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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
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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

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