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    PITPNM3 PITPNM family member 3 [ Homo sapiens (human) ]

    Gene ID: 83394, updated on 3-Apr-2024

    Summary

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    Official Symbol
    PITPNM3provided by HGNC
    Official Full Name
    PITPNM family member 3provided by HGNC
    Primary source
    HGNC:HGNC:21043
    See related
    Ensembl:ENSG00000091622 MIM:608921; AllianceGenome:HGNC:21043
    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
    NIR1; ACKR6; CORD5; RDGBA3
    Summary
    This gene encodes a member of a family of membrane-associated phosphatidylinositol transfer domain-containing proteins. The calcium-binding protein has phosphatidylinositol (PI) transfer activity and interacts with the protein tyrosine kinase PTK2B (also known as PYK2). The protein is homologous to a Drosophila protein that is implicated in the visual transduction pathway in flies. Mutations in this gene result in autosomal dominant cone dystrophy. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]
    Expression
    Biased expression in spleen (RPKM 27.1), ovary (RPKM 12.0) and 6 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    17p13.2-p13.1
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (6451263..6556555, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (6350993..6456410, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (6354583..6459875, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985017 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:6347155-6347733 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:6347797-6348024 Neighboring gene aryl hydrocarbon receptor interacting protein like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6350771-6351437 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:6357121-6357839 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8075 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6360909-6361690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6361691-6362472 Neighboring gene PICALM interacting mitotic regulator Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6367015-6367566 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6367567-6368118 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6373134-6373634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6374667-6375190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6377377-6377969 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6377970-6378561 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:6396251-6396752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6400873-6401763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6404362-6404908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6447205-6447705 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6452242-6452960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6458140-6458786 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6471007-6471507 Neighboring gene KIAA0753 Neighboring gene RNA, 5S ribosomal pseudogene 435 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6540081-6540863 Neighboring gene uncharacterized LOC122526780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:6540864-6541645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11584 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:6543558-6544439

    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
    • 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. Ocular phenotype of CORD5, an autosomal dominant retinal dystrophy associated with PITPNM3 p.Q626H mutation. Reinis A, et al. Acta Ophthalmol, 2013 May. PMID 22405330
    2. PITPNM3 is an uncommon cause of cone and cone-rod dystrophies. Köhn L, et al. Ophthalmic Genet, 2010 Sep. PMID 20590364, Free PMC Article
    3. Mutation in the PYK2-binding domain of PITPNM3 causes autosomal dominant cone dystrophy (CORD5) in two Swedish families. Köhn L, et al. Adv Exp Med Biol, 2008. PMID 18188949
    4. Mutation in the PYK2-binding domain of PITPNM3 causes autosomal dominant cone dystrophy (CORD5) in two Swedish families. Köhn L, et al. Eur J Hum Genet, 2007 Jun. PMID 17377520
    5. CCL18-NIR1 promotes oral cancer cell growth and metastasis by activating the JAK2/STAT3 signaling pathway. Jiang X, et al. BMC Cancer, 2020 Jul 8. PMID 32641093, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Chemokine CCL18 Promotes Phagocytosis Through Its Receptor CCR8 Rather than PITPNM3 in Human Microglial Cells.
      Title: Chemokine CCL18 Promotes Phagocytosis Through Its Receptor CCR8 Rather than PITPNM3 in Human Microglial Cells.
    2. CCL18-NIR1 promotes oral cancer cell growth and metastasis by activating the JAK2/STAT3 signaling pathway.
      Title: CCL18-NIR1 promotes oral cancer cell growth and metastasis by activating the JAK2/STAT3 signaling pathway.
    3. Mitofusin-2 (Mfn-2) Might Have Anti-Cancer Effect through Interaction with Transcriptional Factor SP1 and Consequent Regulation on Phosphatidylinositol Transfer Protein 3 (PITPNM3) Expression.
      Title: Mitofusin-2 (Mfn-2) Might Have Anti-Cancer Effect through Interaction with Transcriptional Factor SP1 and Consequent Regulation on Phosphatidylinositol Transfer Protein 3 (PITPNM3) Expression.
    4. CCL18 can increase the invasive ability of non-small cell lung cancer cells by binding to its receptor Nir1.
      Title: CC chemokine ligand 18(CCL18) promotes migration and invasion of lung cancer cells by binding to Nir1 through Nir1-ELMO1/DOC180 signaling pathway.
    5. CCL18 enhances hepatocellular carcinoma (HCC) cell migration, invasion, and epithelial-mesenchymal transition (EMT) through the expression of PITPNM3 and the activation of the NF-kappaB signaling pathway.
      Title: CCL18/PITPNM3 enhances migration, invasion, and EMT through the NF-κB signaling pathway in hepatocellular carcinoma.
    6. Data indicate that PYK2 N-terminal domain interacting receptor 1 (Nir1) could induce epithelial-mesenchymal transition by stabilising Snail via the PI3K/Akt/GSK3beta/Snail signalling pathway through binding to CCL18.
      Title: Nir1 promotes invasion of breast cancer cells by binding to chemokine (C-C motif) ligand 18 through the PI3K/Akt/GSK3β/Snail signalling pathway.
    7. Our observations of the PITPNM3 p.Q626H mutation carriers confirm that CORD5 is a disease not to mix with other retinal degenerations mapped to 17p13.
      Title: Ocular phenotype of CORD5, an autosomal dominant retinal dystrophy associated with PITPNM3 p.Q626H mutation.
    8. CCL18 derived from Tumor-associated macrophages (TAMs) lays a critical role in promoting breast cancer metastasis via its receptor, PITPNM3.
      Title: CCL18 from tumor-associated macrophages promotes breast cancer metastasis via PITPNM3.
    9. Thus, mutations in PITPNM3 do not appear to be a major cause of cone or cone-rod dystrophy.
      Title: PITPNM3 is an uncommon cause of cone and cone-rod dystrophies.
    10. Mutation in the PYK2-binding domain of PITPNM3 causes autosomal dominant cone dystrophy (CORD5) in two Swedish families.
      Title: Mutation in the PYK2-binding domain of PITPNM3 causes autosomal dominant cone dystrophy (CORD5) in two Swedish families.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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

