The protein encoded by this gene is thought to be an effector for RAB3A, which is a small G protein that acts in the late stages of neurotransmitter exocytosis. The encoded protein may be involved in neurotransmitter release and synaptic vesicle traffic. [provided by RefSeq, Dec 2016] See more...

Aliases for RPH3A Gene

Aliases for RPH3A Gene

  • Rabphilin 3A 2 3 5
  • Exophilin-1 2 3 4
  • Rabphilin-3A 3 4
  • KIAA0985 2 4
  • Rabphilin 3A Homolog (Mouse) 2
  • Rabphilin 3A Homolog 3
  • Rabphilin 2
  • RPH3A 5

External Ids for RPH3A Gene

Previous GeneCards Identifiers for RPH3A Gene

  • GC12P112124
  • GC12P112748
  • GC12P113012
  • GC12P111641
  • GC12P111627
  • GC12P111692
  • GC12P113229
  • GC12P110241

Summaries for RPH3A Gene

Entrez Gene Summary for RPH3A Gene

  • The protein encoded by this gene is thought to be an effector for RAB3A, which is a small G protein that acts in the late stages of neurotransmitter exocytosis. The encoded protein may be involved in neurotransmitter release and synaptic vesicle traffic. [provided by RefSeq, Dec 2016]

GeneCards Summary for RPH3A Gene

RPH3A (Rabphilin 3A) is a Protein Coding gene. Diseases associated with RPH3A include Infundibulo-Neurohypophysitis and Martsolf Syndrome. Among its related pathways are Deregulation of Rab and Rab Effector Genes in Bladder Cancer. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is DOC2B.

UniProtKB/Swiss-Prot Summary for RPH3A Gene

  • Plays an essential role in docking and fusion steps of regulated exocytosis (By similarity). At the presynaptic level, RPH3A is recruited by RAB3A to the synaptic vesicle membrane in a GTP-dependent manner where it modulates synaptic vesicle trafficking and calcium-triggered neurotransmitter release (By similarity). In the post-synaptic compartment, forms a ternary complex with GRIN2A and DLG4 and regulates NMDA receptor stability. Plays also a role in the exocytosis of arginine vasopressin hormone (By similarity).

Gene Wiki entry for RPH3A Gene

Additional gene information for RPH3A Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RPH3A Gene

Genomics for RPH3A Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RPH3A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J112794 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 604.4 +221.5 221481 0.8 REST ZNF143 RAD21 ZBTB26 HDAC2 ZBTB48 AFF1 MYRF MIER1 EHMT2 RPH3A OAS3 HSALNG0094122 lnc-RPL6-1 OAS1
GH12J112837 Enhancer 0.9 Ensembl ENCODE 29.7 +268.1 268113 3.8 FOXA1 GABPA TCF7 SP1 NFE2 ATF3 NR3C1 ZNF316 FOXA2 MAFF RPH3A OAS1 OAS3 HECTD4 HSALNG0094123 HSALNG0094122
GH12J112870 Enhancer 0.6 Ensembl ENCODE 33.2 +300.6 300621 1.2 MNT SPI1 HLF MAX RPH3A OAS3 HSALNG0094123 NONHSAG012341.2 OAS1
GH12J112842 Enhancer 0.6 Ensembl 30.7 +272.4 272381 2.3 ZIC2 ZKSCAN1 NFIC FOSL2 POLR2A RCOR1 YY1 JUN GLIS1 SMARCA4 RPH3A OAS3 HSALNG0094123 HSALNG0094122 OAS1
GH12J112597 Enhancer 1.3 FANTOM5 Ensembl ENCODE 12.5 +29.1 29120 3.4 GATAD2A TFE3 SOX13 RCOR2 RXRB SP1 CEBPA CEBPB NFE2 ZKSCAN8 RPH3A OAS2 OAS3 ALDH2 OAS1 TRAFD1 piR-55985-035
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RPH3A on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RPH3A

