RPH3A rabphilin 3A [Homo sapiens (human)] - Gene

Summary

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

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_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
Rab27/Rabphilin3a/GRAB/Rab3 constitutes a signaling module in sperm exocytosis.
Title: Grab recruitment by Rab27A-Rabphilin3a triggers Rab3A activation in human sperm exocytosis.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D12S1857 (e-PCR)
- UniSTS:43022

WI-11137 (e-PCR)
- UniSTS:41526

SHGC-144673 (e-PCR)
- UniSTS:172344

WI-10614 (e-PCR)
- UniSTS:45179

D12S861 (e-PCR)
- UniSTS:39058

RPH3A_9282 (e-PCR)
- UniSTS:468656

REN53801 (e-PCR)
- UniSTS:378601

A004U31 (e-PCR)
- UniSTS:37116

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

NG_052871.1 RefSeqGene

Range

221652..328785

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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

NR_145126.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC004465, AC004551
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

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

112575236..112898881

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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