    Associated conditions

    Description Tests
    Cone-rod dystrophy 5
    MedGen: C1832976 OMIM: 600977 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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

    • MGC157740, MGC157741

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables lipid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylinositol transfer activity TAS
    Traceable Author Statement
    more info
    		  
    enables phospholipase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables receptor tyrosine kinase binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in intermembrane lipid transfer IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phosphatidylinositol biosynthetic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in phospholipid transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cell body IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cell projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in endomembrane system IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    membrane-associated phosphatidylinositol transfer protein 3
    Names
    NIR-1
    PITPnm 3
    PYK2 N-terminal domain-interacting receptor 1
    atypical chemokine receptor 6
    cone rod dystrophy 5
    phosphatidylinositol transfer protein, membrane-associated 3
    retinal degeneration B 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.

    Genomic

    1. NG_016020.1 RefSeqGene

      Range
      5003..110295
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001165966.2 → NP_001159438.1  membrane-associated phosphatidylinositol transfer protein 3 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AC055872, AI333030, BC035799, BC128583
      Consensus CDS
      CCDS54080.1
      UniProtKB/TrEMBL
      A1A5C9
      Related
      ENSP00000407882.3, ENST00000421306.7
      Conserved Domains (2) summary
      smart00775
      Location:703 → 833
      LNS2; This domain is found in Saccharomyces cerevisiae protein SMP2, proteins with an N-terminal lipin domain and phosphatidylinositol transfer proteins
      pfam02862
      Location:357 → 557
      DDHD; DDHD domain

    2. NM_031220.4 → NP_112497.2  membrane-associated phosphatidylinositol transfer protein 3 isoform 1

      See identical proteins and their annotated locations for NP_112497.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC055872, AF334586, AI333030, BC035799
      Consensus CDS
      CCDS11076.1
      UniProtKB/Swiss-Prot
      A1A5D0, F8WEW5, Q59GH9, Q9BZ71, Q9NPQ4
      UniProtKB/TrEMBL
      A1A5C9
      Related
      ENSP00000262483.8, ENST00000262483.13
      Conserved Domains (2) summary
      smart00775
      Location:739 → 869
      LNS2; This domain is found in Saccharomyces cerevisiae protein SMP2, proteins with an N-terminal lipin domain and phosphatidylinositol transfer proteins
      pfam02862
      Location:393 → 593
      DDHD; DDHD domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      6451263..6556555 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011524015.4 → XP_011522317.1  membrane-associated phosphatidylinositol transfer protein 3 isoform X1

      UniProtKB/TrEMBL
      A1A5C9
      Conserved Domains (2) summary
      pfam02862
      Location:393 → 593
      DDHD; DDHD domain
      cl21460
      Location:739 → 830
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    2. XM_011524016.4 → XP_011522318.1  membrane-associated phosphatidylinositol transfer protein 3 isoform X2

      Conserved Domains (2) summary
      pfam02862
      Location:393 → 593
      DDHD; DDHD domain
      cl21460
      Location:739 → 770
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    3. XM_011524017.4 → XP_011522319.1  membrane-associated phosphatidylinositol transfer protein 3 isoform X3

      Conserved Domains (1) summary
      pfam02862
      Location:393 → 495
      DDHD; DDHD domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      6350993..6456410 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054317461.1 → XP_054173436.1  membrane-associated phosphatidylinositol transfer protein 3 isoform X1

    2. XM_054317462.1 → XP_054173437.1  membrane-associated phosphatidylinositol transfer protein 3 isoform X2

    3. XM_054317463.1 → XP_054173438.1  membrane-associated phosphatidylinositol transfer protein 3 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BZ71.2 GenPept UniProtKB/Swiss-Prot:Q9BZ71

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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