Hps3 MGI Mouse Gene Detail - MGI:2153839 - HPS3, biogenesis of lysosomal organelles complex 2 subunit 1

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Hps3 Gene Detail

Symbol

Hps3
Name

HPS3, biogenesis of lysosomal organelles complex 2 subunit 1
Synonyms

Hermansky-Pudlak syndrome 3

Feature Type

protein coding gene
IDs

MGI:2153839
NCBI Gene: 12807
Alliance

gene page
Transcription Start Sites

2 TSS
Candidate for QTL

3 QTL

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Sequence Map

Chr3:20050109-20089478 bp, - strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 3, 6.12 cM
Mapping Data

5 experiments

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SNPs within 2kb

298 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates	Select Strains
C57BL/6J	MGI_C57BL6J_2153839	protein coding gene	Chr3:20050109-20089479 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0027098	protein coding gene	Chr3:17199740-17243466 (-)
A/J	MGP_AJ_G0027058	protein coding gene	Chr3:17121225-17163991 (-)
AKR/J	MGP_AKRJ_G0027027	protein coding gene	Chr3:17289622-17332385 (-)
BALB/cJ	MGP_BALBcJ_G0027070	protein coding gene	Chr3:16875642-16916214 (-)
C3H/HeJ	MGP_C3HHeJ_G0026811	protein coding gene	Chr3:17314107-17355517 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0027515	protein coding gene	Chr3:18288466-18335785 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0024877	protein coding gene	Chr3:15189370-15226063 (-)
CAST/EiJ	MGP_CASTEiJ_G0026266	protein coding gene	Chr3:17224688-17265214 (-)
CBA/J	MGP_CBAJ_G0026789	protein coding gene	Chr3:18688930-18731609 (-)
DBA/2J	MGP_DBA2J_G0026923	protein coding gene	Chr3:16742724-16782667 (-)
FVB/NJ	MGP_FVBNJ_G0026891	protein coding gene	Chr3:16397665-16438686 (-)
LP/J	MGP_LPJ_G0027035	protein coding gene	Chr3:17852591-17894035 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0026912	protein coding gene	Chr3:20762599-20804434 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0027575	protein coding gene	Chr3:17082541-17122484 (-)
PWK/PhJ	MGP_PWKPhJ_G0025999	protein coding gene	Chr3:16439166-16481845 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0025808	protein coding gene	Chr3:16877498-16923720 (-)
WSB/EiJ	MGP_WSBEiJ_G0026339	protein coding gene	Chr3:17080818-17131950 (-)

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Human Ortholog

HPS3, HPS3 biogenesis of lysosomal organelles complex 2 subunit 1

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

HPS3, HPS3 biogenesis of lysosomal organelles complex 2 subunit 1
Synonyms

BLOC2S1, SUTAL
Links

HGNC:15597

NCBI Gene ID: 84343

neXtProt AC: NX_Q969F9

UniProt: Q969F9
Chr Location

3q24; chr3:149129638-149173732 (+) GRCh38

MGI Vertebrate Homology

Hps3 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: HPS3
Protein SuperFamily

BLOC-2_complex_Hps3
Gene Tree

Hps3

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Diseases

2 with Hps3 mouse models; 2 with human HPS3 associations

Human Disease

Mouse Models

Human and Mouse genes associated with disease

Human and Mouse genes associated with disease

Hermansky-Pudlak syndrome 3

IDs

View 3 models

Mouse gene associated with disease

platelet storage pool deficiency

IDs

View 2 models

Human gene associated with disease

Hermansky-Pudlak syndrome

IDs

Click on a disease name to see all genes associated with that disease.

Mutations/Alleles

2 with disease annotations

References

5 with disease annotations

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Phenotype Summary

15 phenotypes from 7 alleles in 8 genetic backgrounds
2 phenotypes from multigenic genotypes
5 images
31 phenotype references

Phenotype Overview

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

16
Chemically induced (ENU)

3
Gene trapped

1
Radiation induced

1
Spontaneous

7
Targeted

4
Genomic Mutations

1 involving Hps3
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

54 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygotes for spontaneous null mutations exhibit hypopigmentation and prolonged bleeding associated with a platelet defect.

