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Aliases for JPH3 Gene

Aliases for JPH3 Gene

  • Junctophilin 3 2 3 5
  • Trinucleotide Repeat Containing 22 2 3
  • Junctophilin Type 3 3 4
  • TNRC22 3 4
  • JP-3 3 4
  • JP3 3 4
  • Trinucleotide Repeat-Containing Gene 22 Protein 4
  • Junctophilin-3 3
  • CAGL237 3
  • HDL2 3

External Ids for JPH3 Gene

Previous HGNC Symbols for JPH3 Gene

  • TNRC22

Previous GeneCards Identifiers for JPH3 Gene

  • GC16P078973
  • GC16P088667
  • GC16P087377
  • GC16P087417
  • GC16P086194
  • GC16P073377

Summaries for JPH3 Gene

Entrez Gene Summary for JPH3 Gene

  • Junctional complexes between the plasma membrane and endoplasmic/sarcoplasmic reticulum are a common feature of all excitable cell types and mediate cross talk between cell surface and intracellular ion channels. The protein encoded by this gene is a component of junctional complexes and is composed of a C-terminal hydrophobic segment spanning the endoplasmic/sarcoplasmic reticulum membrane and a remaining cytoplasmic domain that shows specific affinity for the plasma membrane. CAG/CTG repeat expansion from normally 6-28 repeats to 40-59 repeats in the 3' UTR of this gene have been associated with Huntington disease-like 2 (HDL2). This gene is a member of the junctophilin gene family. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Jul 2016]

GeneCards Summary for JPH3 Gene

JPH3 (Junctophilin 3) is a Protein Coding gene. Diseases associated with JPH3 include Huntington Disease-Like 2 and Huntington Disease. Gene Ontology (GO) annotations related to this gene include calcium-release channel activity. An important paralog of this gene is JPH1.

UniProtKB/Swiss-Prot for JPH3 Gene

  • Junctophilins contribute to the formation of junctional membrane complexes (JMCs) which link the plasma membrane with the endoplasmic or sarcoplasmic reticulum in excitable cells. Provides a structural foundation for functional cross-talk between the cell surface and intracellular calcium release channels. JPH3 is brain-specific and appears to have an active role in certain neurons involved in motor coordination and memory.

Gene Wiki entry for JPH3 Gene

Additional gene information for JPH3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for JPH3 Gene

Genomics for JPH3 Gene

GeneHancer (GH) Regulatory Elements for JPH3 Gene

Promoters and enhancers for JPH3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J087601 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 650.7 +1.3 1332 4.1 CTCF MXI1 KLF1 ZNF777 SIN3A ZIC2 ETS1 ZNF335 ZNF121 GLIS2 JPH3 ENSG00000269935 PIR44736
GH16J087550 Enhancer 0.8 ENCODE 11.6 -51.3 -51285 0.2 RB1 KLF14 RAD21 ARID2 EGR1 ZNF143 EGR2 SMARCC1 RXRA SP5 JPH3 FBXO31 PIR35253
GH16J087574 Enhancer 0.7 ENCODE 12.1 -26.4 -26390 1.2 CTCF KLF1 ZNF211 ZBTB40 ZFHX2 EGR1 VEZF1 EGR2 ZNF263 ZNF331 BANP ZC3H18 JPH3 KLHDC4 PIR35253
GH16J087507 Enhancer 0.7 Ensembl 11.5 -94.2 -94193 1.1 SOX13 IRF2 SAP130 ERF ZNF644 ZNF7 YY1 ZNF614 SCRT2 HNF4G JPH3 LOC100129215 PIR35253 LOC101928737
GH16J087576 Enhancer 0.4 ENCODE 12.1 -25.4 -25425 0.2 EGR1 VEZF1 JPH3 KLHDC4 MAP1LC3B PIR35253
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around JPH3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the JPH3 gene promoter:
  • NRSF form 2
  • NRSF form 1
  • Egr-2
  • PPAR-alpha
  • POU3F1
  • Egr-1
  • Pax-4a
  • Zic1
  • HNF-4alpha2
  • HNF-4alpha1

Genomic Locations for JPH3 Gene

Genomic Locations for JPH3 Gene
96,322 bases
Plus strand
96,322 bases
Plus strand

Genomic View for JPH3 Gene

Genes around JPH3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
JPH3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for JPH3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for JPH3 Gene

Proteins for JPH3 Gene

  • Protein details for JPH3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • D3DUN2
    • Q8N471
    • Q9HDC3
    • Q9HDC4

    Protein attributes for JPH3 Gene

    748 amino acids
    Molecular mass:
    81469 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for JPH3 Gene


neXtProt entry for JPH3 Gene

Post-translational modifications for JPH3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for JPH3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for JPH3 Gene

Domains & Families for JPH3 Gene

Gene Families for JPH3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted membrane proteins

