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RPH3A rabphilin 3A [ Homo sapiens (human) ]

Gene ID: 22895, updated on 14-Nov-2024

Summary

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Official Symbol
RPH3Aprovided by HGNC
Official Full Name
rabphilin 3Aprovided by HGNC
Primary source
HGNC:HGNC:17056
See related
Ensembl:ENSG00000089169 MIM:612159; AllianceGenome:HGNC:17056
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
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]
Expression
Biased expression in brain (RPKM 30.1) and adrenal (RPKM 1.7) See more
Orthologs
mouse all
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Genomic context

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See RPH3A in Genome Data Viewer
Location:
12q24.13
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (112575236..112898881)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (112552138..112875587)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (113013040..113336686)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903023 Neighboring gene protein tyrosine phosphatase non-receptor type 11 Neighboring gene uncharacterized LOC124903024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:112954684-112955184 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:113015949-113016468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113018366-113018890 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:113039985-113040713 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:113055106-113055606 Neighboring gene NANOG hESC enhancer GRCh37_chr12:113079622-113080142 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113147969-113148469 Neighboring gene microRNA 1302-1 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:113185662-113186162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113229645-113230186 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:113306366-113306564 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7052 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24142 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24146 and experimental_24152 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24159 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24163 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24171 and experimental_24176 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24264 and experimental_24270 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24215 and experimental_24231 Neighboring gene Sharpr-MPRA regulatory region 3381 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24293 and experimental_24295 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24298, experimental_24301 and experimental_24306 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24317/24320 and experimental_24338 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24357 and experimental_24368 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24404 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24448 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_24456 and experimental_24461 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24463 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24487 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7053 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24505 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4887 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24515 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24520 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24535 Neighboring gene MPRA-validated peak1965 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113400746-113401246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:113401247-113401747 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24547 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24553 Neighboring gene 2'-5'-oligoadenylate synthetase 1 Neighboring gene 2'-5'-oligoadenylate synthetase 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Missense variants in RPH3A cause defects in excitatory synaptic function and are associated with a clinically variable neurodevelopmental disorder. Pavinato L, et al. Genet Med, 2023 Nov. PMID 37403762
  2. De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia. Kirov G, et al. Mol Psychiatry, 2012 Feb. PMID 22083728, Free PMC Article
  3. Decreased rabphilin 3A immunoreactivity in Alzheimer's disease is associated with Aβ burden. Tan MG, et al. Neurochem Int, 2014 Jan. PMID 24200817
  4. Rabphilin-3A as a Targeted Autoantigen in Lymphocytic Infundibulo-neurohypophysitis. Iwama S, et al. J Clin Endocrinol Metab, 2015 Jul. PMID 25919460, Free PMC Article
  5. Clinical significance of a novel single nucleotide polymorphism in the 5' untranslated region of the Rabphillin-3A-Like gene in colorectal adenocarcinoma. Katkoori VR, et al. Front Biosci, 2008 Jan 1. PMID 17981610, Free PMC Article