Top Transcription factor binding sites by QIAGEN in the RPH3A gene promoter:
  • AML1a
  • ATF-2
  • CRE-BP1
  • Evi-1
  • HNF-1
  • HNF-1A
  • Lmo2
  • PPAR-alpha
  • Roaz
  • STAT5B

Genomic Locations for RPH3A Gene

Genomic Locations for RPH3A Gene
chr12:112,570,380-112,898,881
(GRCh38/hg38)
Size:
328,502 bases
Orientation:
Plus strand
chr12:113,008,184-113,336,686
(GRCh37/hg19)
Size:
328,503 bases
Orientation:
Plus strand

Genomic View for RPH3A Gene

Genes around RPH3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RPH3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RPH3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RPH3A Gene

Proteins for RPH3A Gene

  • Protein details for RPH3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y2J0-RP3A_HUMAN
    Recommended name:
    Rabphilin-3A
    Protein Accession:
    Q9Y2J0
    Secondary Accessions:
    • B7Z3C3
    • Q96AE0

    Protein attributes for RPH3A Gene

    Size:
    694 amino acids
    Molecular mass:
    76872 Da
    Cofactor:
    Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
    Quaternary structure:
    • Interacts with RAB3B, RAB3C, RAB3D, RAB8A, RAB27A and RAB27B (By similarity). Interacts with RAB3A; this interaction recruits RPH3A to synaptic vesicules (PubMed:15207266). Interacts (via C2B domain) with SNAP25 (By similarity). Interacts with deubiquitinating enzyme CAND1; this interaction results in the deubiquitination of RPH3A (By similarity). Interacts with GRIN2A and DLG4; this ternary complex regulates NMDA receptor composition at postsynaptic membranes (By similarity). Interacts with SNCA (PubMed:15207266).
    SequenceCaution:
    • Sequence=BAA76829.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for RPH3A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RPH3A Gene

Post-translational modifications for RPH3A Gene

  • Ubiquitinated. Deubiquitinated by CAND1 to prevent its degradation.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RPH3A Gene

Domains & Families for RPH3A Gene

Gene Families for RPH3A Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RPH3A Gene

InterPro:
Blocks:
  • C2 domain
  • Zn-finger, FYVE type
  • Synaptotagmin signature
  • Rabphilin-3A effector
ProtoNet:

Suggested Antigen Peptide Sequences for RPH3A Gene

GenScript: Design optimal peptide antigens:
  • RPH3A protein (Q6PJY8_HUMAN)
  • RPH3A protein (Q6PKD5_HUMAN)
  • Exophilin-1 (RP3A_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y2J0

UniProtKB/Swiss-Prot:

RP3A_HUMAN :
  • Binds calcium via the C2 domains. The calcium-bound C2 domains mediate interactions with phospholipid bilayers (By similarity).
Domain:
  • Binds calcium via the C2 domains. The calcium-bound C2 domains mediate interactions with phospholipid bilayers (By similarity).
genes like me logo Genes that share domains with RPH3A: view

Function for RPH3A Gene

Molecular function for RPH3A Gene

UniProtKB/Swiss-Prot Function:
Plays an essential role in docking and fusion steps of regulated exocytosis (By similarity). At the presynaptic level, RPH3A is recruited by RAB3A to the synaptic vesicle membrane in a GTP-dependent manner where it modulates synaptic vesicle trafficking and calcium-triggered neurotransmitter release (By similarity). In the post-synaptic compartment, forms a ternary complex with GRIN2A and DLG4 and regulates NMDA receptor stability. Plays also a role in the exocytosis of arginine vasopressin hormone (By similarity).

Phenotypes From GWAS Catalog for RPH3A Gene

Gene Ontology (GO) - Molecular Function for RPH3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding ISS --
GO:0005515 protein binding IPI 11377421
GO:0005544 calcium-dependent phospholipid binding ISS --
GO:0005546 phosphatidylinositol-4,5-bisphosphate binding ISS --
GO:0008270 zinc ion binding ISS --
genes like me logo Genes that share ontologies with RPH3A: view
genes like me logo Genes that share phenotypes with RPH3A: view

Animal Models for RPH3A Gene

MGI Knock Outs for RPH3A:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RPH3A

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RPH3A Gene

Localization for RPH3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for RPH3A Gene

Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane. Cell projection, dendritic spine. Cell junction, synapse, postsynaptic cell membrane. Membrane. Peripheral membrane protein.