Protein Domains for JPH3 Gene


Suggested Antigen Peptide Sequences for JPH3 Gene

Graphical View of Domain Structure for InterPro Entry



  • The MORN (membrane occupation and recognition nexus) repeats contribute to the plasma membrane binding, possibly by interacting with phospholipids.
  • Belongs to the junctophilin family.
  • The MORN (membrane occupation and recognition nexus) repeats contribute to the plasma membrane binding, possibly by interacting with phospholipids.
  • Belongs to the junctophilin family.
genes like me logo Genes that share domains with JPH3: view

Function for JPH3 Gene

Molecular function for JPH3 Gene

UniProtKB/Swiss-Prot Function:
Junctophilins contribute to the formation of junctional membrane complexes (JMCs) which link the plasma membrane with the endoplasmic or sarcoplasmic reticulum in excitable cells. Provides a structural foundation for functional cross-talk between the cell surface and intracellular calcium release channels. JPH3 is brain-specific and appears to have an active role in certain neurons involved in motor coordination and memory.

Phenotypes From GWAS Catalog for JPH3 Gene

Gene Ontology (GO) - Molecular Function for JPH3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0015278 calcium-release channel activity IEA --
genes like me logo Genes that share ontologies with JPH3: view
genes like me logo Genes that share phenotypes with JPH3: view

Human Phenotype Ontology for JPH3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for JPH3 Gene

MGI Knock Outs for JPH3:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for JPH3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for JPH3 Gene

Localization for JPH3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for JPH3 Gene

Cell membrane; Peripheral membrane protein. Endoplasmic reticulum membrane; Single-pass type IV membrane protein. Note=Localized predominantly on the plasma membrane. The transmembrane domain is anchored in endoplasmic reticulum membrane, while the N-terminal part associates with the plasma membrane (By similarity). {ECO:0000250}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for JPH3 gene
Compartment Confidence
endoplasmic reticulum 5
plasma membrane 4
cytosol 3
extracellular 1
mitochondrion 1
peroxisome 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for JPH3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA,IBA --
GO:0005789 endoplasmic reticulum membrane IEA,IBA --
GO:0005886 plasma membrane IEA --
GO:0014701 junctional sarcoplasmic reticulum membrane TAS 19095005
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with JPH3: view

Pathways & Interactions for JPH3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for JPH3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007612 learning IEA --
GO:0007613 memory IEA --
GO:0035640 exploration behavior IEA --
GO:0040011 locomotion IEA --
GO:0048167 regulation of synaptic plasticity IBA --
genes like me logo Genes that share ontologies with JPH3: view

No data available for Pathways by source and SIGNOR curated interactions for JPH3 Gene

Drugs & Compounds for JPH3 Gene

(1) Additional Compounds for JPH3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with JPH3: view

Transcripts for JPH3 Gene

mRNA/cDNA for JPH3 Gene

(3) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(1) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for JPH3 Gene

Junctophilin 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for JPH3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for JPH3 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10
SP2: - -
SP3: -

Relevant External Links for JPH3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for JPH3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for JPH3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for JPH3 Gene

This gene is overexpressed in Brain - Cortex (x6.6), Brain - Frontal Cortex (BA9) (x5.8), Brain - Anterior cingulate cortex (BA24) (x5.7), Brain - Hippocampus (x5.6), Brain - Amygdala (x4.6), and Brain - Nucleus accumbens (basal ganglia) (x4.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for JPH3 Gene

Protein tissue co-expression partners for JPH3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of JPH3 Gene:


SOURCE GeneReport for Unigene cluster for JPH3 Gene:


mRNA Expression by UniProt/SwissProt for JPH3 Gene:

Tissue specificity: Specifically expressed in brain.

Evidence on tissue expression from TISSUES for JPH3 Gene

  • Nervous system(4.8)

Phenotype-based relationships between genes and organs from Gene ORGANizer for JPH3 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
  • skeletal muscle
Head and neck:
  • brain
  • cerebellum
  • head
  • spinal cord
genes like me logo Genes that share expression patterns with JPH3: view

No data available for Protein differential expression in normal tissues for JPH3 Gene

Orthologs for JPH3 Gene

This gene was present in the common ancestor of animals.

Orthologs for JPH3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia JPH3 34 33
  • 98.91 (n)
(Bos Taurus)
Mammalia JPH3 34 33
  • 90.86 (n)
(Canis familiaris)
Mammalia JPH3 34 33
  • 90.24 (n)
(Monodelphis domestica)
Mammalia JPH3 34
  • 89 (a)
(Rattus norvegicus)
Mammalia Jph3 33
  • 88.83 (n)
(Mus musculus)
Mammalia Jph3 16 34 33
  • 88.8 (n)
(Ornithorhynchus anatinus)
Mammalia JPH3 34
  • 88 (a)
(Gallus gallus)
Aves JPH3 34 33
  • 83.38 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia jph3 33
  • 78.21 (n)
(Danio rerio)
Actinopterygii LOC569861 33
  • 69.06 (n)
jph3 34
  • 66 (a)
JPH3 (2 of 2) 34
  • 48 (a)
fruit fly
(Drosophila melanogaster)
Insecta jp 34 35
  • 25 (a)
(Caenorhabditis elegans)
Secernentea jph-1 34
  • 34 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 56 (a)
Species where no ortholog for JPH3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for JPH3 Gene