See all (46) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Missense variants in RPH3A cause defects in excitatory synaptic function and are associated with a clinically variable neurodevelopmental disorder.
    Title: Missense variants in RPH3A cause defects in excitatory synaptic function and are associated with a clinically variable neurodevelopmental disorder.
  2. Protein and fat intake interacts with the haplotype of PTPN11_rs11066325, RPH3A_rs886477, and OAS3_rs2072134 to modulate serum HDL concentrations in middle-aged people.
    Title: Protein and fat intake interacts with the haplotype of PTPN11_rs11066325, RPH3A_rs886477, and OAS3_rs2072134 to modulate serum HDL concentrations in middle-aged people.
  3. Small GTPase ARF6 Is a Coincidence-Detection Code for RPH3A Polarization in Neutrophil Polarization.
    Title: Small GTPase ARF6 Is a Coincidence-Detection Code for RPH3A Polarization in Neutrophil Polarization.
  4. Rab27/Rabphilin3a/GRAB/Rab3 constitutes a signaling module in sperm exocytosis.
    Title: Grab recruitment by Rab27A-Rabphilin3a triggers Rab3A activation in human sperm exocytosis.
  5. Findings indicate that Rph3A activity is linked to the aberrant synaptic localization of GluN2A-expressing NMDARs characterizing levodopa-induced dyskinesias; suggest that Rph3A/GluN2A complex could represent an innovative therapeutic target for those pathological conditions where NMDAR composition is significantly altered.
    Title: Rabphilin 3A: A novel target for the treatment of levodopa-induced dyskinesias.
  6. Rabphilin-3A is a major autoantigen in Lymphocytic infundibulo-neurohypophysitis (LINH). Autoantibodies to rabphilin-3A may serve as biomarker for the diagnosis of LINH and be useful for the differential diagnosis of Central diabetes insipidus.
    Title: Rabphilin-3A as a Targeted Autoantigen in Lymphocytic Infundibulo-neurohypophysitis.
  7. rabphilin 3A loss correlated with dementia severity, cholinergic deafferentation, and increased beta-amyloid concentrations
    Title: Decreased rabphilin 3A immunoreactivity in Alzheimer's disease is associated with Aβ burden.
  8. Structural insights into the Ca2+ and PI(4,5)P2 binding modes of the C2 domains of rabphilin 3A and synaptotagmin 1.
    Title: Structural insights into the Ca2+ and PI(4,5)P2 binding modes of the C2 domains of rabphilin 3A and synaptotagmin 1.
  9. We found a reduction in rabphilin 3a, a protein involved in vesicle docking and recycling, in Huntington disease[HD] brains of grade III and IV. A deficient pre-synaptic transmitter release may underlie some symptoms of HD.
    Title: Loss of SNAP-25 and rabphilin 3a in sensory-motor cortex in Huntington's disease.
  10. Rabphilin-3A and Rab3A are present in normal mouse, rat, and human kidneys, with an exclusively glomerular expression and a comma-like pattern of positivity along the glomerular capillary wall, suggestive for podocyte staining.
    Title: Glomerular podocytes possess the synaptic vesicle molecule Rab3A and its specific effector rabphilin-3a.
Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2018-07-25)

ClinGen Genome Curation Page
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated 2018-07-25)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
New gene functions in megakaryopoiesis and platelet formation.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0985

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables calcium-dependent phospholipid binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables inositol 1,4,5 trisphosphate binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables phosphate ion binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables phosphatidylinositol phosphate binding TAS
Traceable Author Statement
more info
 PubMed 
enables phosphatidylinositol-4,5-bisphosphate binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-containing complex binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables selenium binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables small GTPase binding IEA
Inferred from Electronic Annotation
more info
  
enables zinc ion binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in calcium-dependent activation of synaptic vesicle fusion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in intracellular protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of calcium ion-dependent exocytosis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in spontaneous neurotransmitter secretion IEA
Inferred from Electronic Annotation
more info
  
involved_in synaptic vesicle priming IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
colocalizes_with Golgi apparatus ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in cytosol ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in dendritic spine IEA
Inferred from Electronic Annotation
more info
  
located_in extrinsic component of membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in extrinsic component of synaptic vesicle membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in neuron projection IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in neuron projection ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in postsynaptic membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of protein-containing complex ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in secretory granule ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in synapse IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in synapse ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in synaptic vesicle TAS
Traceable Author Statement
more info
 PubMed 
located_in synaptic vesicle membrane ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
rabphilin-3A
Names
exophilin-1
rabphilin 3A homolog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_052871.1 RefSeqGene

    Range
    221652..328785
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001143854.2 → NP_001137326.1  rabphilin-3A isoform 1

