G	11: 77,881,186 (GRCm38)	S371P	probably damaging	Het
Plekhg1	T	C	10: 3,873,343 (GRCm38)	S159P		Het
Psme4	C	T	11: 30,874,226 (GRCm38)	P1737S	probably benign	Het
Pygm	G	A	19: 6,388,863 (GRCm38)	D328N	probably benign	Het
Rabgef1	A	T	5: 130,190,960 (GRCm38)	E88V	probably benign	Het
Rims2	G	T	15: 39,437,032 (GRCm38)	R245L	probably benign	Het
Slc38a4	T	C	15: 97,010,345 (GRCm38)	I172V	probably damaging	Het
Slc4a10	T	A	2: 62,268,665 (GRCm38)	Y586N	probably damaging	Het
Snap91	C	T	9: 86,879,557 (GRCm38)		probably benign	Het
Sorcs1	C	T	19: 50,190,042 (GRCm38)	V881I	probably benign	Het
Spef2	A	T	15: 9,601,640 (GRCm38)	V1512E	unknown	Het
Sufu	T	C	19: 46,453,277 (GRCm38)	I292T	possibly damaging	Het
Tet1	T	C	10: 62,813,671 (GRCm38)	N87D	possibly damaging	Het
Tmem108	T	C	9: 103,499,534 (GRCm38)	T239A	not run	Het
Tmem121	A	T	12: 113,188,494 (GRCm38)	K111*	probably null	Het
Tpp2	T	A	1: 43,968,888 (GRCm38)	D417E	probably damaging	Het
Tpr	G	A	1: 150,439,256 (GRCm38)	E2025K	possibly damaging	Het
Trappc3	C	T	4: 126,275,152 (GRCm38)	A145V	possibly damaging	Het
Ttn	T	C	2: 76,890,981 (GRCm38)	D6754G	probably null	Het
Unc13c	T	A	9: 73,629,191 (GRCm38)	M1627L	probably benign	Het
Ush2a	A	G	1: 188,810,217 (GRCm38)	I3327V	probably benign	Het
Vmn1r74	C	T	7: 11,846,967 (GRCm38)	Q65*	probably null	Het
Wdr18	G	A	10: 79,960,368 (GRCm38)	R69H	probably damaging	Het
Zbed5	G	T	5: 129,900,438 (GRCm38)	D132Y	probably damaging	Het
Zfp644	A	T	5: 106,637,582 (GRCm38)	Y366*	probably null	Het
Zfyve26	T	C	12: 79,246,171 (GRCm38)	N2068S	probably damaging	Het
Zic2	T	C	14: 122,476,091 (GRCm38)	F139S	probably damaging	Het
Zmynd11	T	C	13: 9,710,162 (GRCm38)	Q141R	probably benign	Het
Zrsr2-ps1	A	G	11: 22,973,388 (GRCm38)	E54G	probably benign	Het
Zscan10	G	A	17: 23,609,482 (GRCm38)	D333N	probably benign	Het