Gene Tree for JPH3 (if available)
Gene Tree for JPH3 (if available)
Evolutionary constrained regions (ECRs) for JPH3: view image

Paralogs for JPH3 Gene

Paralogs for JPH3 Gene

(5) SIMAP similar genes for JPH3 Gene using alignment to 2 proteins:

  • F8W9A3_HUMAN
genes like me logo Genes that share paralogs with JPH3: view

Variants for JPH3 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for JPH3 Gene

Isoform 2 length of the poly-Ala region is variable (6 to 27 CTG/CAG triplets) in the normal population and may be expanded (41 to 58 CTG/CAG triplets) in patients suffering from Huntington disease-like type 2.

Sequence variations from dbSNP and Humsavar for JPH3 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1000001462 -- 87,691,319(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000033381 -- 87,616,463(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000047395 -- 87,612,278(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000049169 -- 87,657,089(+) A/T genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for JPH3 Gene

Variant ID Type Subtype PubMed ID
dgv503n67 CNV gain 20364138
dgv504n67 CNV gain 20364138
dgv871e212 CNV loss 25503493
esv1008276 CNV insertion 20482838
esv2229873 CNV deletion 18987734
esv24856 CNV loss 19812545
esv2658391 CNV deletion 23128226
esv2669244 CNV deletion 23128226
esv2677149 CNV deletion 23128226
esv2714925 CNV deletion 23290073
esv2714926 CNV deletion 23290073
esv2714927 CNV deletion 23290073
esv2714928 CNV deletion 23290073
esv2714930 CNV deletion 23290073
esv2714931 CNV deletion 23290073
esv29774 CNV loss 19812545
esv3553849 CNV deletion 23714750
esv3639521 CNV gain 21293372
esv3639522 CNV loss 21293372
esv3639523 CNV loss 21293372
esv990733 CNV deletion 20482838
nsv103166 CNV deletion 16902084
nsv103793 CNV deletion 16902084
nsv1062946 CNV gain 25217958
nsv1070780 CNV deletion 25765185
nsv1136224 CNV deletion 24896259
nsv1138482 CNV deletion 24896259
nsv1138483 CNV deletion 24896259
nsv1144778 CNV deletion 24896259
nsv428330 CNV gain 18775914
nsv471110 CNV loss 18288195
nsv510695 CNV deletion 20534489
nsv527983 CNV loss 19592680
nsv573534 CNV loss 21841781
nsv827816 CNV gain 20364138
nsv952065 CNV deletion 24416366

Variation tolerance for JPH3 Gene

Residual Variation Intolerance Score: 67.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.29; 53.09% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for JPH3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

Disorders for JPH3 Gene

MalaCards: The human disease database

(9) MalaCards diseases for JPH3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search JPH3 in MalaCards View complete list of genes associated with diseases


  • Huntington disease-like 2 (HDL2) [MIM:606438]: Huntington disease (HD) is a neurodegenerative disorder resulting primarily from the loss of medium spiny projection neurons in the striatum, especially in the caudate nucleus, and, to a lesser extent, atrophy of mesencephalic and cortical structures. The typical clinical picture of HD combines familial adult onset chorea and subcortical dementia that usually begin during the fourth decade of life. {ECO:0000269 PubMed:11914418, ECO:0000269 PubMed:14557581}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for JPH3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with JPH3: view

No data available for Genatlas for JPH3 Gene

Publications for JPH3 Gene

  1. Characterization of human junctophilin subtype genes. (PMID: 10891348) Nishi M … Takeshima H (Biochemical and biophysical research communications 2000) 2 3 4 22 58
  2. Searching for mutation in the JPH3, ATN1 and TBP genes in Polish patients suspected of Huntington's disease and without mutation in the IT15 gene. (PMID: 18651325) Sułek-Piatkowska A … Zaremba J (Neurologia i neurochirurgia polska 2008) 3 22 44 58
  3. Exclusion of mutations in the PRNP, JPH3, TBP, ATN1, CREBBP, POU3F2 and FTL genes as a cause of disease in Portuguese patients with a Huntington-like phenotype. (PMID: 16858508) Costa Mdo C … Maciel P (Journal of human genetics 2006) 3 22 44 58
  4. Huntington's disease-like phenotype due to trinucleotide repeat expansions in the TBP and JPH3 genes. (PMID: 12805114) Stevanin G … Durr A (Brain : a journal of neurology 2003) 3 22 44 58
  5. CAG/CTG repeat expansions at the Huntington's disease-like 2 locus are rare in Huntington's disease patients. (PMID: 11914418) Stevanin G … Brice A (Neurology 2002) 3 4 22 58

Products for JPH3 Gene

Sources for JPH3 Gene

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