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All GO Annotations

13
GO References

8

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	non-membrane-bounded organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

706
cDNA Data

49
Literature Summary

1

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase hps3

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All Sequences

96
RefSeq

31
UniProt

7
CCDS

CCDS17260.1, CCDS50872.1

Ensembl

ENSMUSG00000027615 (Evidence)
NCBI Gene

12807

Representative Sequences				Length	Strain/Species	Flank
	genomic	12807	NCBI Gene Model \| MGI Sequence Detail	39370	C57BL/6J	± kb
	transcript	NM_001409881	RefSeq \| MGI Sequence Detail	4141	ZRU/MplStud
	polypeptide	Q91VB4	UniProt \| EBI \| MGI Sequence Detail	1002	Not Applicable

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UniProt

7 Sequences
Protein Ontology

PR:000008737 BLOC-2 complex member HPS3

(term hierarchy)
InterPro Domains

IPR029438 BLOC-2 complex member HPS3, C-terminal domain

IPR029437 BLOC-2 complex member HPS3, N-terminal domain

IPR017216 Hermansky-Pudlak syndrome 3 protein

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All nucleic 52

cDNA 52

Microarray probesets 4

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MGD-MRK-2045, MGI:88441

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Summaries

All 61

Developmental Gene Expression 1

Diseases 5

Gene Ontology 8

Phenotypes 31
Earliest

J:9300 Novak EK, et al., Cocoa: a new mouse model for platelet storage pool deficiency. Br J Haematol. 1988 Jul;69(3):371-8
Latest

J:302829 Lu J, et al., Mouse models for human hyperuricaemia: a critical review. Nat Rev Rheumatol. 2019 Jul;15(7):413-426

TSS for Hps3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr32706	Chr3:20089449-20089489 (-)	9 bp
Tssr32705	Chr3:20089433-20089447 (-)	38 bp

Hps3 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Bglq3	Chr3, 76.22 cM		J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome 3, Hps3 (12.5 cM) showed differential expression between A/a and A/A animals on the unrestricted diet. Diabesity QTL Insq3 (2.6 cM) maps near this candidate gene.Candidate genes for diabesity QTLs Bglq3 (49 cM) and Wt10q2 (61 cM) are Fabp2 (55 cM) and Ampd2 (50.4 cM). Fabp2 shows differential expression between the restricted and unrestricted diets on the A/a background and Ampd2 shows differential expression between the restricted and unrestricted diets on the A/A background.
Insq3	Chr3, syntenic		J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome 3, Hps3 (12.5 cM) showed differential expression between A/a and A/A animals on the unrestricted diet. Diabesity QTL Insq3 (2.6 cM) maps near this candidate gene.Candidate genes for diabesity QTLs Bglq3 (49 cM) and Wt10q2 (61 cM) are Fabp2 (55 cM) and Ampd2 (50.4 cM). Fabp2 shows differential expression between the restricted and unrestricted diets on the A/a background and Ampd2 shows differential expression between the restricted and unrestricted diets on the A/A background.
Wt10q2	Chr3, syntenic		J:91835	The correlation between gene expression and dietary interaction was examined in a population of (BALB/cStCrlfC3H/Nctr x VY/WffC3Hf/Nctr-A(vy)/a)F1 animals. A/a and A/A animals were placed on a 70% (calorie restricted) or 100% (non-restricted) diet andliver mRNA levels were assessed for over 18,000 genes using DNA microarrays. Twenty-eight known genes showing statistically significant differential expression between the 70% and 100% calorie diets and A/a and A/A genotypes mapped near known diabesity QTLs. These genes may be considered further for candidate genes. On mouse Chromosome 3, Hps3 (12.5 cM) showed differential expression between A/a and A/A animals on the unrestricted diet. Diabesity QTL Insq3 (2.6 cM) maps near this candidate gene.Candidate genes for diabesity QTLs Bglq3 (49 cM) and Wt10q2 (61 cM) are Fabp2 (55 cM) and Ampd2 (50.4 cM). Fabp2 shows differential expression between the restricted and unrestricted diets on the A/a background and Ampd2 shows differential expression between the restricted and unrestricted diets on the A/A background.

*cM position of peak correlated region/marker

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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