Other mutations in Hps3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00545:Hps3	APN	3	20,019,807 (GRCm38)	missense	possibly damaging	0.94
IGL00846:Hps3	APN	3	20,025,792 (GRCm38)	missense	probably benign	0.00
IGL01320:Hps3	APN	3	20,030,469 (GRCm38)	missense	probably benign	0.12
IGL01364:Hps3	APN	3	20,003,305 (GRCm38)	missense	possibly damaging	0.58
IGL01751:Hps3	APN	3	20,010,966 (GRCm38)	missense	probably damaging	1.00
IGL01843:Hps3	APN	3	20,029,001 (GRCm38)	missense	probably benign	0.05
IGL02294:Hps3	APN	3	20,014,048 (GRCm38)	missense	probably damaging	1.00
IGL02581:Hps3	APN	3	20,003,221 (GRCm38)	intron	probably benign
Blue	UTSW	3	20,030,796 (GRCm38)	missense	probably damaging	1.00
earl_grey	UTSW	3	20,017,173 (GRCm38)	intron	probably benign
gandalf	UTSW	3	20,012,796 (GRCm38)	nonsense	probably null
pam_gray	UTSW	3	20,017,173 (GRCm38)	intron	probably benign
R0107:Hps3	UTSW	3	20,030,796 (GRCm38)	missense	probably damaging	1.00
R0245:Hps3	UTSW	3	20,012,796 (GRCm38)	nonsense	probably null
R0421:Hps3	UTSW	3	20,029,316 (GRCm38)	missense	probably benign	0.00
R0524:Hps3	UTSW	3	20,012,776 (GRCm38)	missense	probably damaging	1.00
R0763:Hps3	UTSW	3	20,003,279 (GRCm38)	missense	probably damaging	1.00
R1795:Hps3	UTSW	3	20,012,695 (GRCm38)	critical splice donor site	probably null
R1864:Hps3	UTSW	3	20,019,959 (GRCm38)	critical splice acceptor site	probably null
R2029:Hps3	UTSW	3	20,030,527 (GRCm38)	missense	probably benign	0.01
R2101:Hps3	UTSW	3	20,012,783 (GRCm38)	missense	possibly damaging	0.95
R2221:Hps3	UTSW	3	20,002,363 (GRCm38)	missense	probably benign
R2268:Hps3	UTSW	3	20,012,935 (GRCm38)	splice site	probably benign
R2520:Hps3	UTSW	3	20,029,030 (GRCm38)	missense	probably damaging	1.00
R3809:Hps3	UTSW	3	20,018,812 (GRCm38)	missense	probably damaging	1.00
R3888:Hps3	UTSW	3	20,003,223 (GRCm38)	critical splice donor site	probably null
R3942:Hps3	UTSW	3	19,996,939 (GRCm38)	missense	probably damaging	1.00
R4022:Hps3	UTSW	3	20,035,261 (GRCm38)	missense	possibly damaging	0.69
R4156:Hps3	UTSW	3	20,029,229 (GRCm38)	missense	probably damaging	1.00
R4739:Hps3	UTSW	3	20,030,410 (GRCm38)	critical splice acceptor site	probably null
R4823:Hps3	UTSW	3	20,012,726 (GRCm38)	missense	probably benign	0.03
R4912:Hps3	UTSW	3	20,014,173 (GRCm38)	missense	probably damaging	1.00
R5307:Hps3	UTSW	3	20,012,701 (GRCm38)	missense	possibly damaging	0.89
R5859:Hps3	UTSW	3	20,008,870 (GRCm38)	missense	probably benign	0.02
R6140:Hps3	UTSW	3	19,996,987 (GRCm38)	missense	probably damaging	1.00
R6183:Hps3	UTSW	3	20,008,868 (GRCm38)	missense	probably benign	0.04
R6971:Hps3	UTSW	3	20,011,535 (GRCm38)	missense	probably damaging	1.00
R6981:Hps3	UTSW	3	20,022,820 (GRCm38)	missense	probably damaging	1.00
R7120:Hps3	UTSW	3	20,011,541 (GRCm38)	missense	probably damaging	1.00
R7146:Hps3	UTSW	3	20,008,886 (GRCm38)	missense	probably damaging	1.00
R7448:Hps3	UTSW	3	20,035,165 (GRCm38)	missense	probably damaging	0.99
R7452:Hps3	UTSW	3	20,011,428 (GRCm38)	missense	probably damaging	1.00
R7560:Hps3	UTSW	3	20,030,452 (GRCm38)	missense	probably benign	0.29
R7659:Hps3	UTSW	3	20,022,814 (GRCm38)	nonsense	probably null
R7769:Hps3	UTSW	3	20,018,808 (GRCm38)	splice site	probably null
R8050:Hps3	UTSW	3	20,003,328 (GRCm38)	missense	probably benign
R8242:Hps3	UTSW	3	20,014,126 (GRCm38)	missense	possibly damaging	0.59
R8802:Hps3	UTSW	3	20,019,906 (GRCm38)	missense	probably damaging	1.00
R8822:Hps3	UTSW	3	20,003,227 (GRCm38)	missense	probably benign
R8945:Hps3	UTSW	3	20,014,060 (GRCm38)	missense	probably damaging	0.99
R9111:Hps3	UTSW	3	20,030,411 (GRCm38)	critical splice acceptor site	probably null
R9131:Hps3	UTSW	3	20,029,186 (GRCm38)	missense	probably damaging	0.98
R9645:Hps3	UTSW	3	20,030,667 (GRCm38)	missense	probably benign	0.01
R9728:Hps3	UTSW	3	20,010,964 (GRCm38)	missense	probably benign	0.06
X0021:Hps3	UTSW	3	20,030,749 (GRCm38)	missense	probably benign	0.14
X0066:Hps3	UTSW	3	20,015,988 (GRCm38)	missense	probably damaging	1.00
Z1177:Hps3	UTSW	3	20,008,901 (GRCm38)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GGCATGCCACTATAGATACCAGG -3'
(R):5'- TGAGATGCCAATGTCTGAGGC -3'

Sequencing Primer
(F):5'- TCCGCCTCTTTCAATGGA -3'
(R):5'- AATGTCTGAGGCCCCTTTG -3'

Posted On

2019-06-26