Subcellular locations from

COMPARTMENTS
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 RPH3A gene
Compartment Confidence
plasma membrane 4
cytosol 4
cytoskeleton 2
endosome 2
extracellular 1
mitochondrion 1
nucleus 1
endoplasmic reticulum 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for RPH3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005794 colocalizes_with Golgi apparatus ISS --
GO:0005829 cytosol ISS --
GO:0005886 plasma membrane IEA --
GO:0008021 synaptic vesicle TAS 10099709
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with RPH3A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for RPH3A Gene

Pathways & Interactions for RPH3A Gene

genes like me logo Genes that share pathways with RPH3A: view

Pathways by source for RPH3A Gene

Gene Ontology (GO) - Biological Process for RPH3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IEA --
GO:0015031 protein transport IEA --
GO:0061669 spontaneous neurotransmitter secretion IEA --
genes like me logo Genes that share ontologies with RPH3A: view

No data available for SIGNOR curated interactions for RPH3A Gene

Drugs & Compounds for RPH3A Gene

(6) Drugs for RPH3A Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(4) Additional Compounds for RPH3A Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with RPH3A: view

Transcripts for RPH3A Gene

mRNA/cDNA for RPH3A Gene

6 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
27 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RPH3A

Alternative Splicing Database (ASD) splice patterns (SP) for RPH3A Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15a · 15b ^ 16 ^ 17 ^ 18a · 18b ·
SP1: - - - - - -
SP2: - - - - -
SP3: - -
SP4: - - - - - - - - - - - - - - - - - -
SP5: - -
SP6:
SP7: -
SP8:

ExUns: 18c ^ 19 ^ 20 ^ 21a · 21b ^ 22a · 22b ^ 23 ^ 24
SP1: -
SP2: -
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:

Relevant External Links for RPH3A Gene

GeneLoc Exon Structure for
RPH3A

Expression for RPH3A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RPH3A Gene

mRNA differential expression in normal tissues according to GTEx for RPH3A Gene

This gene is overexpressed in Brain - Cortex (x8.9), Brain - Frontal Cortex (BA9) (x8.7), Brain - Anterior cingulate cortex (BA24) (x7.0), Brain - Cerebellar Hemisphere (x4.9), and Brain - Cerebellum (x4.3).

Protein differential expression in normal tissues from HIPED for RPH3A Gene

This gene is overexpressed in Serum (35.6), Frontal cortex (20.4), and Cerebrospinal fluid (6.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for RPH3A Gene



Protein tissue co-expression partners for RPH3A Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RPH3A

SOURCE GeneReport for Unigene cluster for RPH3A Gene:

Hs.21239

Evidence on tissue expression from TISSUES for RPH3A Gene

  • Nervous system(5)
  • Adrenal gland(2.5)
genes like me logo Genes that share expression patterns with RPH3A: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RPH3A Gene

Orthologs for RPH3A Gene

This gene was present in the common ancestor of animals.

Orthologs for RPH3A Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RPH3A 30 31
  • 98.69 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RPH3A 30 31
  • 90.11 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia RPH3A 30 31
  • 88.89 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rph3a 30
  • 83.21 (n)
Mouse
(Mus musculus)
Mammalia Rph3a 30 17 31
  • 83.06 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia RPH3A 31
  • 82 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia RPH3A 31
  • 81 (a)
OneToOne
Chicken
(Gallus gallus)
Aves RPH3A 30 31
  • 72.16 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RPH3A 31
  • 72 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100487950 30
  • 68.14 (n)
Zebrafish
(Danio rerio)
Actinopterygii rph3ab 30
  • 68.7 (n)
RPH3A (2 of 2) 31
  • 61 (a)
OneToMany
RPH3A (1 of 2) 31
  • 58 (a)
OneToMany
Fruit Fly
(Drosophila melanogaster)
Insecta Rph 30 31
  • 53.7 (n)
OneToMany
rabphilin-3A 32
  • 39 (a)
Worm
(Caenorhabditis elegans)
Secernentea rbf-1 30 31
  • 53.39 (n)
OneToMany
Species where no ortholog for RPH3A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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 Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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 RPH3A Gene