    See identical proteins and their annotated locations for NP_001137326.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1). Variants 1, 3, 4, and 5 all encode the same isoform (1).
    Source sequence(s)
    AB023202, BU738474, DA332963
    Consensus CDS
    CCDS44979.1
    UniProtKB/Swiss-Prot
    B7Z3C3, Q96AE0, Q9Y2J0
    UniProtKB/TrEMBL
    B7Z9Z7
    Related
    ENSP00000374036.4, ENST00000389385.9
    Conserved Domains (3) summary
    cd04035
    Location:393 → 516
    C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
    cd08384
    Location:553 → 685
    C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain
    cd15762
    Location:92 → 171
    FYVE_RP3A; FYVE-related domain found in rabphilin-3A and similar proteins

  2. NM_001347952.2 → NP_001334881.1  rabphilin-3A isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 3, 4, and 5 all encode the same isoform (1).
    Source sequence(s)
    AC004216, AC004465, AC004551
    Consensus CDS
    CCDS44979.1
    UniProtKB/Swiss-Prot
    B7Z3C3, Q96AE0, Q9Y2J0
    UniProtKB/TrEMBL
    B7Z9Z7
    Related
    ENSP00000440384.2, ENST00000543106.6

  3. NM_001347953.1 → NP_001334882.1  rabphilin-3A isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 3, 4, and 5 all encode the same isoform (1).
    Source sequence(s)
    AC004465, AC004551
    Consensus CDS
    CCDS44979.1
    UniProtKB/Swiss-Prot
    B7Z3C3, Q96AE0, Q9Y2J0
    UniProtKB/TrEMBL
    B7Z9Z7
    Related
    ENSP00000405357.3, ENST00000415485.7

  4. NM_001347954.2 → NP_001334883.1  rabphilin-3A isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1, 3, 4, and 5 all encode the same isoform (1).
    Source sequence(s)
    AC004465, AC004551
    Consensus CDS
    CCDS44979.1
    UniProtKB/Swiss-Prot
    B7Z3C3, Q96AE0, Q9Y2J0
    UniProtKB/TrEMBL
    B7Z9Z7

  5. NM_001347955.2 → NP_001334884.1  rabphilin-3A isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC004465, AC004551
    UniProtKB/TrEMBL
    F8VP47

  6. NM_014954.4 → NP_055769.2  rabphilin-3A isoform 2

    See identical proteins and their annotated locations for NP_055769.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is 4 aa shorter compared to isoform 1.
    Source sequence(s)
    AB023202, BU738474, DA332963
    Consensus CDS
    CCDS31904.1
    UniProtKB/TrEMBL
    B7Z9Z7
    Related
    ENSP00000448297.1, ENST00000551052.5
    Conserved Domains (4) summary
    cd04035
    Location:389 → 512
    C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
    cd08384
    Location:549 → 681
    C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain
    cd15762
    Location:88 → 167
    FYVE_RP3A; FYVE-related domain found in rabphilin-3A and similar proteins
    cl26386
    Location:165 → 349
    DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III

RNA

  1. NR_145126.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC004465, AC004551

  2. NR_145127.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC004465, AC004551

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    112575236..112898881
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047428540.1 → XP_047284496.1  rabphilin-3A isoform X1

  2. XM_017019034.3 → XP_016874523.1  rabphilin-3A isoform X2

    Conserved Domains (2) summary
    cd04035
    Location:45 → 168
    C2A_Rabphilin_Doc2; C2 domain first repeat present in Rabphilin and Double C2 domain
    cd08384
    Location:205 → 337
    C2B_Rabphilin_Doc2; C2 domain second repeat present in Rabphilin and Double C2 domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    112552138..112875587
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054371454.1 → XP_054227429.1  rabphilin-3A isoform X3

    UniProtKB/Swiss-Prot
    B7Z3C3, Q96AE0, Q9Y2J0

  2. XM_054371455.1 → XP_054227430.1  rabphilin-3A isoform X1

  3. XM_054371456.1 → XP_054227431.1  rabphilin-3A isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y2J0.1 GenPept UniProtKB/Swiss-Prot:Q9Y2J0

Gene LinkOut

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