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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 Metabolism and Glycerophospholipid biosynthesis. 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.

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

Genomics for PITPNM3 Gene

Regulatory Elements for PITPNM3 Gene

Enhancers for PITPNM3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17F006471 1.4 FANTOM5 Ensembl ENCODE 10.9 +84.2 84189 2.5 ARID4B RAD21 RFX5 SCRT2 ZNF143 RCOR1 FOS CREM MIXL1 EGR2 FAM64A PITPNM3 AIPL1 WSCD1 PIR55314 PIR59656
GH17F006505 1.1 Ensembl ENCODE 11.4 +48.1 48108 6.0 BRCA1 RAD21 YY1 RFX5 ZNF366 ZNF143 RCOR1 FOS EGR2 ZNF654 PITPNM3 TXNDC17 ENSG00000274860 PIR55314
GH17F006598 0.9 Ensembl ENCODE 11.5 -42.9 -42944 1.4 MAFG MAX ZNF316 SMARCA4 IKZF1 NFE2L1 NFE2 MAFK EMSY SPI1 KIAA0753 PITPNM3 TXNDC17 ENSG00000256806 MED31 SLC13A5 GC17M006601 RNA5SP435 GC17M006460
GH17F006523 0.9 Ensembl ENCODE 11.2 +33.1 33142 0.4 JUN BHLHE40 MAX USF2 THRB TEAD3 ZNF664 SREBF1 JUND GLIS1 PITPNM3 FAM64A SLC13A5 GC17P006523 GC17P006524 GC17P006525
GH17F006474 0.8 ENCODE 10.9 +80.6 80568 3.2 ESRRA CBX3 TAL1 JUN RAD21 GATA3 ZNF366 SMC3 NR2F6 CHD2 FAM64A PITPNM3 ENSG00000262089 PIR55314 PIR59656
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PITPNM3 on UCSC Golden Path with GeneCards custom track

Promoters for PITPNM3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001339953 157 1201 SP3 ZMYM3 ZNF16 ZNF48 ZNF623 E2F1 ZFHX2 PATZ1 KDM1A FOS

Genomic Location for PITPNM3 Gene

6,450,344 bp from pter
6,556,557 bp from pter
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

Protein Domains for PITPNM3 Gene

Suggested Antigen Peptide Sequences for PITPNM3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 DDHD domain.
  • Belongs to the PtdIns transfer protein family. PI transfer class IIA subfamily.
  • Contains 1 DDHD domain.
  • 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.

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

miRNA for PITPNM3 Gene

miRTarBase miRNAs that target PITPNM3

Inhibitory RNA Products

Flow Cytometry 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

Gene Ontology (GO) - Cellular Components for PITPNM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
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:0006810 transport IEA --
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 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-stearidonoyl-sn-glycero-3-phosphocholine
  • GPCho(16:0/18:4)
  • GPCho(16:0/18:4n3)
  • GPCho(16:0/18:4w3)
  • GPCho(34:4)
  • 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:

Inhibitory RNA Products

Flow Cytometry 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 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.
genes like me logo Genes that share expression patterns with PITPNM3: view

Primer Products

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 35
  • 98.26 (n)
(Bos Taurus)
Mammalia PITPNM3 34 35
  • 90.12 (n)
(Rattus norvegicus)
Mammalia Pitpnm3 34
  • 89.9 (n)
(Mus musculus)
Mammalia Pitpnm3 34 16 35
  • 89.59 (n)
(Canis familiaris)
Mammalia PITPNM3 34 35
  • 89.17 (n)
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 88 (a)
-- 35
  • 87 (a)
-- 35
  • 81 (a)
-- 35
  • 77 (a)
-- 35
  • 76 (a)
-- 35
  • 49 (a)
(Monodelphis domestica)
Mammalia PITPNM3 35
  • 63 (a)
(Gallus gallus)
Aves PITPNM3 34 35
  • 70.73 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia pitpnm3 34
  • 69.71 (n)
(Danio rerio)
Actinopterygii PITPNM3 (1 of 2) 35
  • 66 (a)
wu:fb08f09 34
  • 65.46 (n)
pitpnm3 35
  • 65 (a)
plrdgb 34
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 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 Sequence Context AA Info Type
rs76024428 Cone-rod dystrophy 5 (CORD5) [MIM:600977], Pathogenic 6,468,237(-) ACTCA(C/G)GTCAA reference, missense
rs138671220 Uncertain significance 6,474,566(+) CCGCC(A/G)GGGTC reference, missense
rs139119218 Uncertain significance 6,470,345(+) AGGCC(A/G)TGAGG reference, missense, utr-variant-3-prime
rs139901820 Uncertain significance 6,455,563(+) ATCAT(A/G)CGCGA reference, synonymous-codon
rs146899730 Uncertain significance 6,461,508(+) ATGTC(C/T)GGCCG downstream-variant-500B, reference, synonymous-codon

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

Variant ID Type Subtype PubMed ID
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
esv1197663 CNV deletion 17803354
nsv952115 CNV deletion 24416366
nsv574278 CNV gain 21841781
nsv526449 CNV loss 19592680
nsv524539 CNV loss 19592680
nsv519881 CNV loss 19592680

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)

Relevant External Links 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

(4) MalaCards diseases for PITPNM3 Gene - From: OMIM, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
cone-rod dystrophy 5
  • cord5
retinitis pigmentosa
  • retinitis pigmentosa 1
cone dystrophy
  • retinal cone dystrophy
cone-rod dystrophy
  • cone-rod retinal dystrophy-2
- 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. {ECO:0000269 PubMed:17377520}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PITPNM3

Genetic Association Database (GAD)
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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. (Mol. Cell. Biol. 1999) 2 3 4 22 64
  2. Mutation in the PYK2-binding domain of PITPNM3 causes autosomal dominant cone dystrophy (CORD5) in two Swedish families. (PMID: 17377520) Koehn L. … Golovleva I. (Eur. J. Hum. Genet. 2007) 3 4 64
  3. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein M.Y. … Mann M. (Cell 2015) 3 64
  4. An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. (PMID: 24275569) Bian Y. … Zou H. (J. Proteomics 2014) 4 64
  5. Ocular phenotype of CORD5, an autosomal dominant retinal dystrophy associated with PITPNM3 p.Q626H mutation. (PMID: 22405330) Reinis A. … Sandgren O. (Acta Ophthalmol 2013) 3 64

Products for PITPNM3 Gene

Sources for PITPNM3 Gene