PITPNM3 Gene

HGNC Family	G protein-coupled receptors
Name	PITPNM family member 3
Description	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]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nPITPNM3 functions as a critical mediator in both cancer invasion and retinal signaling. In breast and hepatocellular carcinomas, PITPNM3 serves as a functional receptor for the chemokine CCL18, which is abundantly expressed by tumor‐associated macrophages. Binding of CCL18 to PITPNM3 activates downstream intracellular calcium signaling and NF‑κB pathways, thereby facilitating integrin clustering, cell migration, invasion, and epithelial–mesenchymal transition, all of which ultimately promote tumor metastasis."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn addition to its role in tumor progression, PITPNM3 has been implicated in phototransduction processes within the retina. Mutations in PITPNM3—such as the Q626H alteration identified in families with autosomal dominant cone dystrophy—highlight its importance in maintaining cone photoreceptor function. Although PITPNM3 is homologous to the Drosophila retinal degeneration B (rdgB) gene, in humans the mutation in its C‑terminal region that interacts with nonreceptor tyrosine kinases (e.g., PYK2) suggests a novel mechanism in mammalian photoreceptor signaling."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "3", "end_ref": "5"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n"}, {"type": "p", "children": [{"type": "t", "text": "\nMoreover, the oncogenic potential of PITPNM3 is further supported by evidence from hepatic carcinoma cell studies, where its expression is positively regulated by the transcription factor SP1 and negatively modulated by mitofusin‑2 (Mfn‑2). This regulation impacts tumor growth, as enhanced PITPNM3 expression correlates with increased tumorigenicity, whereas suppression via Mfn‑2 leads to tumor inhibition."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "6"}]}, {"type": "t", "text": " In contrast, in microglial cells, although PITPNM3 is expressed, it appears not to be the dominant receptor mediating CCL18-induced phagocytosis, a process primarily driven by CCR8, thereby illustrating a context-specific role of PITPNM3 in cell signaling."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Jingqi Chen, Yandan Yao, Chang Gong, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CCL18 from tumor-associated macrophages promotes breast cancer metastasis via PITPNM3."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cancer Cell (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.ccr.2011.02.006"}], "href": "https://doi.org/10.1016/j.ccr.2011.02.006"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21481794"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21481794"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Zeyu Lin, Wenbin Li, Heyun Zhang, et al. "}, {"type": "b", "children": [{"type": "t", "text": "CCL18/PITPNM3 enhances migration, invasion, and EMT through the NF-κB signaling pathway in hepatocellular carcinoma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Tumour Biol (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s13277-015-4172-x"}], "href": "https://doi.org/10.1007/s13277-015-4172-x"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26449829"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26449829"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Linda Köhn, Konstantin Kadzhaev, Marie S I Burstedt, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Mutation in the PYK2-binding domain of PITPNM3 causes autosomal dominant cone dystrophy (CORD5) in two Swedish families."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Eur J Hum Genet (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/sj.ejhg.5201817"}], "href": "https://doi.org/10.1038/sj.ejhg.5201817"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17377520"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17377520"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Linda Köhn, Susanne Kohl, Sara J Bowne, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PITPNM3 is an uncommon cause of cone and cone-rod dystrophies."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Ophthalmic Genet (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.3109/13816810.2010.486776"}], "href": "https://doi.org/10.3109/13816810.2010.486776"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20590364"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20590364"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Ainars Reinis, Irina Golovleva, Linda Köhn, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Ocular phenotype of CORD5, an autosomal dominant retinal dystrophy associated with PITPNM3 p.Q626H mutation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Acta Ophthalmol (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1111/j.1755-3768.2011.02381.x"}], "href": "https://doi.org/10.1111/j.1755-3768.2011.02381.x"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "22405330"}], "href": "https://pubmed.ncbi.nlm.nih.gov/22405330"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Tao Tang, Xuxiong Tao, Xing Bao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "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."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Med Sci Monit (2020)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.12659/MSM.918599"}], "href": "https://doi.org/10.12659/MSM.918599"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31955176"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31955176"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Dengfeng Ding, Li Zhang, Xu Liu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Chemokine "}, {"type": "a", "children": [{"type": "t", "text": "i"}], "href": "i"}, {"type": "t", "text": "CCL18"}, {"type": "a", "children": [{"type": "t", "text": "/i"}], "href": "/i"}, {"type": "t", "text": " Promotes Phagocytosis Through Its Receptor CCR8 Rather than PITPNM3 in Human Microglial Cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Interferon Cytokine Res (2022)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1089/jir.2021.0123"}], "href": "https://doi.org/10.1089/jir.2021.0123"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "35041514"}], "href": "https://pubmed.ncbi.nlm.nih.gov/35041514"}]}]}]}
Synonyms	NIR1, RDGBA3, ACKR6
Proteins	PITM3_HUMAN
NCBI Gene ID	83394
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

PITPNM3 has 6,453 functional associations with biological entities spanning 9 categories (molecular profile, organism, chemical, disease, phenotype or trait, functional term, phrase or reference, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 112 datasets.

Click the + buttons to view associations for PITPNM3 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

PITPNM3 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of PITPNM3 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of PITPNM3 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of PITPNM3 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of PITPNM3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of PITPNM3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of PITPNM3 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of PITPNM3 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of PITPNM3 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of PITPNM3 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of PITPNM3 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of PITPNM3 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of PITPNM3 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of PITPNM3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of PITPNM3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	ClinVar Gene-Phenotype Associations 2025	phenotypes associated with PITPNM3 gene from the curated ClinVar Gene-Phenotype Associations 2025 dataset.
	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	gene perturbations changing expression of PITPNM3 gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
	CM4AI U2OS Cell Map Protein Localization Assemblies	assemblies containing PITPNM3 protein from integrated AP-MS and IF data from the CM4AI U2OS Cell Map Protein Localization Assemblies dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of PITPNM3 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing PITPNM3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores 2025	cellular components containing PITPNM3 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with PITPNM3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with PITPNM3 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Disease Associations	diseases associated with PITPNM3 gene/protein from the curated CTD Gene-Disease Associations dataset.
	dbGAP Gene-Trait Associations	traits associated with PITPNM3 gene in GWAS and other genetic association datasets from the dbGAP Gene-Trait Associations dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by PITPNM3 gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores	diseases involving PITPNM3 gene from the DISEASES Curated Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores 2025	diseases involving PITPNM3 gene from the DISEASES Curated Gene-Disease Association Evidence Scores 2025 dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with PITPNM3 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with PITPNM3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with PITPNM3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with PITPNM3 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with PITPNM3 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at PITPNM3 gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of PITPNM3 gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of PITPNM3 gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing PITPNM3 from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD Gene-Disease Associations	diseases associated with PITPNM3 gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.
	GAD High Level Gene-Disease Associations	diseases associated with PITPNM3 gene in GWAS and other genetic association datasets from the GAD High Level Gene-Disease Associations dataset.
	GDSC Cell Line Gene Expression Profiles	cell lines with high or low expression of PITPNM3 gene relative to other cell lines from the GDSC Cell Line Gene Expression Profiles dataset.
	GeneRIF Biological Term Annotations	biological terms co-occuring with PITPNM3 gene in literature-supported statements describing functions of genes from the GeneRIF Biological Term Annotations dataset.