ENSEMBL:
Gene Tree for RPH3A (if available)
TreeFam:
Gene Tree for RPH3A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RPH3A: view image

Paralogs for RPH3A Gene

(15) SIMAP similar genes for RPH3A Gene using alignment to 19 proteins:

  • RP3A_HUMAN
  • F8VNP7_HUMAN
  • F8VNU2_HUMAN
  • F8VNW3_HUMAN
  • F8VP47_HUMAN
  • F8VR41_HUMAN
  • F8VRJ1_HUMAN
  • F8VTR7_HUMAN
  • F8VV58_HUMAN
  • F8VVK8_HUMAN
  • F8VZS2_HUMAN
  • F8W045_HUMAN
  • F8W116_HUMAN
  • F8W131_HUMAN
  • F8W1A3_HUMAN
  • F8W1K7_HUMAN
  • J3KR03_HUMAN
  • Q6PJY8_HUMAN
  • Q6PKD5_HUMAN

Pseudogenes.org Pseudogenes for RPH3A Gene

genes like me logo Genes that share paralogs with RPH3A: view

Variants for RPH3A Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RPH3A Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
741613 Benign: not provided 112,869,939(+) C/T NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
781700 Benign: not provided 112,876,673(+) C/G NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
787101 Benign: not provided 112,868,593(+) G/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
801393 Pathogenic: not provided 112,870,006(+) G/C MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
rs869312710 Uncertain Significance: not specified 112,883,315(+) C/G MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT

Additional dbSNP identifiers (rs#s) for RPH3A Gene

Structural Variations from Database of Genomic Variants (DGV) for RPH3A Gene

Variant ID Type Subtype PubMed ID
esv2673292 CNV deletion 23128226
esv2746377 CNV deletion 23290073
esv275176 CNV gain+loss 21479260
esv3381540 CNV insertion 20981092
esv3435630 CNV insertion 20981092
esv3580467 CNV loss 25503493
esv3630788 CNV loss 21293372
esv3630789 CNV loss 21293372
esv987835 CNV insertion 20482838
nsv1042636 CNV gain 25217958
nsv832515 CNV gain 17160897
nsv832516 CNV gain 17160897

Variation tolerance for RPH3A Gene

Residual Variation Intolerance Score: 63.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.03; 68.63% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RPH3A Gene

Human Gene Mutation Database (HGMD)
RPH3A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RPH3A

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RPH3A Gene

Disorders for RPH3A Gene

MalaCards: The human disease database

(3) MalaCards diseases for RPH3A Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
infundibulo-neurohypophysitis
martsolf syndrome
  • cataract-mental retardation-hypogonadism
diabetes insipidus, neurohypophyseal
  • diabetes insipidus, primary central; cdi
- elite association - COSMIC cancer census association via MalaCards
Search RPH3A in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RPH3A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with RPH3A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RPH3A Gene

Publications for RPH3A Gene

  1. Abnormal alpha-synuclein interactions with rab3a and rabphilin in diffuse Lewy body disease. (PMID: 15207266) Dalfó E … Ferrer I (Neurobiology of disease 2004) 3 4 23
  2. Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10231032) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4
  3. Loss of SNAP-25 and rabphilin 3a in sensory-motor cortex in Huntington's disease. (PMID: 17877635) Smith R … Li JY (Journal of neurochemistry 2007) 3 23
  4. Visualization of Rab3A dissociation during exocytosis: a study by total internal reflection microscopy. (PMID: 17149709) Lin CC … Kao LS (Journal of cellular physiology 2007) 3 23
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for RPH3A Gene

Sources for RPH3A Gene