PPFIA3 PTPRF interacting protein alpha 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PPFIA3provided by HGNC
Official Full Name: PTPRF interacting protein alpha 3provided by HGNC
Primary source: HGNC:HGNC:9247
See related: Ensembl:ENSG00000177380 MIM:603144; AllianceGenome:HGNC:9247
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
Also known as: LPNA3
Summary: The protein encoded by this gene is a member of the LAR protein-tyrosine phosphatase-interacting protein (liprin) family. Liprins interact with members of LAR family of transmembrane protein tyrosine phosphatases, which are known to be important for axon guidance and mammary gland development. Liprin family protein has been shown to localize phosphatase LAR to cell focal adhesions and may be involved in the molecular organization of presynaptic active zones. [provided by RefSeq, Jul 2008]
Expression: Biased expression in brain (RPKM 10.8), skin (RPKM 6.5) and 10 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.33

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (49119544..49151026)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (52114278..52145758)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (49622801..49654283)

Chromosome 19 - NC_000019.10 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
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?

A syndromic neurodevelopmental disorder caused by rare variants in PPFIA3.
Title: A syndromic neurodevelopmental disorder caused by rare variants in PPFIA3.
Results found that OSR2, VAV3, and PPFIA3 were significantly hypermethylated in gastric cancer (GC) patients offering a good alternative in a simple, promising, and noninvasive detection of GC.
Title: Detection of OSR2, VAV3, and PPFIA3 Methylation in the Serum of Patients with Gastric Cancer.

Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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

D1S2695 (e-PCR), detects polymorphism
- UniSTS:52049

GDB:182000 (e-PCR)
- UniSTS:155340

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in neurotransmitter secretion	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of short-term neuronal synaptic plasticity	ISS Inferred from Sequence or Structural Similarity more info
involved_in synapse organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic vesicle docking	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in acrosomal vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in epididymosome	ISS Inferred from Sequence or Structural Similarity more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in presynaptic active zone	IBA Inferred from Biological aspect of Ancestor more info
located_in presynaptic active zone	TAS Traceable Author Statement more info	PubMed
located_in presynaptic active zone cytoplasmic component	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: liprin-alpha-3

Names: liprin; protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-3; protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3; protein tyrosine phosphatase, receptor type, f polypeptide, alpha 3

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.

mRNA and Protein(s)

NM_003660.4 → NP_003651.1 liprin-alpha-3

See identical proteins and their annotated locations for NP_003651.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes a functional protein.

Source sequence(s)

AB014554, AI346749, BX111585, DA236900

Consensus CDS

CCDS12758.1

UniProtKB/Swiss-Prot

A8K142, O75145, Q3MJA0, Q9H8B5, Q9UEW4

Related

ENSP00000335614.3, ENST00000334186.9

Conserved Domains (7) summary

cd09562
Location:835 → 905

SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1

cd09565
Location:952 → 1017

SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2

cd09568
Location:1037 → 1108

SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3

smart00454
Location:1040 → 1107

SAM; Sterile alpha motif

pfam09728
Location:239 → 499

Taxilin; Myosin-like coiled-coil protein

cl03951
Location:398 → 498

CDC37_N; Cdc37 N terminal kinase binding

cl12013
Location:237 → 419

BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

RNA

NR_103842.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AB014554, AI346749, BC143470, BX111585, DA236900

Related

ENST00000602655.5

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_000019.10 Reference GRCh38.p14 Primary Assembly

Range

49119544..49151026

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047439582.1 → XP_047295538.1 liprin-alpha-3 isoform X1

UniProtKB/Swiss-Prot

A8K142, O75145, Q3MJA0, Q9H8B5, Q9UEW4
XM_047439583.1 → XP_047295539.1 liprin-alpha-3 isoform X2
XM_017027407.2 → XP_016882896.1 liprin-alpha-3 isoform X2

UniProtKB/Swiss-Prot

O75145

Related

ENSP00000473622.1, ENST00000602351.5

Conserved Domains (8) summary

cd09562
Location:835 → 905

SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1

cd09565
Location:943 → 1008

SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2

cd09568
Location:1028 → 1099

SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3

smart00454
Location:1031 → 1098

SAM; Sterile alpha motif

COG1340
Location:32 → 345

COG1340; Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]

pfam09728
Location:239 → 499

Taxilin; Myosin-like coiled-coil protein

cl03951
Location:398 → 498

CDC37_N; Cdc37 N terminal kinase binding

cl12013
Location:237 → 419

BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature