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Aliases for PITPNM3 Gene

Aliases for PITPNM3 Gene

  • PITPNM Family Member 3 2 3 5
  • Phosphatidylinositol Transfer Protein, Membrane-Associated 3 3 4
  • Atypical Chemokine Receptor 6 2 3
  • Cone Rod Dystrophy 5 2 3
  • PITPnm 3 3 4
  • NIR-1 3 4
  • NIR1 3 4
  • Membrane-Associated Phosphatidylinositol Transfer Protein 3 3
  • PYK2 N-Terminal Domain-Interacting Receptor 1 3
  • Pyk2 N-Terminal Domain-Interacting Receptor 1 4
  • Retinal Degeneration B Alpha 3 3
  • RDGBA3 3
  • CORD5 3
  • ACKR6 3

External Ids for PITPNM3 Gene

Previous HGNC Symbols for PITPNM3 Gene

  • CORD5

Previous GeneCards Identifiers for PITPNM3 Gene

  • GC17M006303
  • GC17M006559
  • GC17M006299
  • GC17M006356
  • GC17M006357
  • GC17M006358
  • GC17M006360
  • GC17M006361

Summaries for PITPNM3 Gene

Entrez Gene Summary for PITPNM3 Gene

  • 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]

GeneCards Summary for PITPNM3 Gene

PITPNM3 (PITPNM Family Member 3) is a Protein Coding gene. Diseases associated with PITPNM3 include Cone-Rod Dystrophy 5 and Retinitis Pigmentosa. Among its related pathways are Glycerophospholipid biosynthesis and Metabolism. Gene Ontology (GO) annotations related to this gene include calcium ion binding and receptor tyrosine kinase binding. An important paralog of this gene is PITPNM2.

UniProtKB/Swiss-Prot for PITPNM3 Gene

  • Catalyzes the transfer of phosphatidylinositol and phosphatidylcholine between membranes (in vitro) (By similarity). Binds calcium ions.

Additional gene information for PITPNM3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PITPNM3 Gene

Genomics for PITPNM3 Gene

GeneHancer (GH) Regulatory Elements for PITPNM3 Gene

Promoters and enhancers for PITPNM3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17I006554 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 550.8 +0.9 926 2.3 ZBTB6 MAX SIN3A ZNF48 E2F1 ZNF335 ZFHX2 GLIS2 POLR2A PATZ1 PITPNM3 GC17M006460 GC17P006525
GH17I006505 Enhancer 1.1 Ensembl ENCODE dbSUPER 11.4 +48.1 48108 6 KLF1 MXI1 JUN MAX ZIC2 RAD21 BRCA1 YY1 RFX5 ZKSCAN1 PITPNM3 TXNDC17 ENSG00000274860 PIR55314 GC17M006460
GH17I006473 Enhancer 1.1 Ensembl ENCODE dbSUPER 11 +83.3 83256 0.6 CTCF USF1 ARID4B SIN3A RAD21 GATAD1 SMC3 ZNF143 ZNF444 BCLAF1 PIMREG PITPNM3 PIR55314 PIR59656 GC17M006460
GH17I006474 Enhancer 0.9 ENCODE dbSUPER 11 +80.6 80568 3.2 SMAD1 ZNF449 NFIB JUN TAL1 RAD21 FOSL1 TCF12 CTBP1 GATA3 PIMREG PITPNM3 ENSG00000262089 PIR55314 PIR59656 GC17M006460
GH17I006599 Enhancer 0.8 Ensembl ENCODE 11.5 -43.1 -43064 1.2 L3MBTL2 MAX MAFG MNT ZNF316 FOXK2 SMARCA4 IKZF1 NFE2 MAFK GC17M006601 RNA5SP435 KIAA0753 PITPNM3 TXNDC17 C17orf100 MED31 SLC13A5 GC17M006460
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PITPNM3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PITPNM3 gene promoter:

Genomic Locations for PITPNM3 Gene

Genomic Locations for PITPNM3 Gene
106,214 bases
Minus strand

Genomic View for PITPNM3 Gene

Genes around PITPNM3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PITPNM3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PITPNM3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PITPNM3 Gene

Proteins for PITPNM3 Gene

  • Protein details for PITPNM3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Membrane-associated phosphatidylinositol transfer protein 3
    Protein Accession:
    Secondary Accessions:
    • A1A5D0
    • F8WEW5
    • Q59GH9
    • Q9NPQ4

    Protein attributes for PITPNM3 Gene

    974 amino acids
    Molecular mass:
    106781 Da
    Quaternary structure:
    • Interacts with PTK2B via its C-terminus.
    • Sequence=BAD92367.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for PITPNM3 Gene


neXtProt entry for PITPNM3 Gene

Post-translational modifications for PITPNM3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PITPNM3 Gene

No data available for DME Specific Peptides for PITPNM3 Gene

Domains & Families for PITPNM3 Gene

Gene Families for PITPNM3 Gene

Protein Domains for PITPNM3 Gene

Suggested Antigen Peptide Sequences for PITPNM3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the PtdIns transfer protein family. PI transfer class IIA subfamily.
  • Belongs to the PtdIns transfer protein family. PI transfer class IIA subfamily.
genes like me logo Genes that share domains with PITPNM3: view

Function for PITPNM3 Gene

Molecular function for PITPNM3 Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the transfer of phosphatidylinositol and phosphatidylcholine between membranes (in vitro) (By similarity). Binds calcium ions.

Phenotypes From GWAS Catalog for PITPNM3 Gene

Gene Ontology (GO) - Molecular Function for PITPNM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding TAS 10022914
GO:0005515 protein binding IPI 21481794
GO:0008289 lipid binding IEA --
GO:0008526 phosphatidylinositol transporter activity TAS 10022914
GO:0030971 receptor tyrosine kinase binding TAS 10022914
genes like me logo Genes that share ontologies with PITPNM3: view
genes like me logo Genes that share phenotypes with PITPNM3: view

Human Phenotype Ontology for PITPNM3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

miRNA for PITPNM3 Gene

miRTarBase miRNAs that target PITPNM3

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for PITPNM3 Gene

Localization for PITPNM3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PITPNM3 Gene

Endomembrane system; Peripheral membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PITPNM3 gene
Compartment Confidence
cytosol 5
nucleus 3
plasma membrane 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PITPNM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol TAS --
GO:0012505 endomembrane system IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane TAS 10022914
genes like me logo Genes that share ontologies with PITPNM3: view

Pathways & Interactions for PITPNM3 Gene

genes like me logo Genes that share pathways with PITPNM3: view

Pathways by source for PITPNM3 Gene

Gene Ontology (GO) - Biological Process for PITPNM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006661 phosphatidylinositol biosynthetic process TAS --
GO:0015914 phospholipid transport IEA --
GO:0046488 phosphatidylinositol metabolic process TAS 10022914
genes like me logo Genes that share ontologies with PITPNM3: view

No data available for SIGNOR curated interactions for PITPNM3 Gene

Drugs & Compounds for PITPNM3 Gene

(1) Drugs for PITPNM3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0

(382) Additional Compounds for PITPNM3 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (2-acetyloxy-3-octadec-9-enoxypropyl) 2-trimethylazaniumylethyl phosphate
  • 2-Acetyl-1-(9Z-octadecenyl)-sn-glycero-3-phosphocholine
  • PC(O-18:1(9Z)/2:0)
Phosphatidylcholines Group A
  • (Z,Z)-(1)-(7-Oleoyl-4-oxido-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-enyl)trimethylammonium 4-oxide
  • (Z,Z)-4-hydroxy-N,N,N-trimethyl-10-oxo-7-[(1-oxo-9-octadecenyl)oxy]-3,5,9-Trioxa-4-phosphaheptacos-18-en-1-aminium 4-oxide hydroxide inner salt
  • 1,2-Dioleoyl-rac-glycero-3-phosphocholine
  • 1,2-Dioleoylglycerol-3-phosphorylcholine
  • 1,2-Dioleoylglyceryl-3-phosphorylcholine
Phosphatidylcholines Group B
  • 1-(1-Enyl-palmitoyl)-2-eicosenoyl-sn-glycero-3-phosphocholine
  • GPCho(16:0/20:1)
  • GPCho(16:0/20:1n9)
  • GPCho(16:0/20:1w9)
  • GPCho(36:1)
  • 1,2-Diacyl-sn-glycero-3-phospho-(1'-myo-inositol-3',4',5'-bisphosphate)
  • 1-Phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate
  • Phosphatidylinositol-3,4,5-trisphosphate
  • 1,2-Dihexadecanoyl-rac-glycero-3-phospho-(1'-myo-inositol)
  • 1,2-Dipalmitoyl-rac-glycero-3-phosphoinositol
  • Phosphatidylinositol(16:0/16:0)
  • Phosphatidylinositol(32:0)
  • PI(16:0/16:0)
genes like me logo Genes that share compounds with PITPNM3: view

Transcripts for PITPNM3 Gene

Unigene Clusters for PITPNM3 Gene

PITPNM family member 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for PITPNM3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20a · 20b
SP1: -
SP3: - -
SP4: -

Relevant External Links for PITPNM3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PITPNM3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PITPNM3 Gene

Protein differential expression in normal tissues from HIPED for PITPNM3 Gene

This gene is overexpressed in Spleen (31.2) and Fetal Brain (26.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PITPNM3 Gene

Protein tissue co-expression partners for PITPNM3 Gene

NURSA nuclear receptor signaling pathways regulating expression of PITPNM3 Gene:


SOURCE GeneReport for Unigene cluster for PITPNM3 Gene:


mRNA Expression by UniProt/SwissProt for PITPNM3 Gene:

Tissue specificity: Detected in brain and spleen, and at low levels in ovary.

Evidence on tissue expression from TISSUES for PITPNM3 Gene

  • Nervous system(4.5)
  • Liver(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PITPNM3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • skeletal muscle
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • head
  • lacrimal apparatus
  • pituitary gland
  • breast
  • ovary
  • penis
  • prostate
  • testicle
  • uterus
  • vagina
  • vulva
  • blood
  • blood vessel
  • hair
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with PITPNM3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for PITPNM3 Gene

Orthologs for PITPNM3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PITPNM3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PITPNM3 34 33
  • 98.26 (n)
(Bos Taurus)
Mammalia PITPNM3 34 33
  • 90.12 (n)
(Rattus norvegicus)
Mammalia Pitpnm3 33
  • 89.9 (n)
(Mus musculus)
Mammalia Pitpnm3 16 34 33
  • 89.59 (n)
(Canis familiaris)
Mammalia PITPNM3 34 33
  • 89.17 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 88 (a)
-- 34
  • 87 (a)
-- 34
  • 81 (a)
-- 34
  • 77 (a)
-- 34
  • 76 (a)
-- 34
  • 49 (a)
(Monodelphis domestica)
Mammalia PITPNM3 34
  • 63 (a)
(Gallus gallus)
Aves PITPNM3 34 33
  • 70.73 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia pitpnm3 33
  • 69.71 (n)
(Danio rerio)
Actinopterygii PITPNM3 (1 of 2) 34
  • 66 (a)
wu:fb08f09 33
  • 65.46 (n)
pitpnm3 34
  • 65 (a)
plrdgb 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 29 (a)
Species where no ortholog for PITPNM3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PITPNM3 Gene

Gene Tree for PITPNM3 (if available)
Gene Tree for PITPNM3 (if available)

Paralogs for PITPNM3 Gene

Paralogs for PITPNM3 Gene

(3) SIMAP similar genes for PITPNM3 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with PITPNM3: view

Variants for PITPNM3 Gene

Sequence variations from dbSNP and Humsavar for PITPNM3 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1011098067 uncertain-significance, Cone-Rod Dystrophy, Dominant 6,451,632(-) C/A/G/T 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1036826283 uncertain-significance, Cone-Rod Dystrophy, Dominant 6,451,291(-) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant
rs11078630 benign, Cone-Rod Dystrophy, Dominant 6,452,099(-) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant
rs111943449 likely-benign, Cone-Rod Dystrophy, Dominant 6,454,514(-) C/A 3_prime_UTR_variant, genic_downstream_transcript_variant
rs112833778 uncertain-significance, Cone-Rod Dystrophy, Dominant 6,453,003(-) TCTCTCTCTCTCTCTCTCTCT/TCTCTCTCTCTCT/TCTCTCTCTCTCTCT/TCTCTCTCTCTCTCTCT/TCTCTCTCTCTCTCTCTCT 3_prime_UTR_variant, genic_downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PITPNM3 Gene

Variant ID Type Subtype PubMed ID
esv1197663 CNV deletion 17803354
esv2539012 CNV deletion 19546169
esv2715587 CNV deletion 23290073
esv3639841 CNV loss 21293372
nsv1070383 CNV deletion 25765185
nsv1126449 CNV deletion 24896259
nsv1131130 CNV deletion 24896259
nsv477788 CNV novel sequence insertion 20440878
nsv477807 CNV novel sequence insertion 20440878
nsv519881 CNV loss 19592680
nsv524539 CNV loss 19592680
nsv526449 CNV loss 19592680
nsv574278 CNV gain 21841781
nsv952115 CNV deletion 24416366

Variation tolerance for PITPNM3 Gene

Residual Variation Intolerance Score: 5.52% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.97; 74.69% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PITPNM3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PITPNM3 Gene

Disorders for PITPNM3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for PITPNM3 Gene - From: HGMD, OMIM, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
cone-rod dystrophy 5
  • cord5
retinitis pigmentosa
  • rp
cone dystrophy
  • cone dystrophy 3
- elite association - COSMIC cancer census association via MalaCards


  • Cone-rod dystrophy 5 (CORD5) [MIM:600977]: An inherited retinal dystrophy characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa, due to cone photoreceptors degenerating at a higher rate than rod photoreceptors. {ECO:0000269 PubMed:17377520}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PITPNM3

genes like me logo Genes that share disorders with PITPNM3: view

No data available for Genatlas for PITPNM3 Gene

Publications for PITPNM3 Gene

  1. Identification of a novel family of targets of PYK2 related to Drosophila retinal degeneration B (rdgB) protein. (PMID: 10022914) Lev S … Schlessinger J (Molecular and cellular biology 1999) 2 3 4 22 58
  2. Mutation in the PYK2-binding domain of PITPNM3 causes autosomal dominant cone dystrophy (CORD5) in two Swedish families. (PMID: 17377520) Köhn L … Golovleva I (European journal of human genetics : EJHG 2007) 3 4 58
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  4. CCL18/PITPNM3 enhances migration, invasion, and EMT through the NF-κB signaling pathway in hepatocellular carcinoma. (PMID: 26449829) Lin Z … Ouyang N (Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine 2016) 3 58
  5. CC chemokine ligand 18(CCL18) promotes migration and invasion of lung cancer cells by binding to Nir1 through Nir1-ELMO1/DOC180 signaling pathway. (PMID: 26756176) Shi L … Zhang P (Molecular carcinogenesis 2016) 3 58

Products for PITPNM3 Gene

Sources for PITPNM3 Gene

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