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FAM46D Gene

protein-coding   GIFtS: 48
GCID: GC0XP079675

Family With Sequence Similarity 46, Member D

  See FAM46D-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Family With Sequence Similarity 46, Member D1 2
Cancer/Testis Antigen 1121 2
CT1.262
CT1122
Protein FAM46D2

External Ids:    HGNC: 283991   Entrez Gene: 1699662   Ensembl: ENSG000001740167   UniProtKB: Q8NEK83   

Export aliases for FAM46D gene to outside databases

Previous GC identifers: GC0XP079397 GC0XP079562 GC0XP073172


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for FAM46D Gene:
Antibodies against the protein encoded by this gene were found only in plasma from cancer patients. While it may
be a target for immunotherapy, the function of this gene is unknown. (provided by RefSeq, Dec 2009)

GeneCards Summary for FAM46D Gene:
FAM46D (family with sequence similarity 46, member D) is a protein-coding gene. Diseases associated with FAM46D include recurrent corneal erosion. An important paralog of this gene is FAM46B.




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000023.10  NC_018934.2  NT_011651.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the FAM46D gene promoter:
         RFX1   POU6F1 (c2)   POU3F2   Evi-1   HNF-1A   C/EBPalpha   HNF-1   FOXJ2 (long isoform)   c-Myb   FOXJ2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidFAM46D promoter sequence
   Search Chromatin IP Primers for FAM46D

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FAM46D


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xq21.1   Ensembl cytogenetic band:  Xq21.1   HGNC cytogenetic band: Xq21.1

FAM46D Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FAM46D gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP079675:  view genomic region     (about GC identifiers)

Start:
79,591,003 bp from pter      End:
79,700,810 bp from pter
Size:
109,808 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: FA46D_HUMAN, Q8NEK8 (See protein sequence)
Recommended Name: Protein FAM46D  
Size: 389 amino acids; 44500 Da
Secondary accessions: Q7Z3F6 Q8NHU1

Explore the universe of human proteins at neXtProt for FAM46D: NX_Q8NEK8

Explore proteomics data for FAM46D at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See FAM46D Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001164045.1  NP_689843.1  

    ENSEMBL proteins: 
     ENSP00000308575   ENSP00000443410  

    FAM46D Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR012937 DUF1693

    Graphical View of Domain Structure for InterPro Entry Q8NEK8

    ProtoNet protein and cluster: Q8NEK8

    1 Blocks protein domain: IPB012937 Protein of unknown function DUF1693

    UniProtKB/Swiss-Prot: FA46D_HUMAN, Q8NEK8
    Similarity: Belongs to the FAM46 family


    Find genes that share domains with FAM46D           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for FAM46D
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for FAM46D

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for FAM46D
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for FAM46D

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    hsa-miR-9 hsa-miR-3688-3p hsa-miR-23b hsa-miR-130a* hsa-miR-23a hsa-miR-3682-3p hsa-miR-23c
    SwitchGear 3'UTR luciferase reporter plasmidFAM46D 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat FAM46D

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    GenScript: all cDNA clones in your preferred vector (see all 2): FAM46D (NM_152630)
    Browse Sino Biological Human cDNA Clones
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FAM46D


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    nucleus2
    cytoskeleton1
    peroxisome1
    plasma membrane1

    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for FAM46D
    Interactions:

        Search GeneGlobe Interaction Network for FAM46D

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for FAM46D (Q8NEK82, 3 ENSP000003085754) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RHOXF2Q9BQY42, 3, ENSP000003604414MINT-66555 I2D: score=4 STRING: ENSP00000360441
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for FAM46D (FA46D)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for FAM46D gene (2 alternative transcripts): 
    NM_001170574.1  NM_152630.4  

    Unigene Cluster for FAM46D:

    Family with sequence similarity 46, member D
    Hs.367959  [show with all ESTs]
    Unigene Representative Sequence: NM_001170574
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000308293(uc004edm.2) ENST00000538312(uc004edl.1)
    miRNA
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    7 qRT-PCR Assays for microRNAs that regulate FAM46D:
    hsa-miR-9 hsa-miR-3688-3p hsa-miR-23b hsa-miR-130a* hsa-miR-23a hsa-miR-3682-3p hsa-miR-23c
    SwitchGear 3'UTR luciferase reporter plasmidFAM46D 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat FAM46D
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    OriGene ORF clones in mouse, rat for FAM46D
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): FAM46D (NM_152630)
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat FAM46D
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for FAM46D
    Pre-validated RT2 qPCR Primer Assay in human, mouse / rat FAM46D
      QuantiTect SYBR Green Assays in human, mouse, rat FAM46D
      QuantiFast Probe-based Assays in human, mouse, rat FAM46D

    Additional mRNA sequence: 

    AK128147.1 AK313875.1 BC028710.2 BC030784.2 BC034979.2 BX537938.1 

    2 DOTS entries:

    DT.100001436  DT.101965209 

    11 AceView cDNA sequences:

    NM_152630 BC030784 BX506299 BX537938 BC028710 BP369557 BG722950 AK128147 
    BX506300 BC034979 BG720732 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    FAM46D expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACCTGACAGT
    FAM46D Expression
    About this image

    FAM46D Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    FAM46D Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.367959
        Custom PCR Arrays for FAM46D
    Primer
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    QuantiFast Probe-based Assays in human, mouse, rat FAM46D
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FAM46D

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for FAM46D gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Fam46d1 , 5 family with sequence similarity 46, member D1, 5 82.47(n)1
    77.32(a)1
      X (47.62 cM)5
    2134491  NM_001163104.21  NP_001156576.11 
     1077925905 
    chicken
    (Gallus gallus)
    Aves FAM46D1 family with sequence similarity 46, member D 70.67(n)
    69.19(a)
      422282  XM_420263.4  XP_420263.1 
    lizard
    (Anolis carolinensis)
    Reptilia FAM46D6
    family with sequence similarity 46, member D
    67(a)
    1 ↔ 1
    GL343826.1(18582-19760)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia fam46d1 family with sequence similarity 46, member D 69.02(n)
    69.71(a)
      100494671  XM_002940435.2  XP_002940481.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1001497011 protein FAM46C-like 64.74(n)
    66.4(a)
      100149701  XM_001920582.4  XP_001920617.4 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG304976
    --
    23(a)
    1 → many
    2R(3624524-3670142)
    worm
    (Caenorhabditis elegans)
    Secernentea pqn-446
    Protein PQN-44, isoform c
    33(a)
    1 → many
    I(5372851-5384508) WBGene00004131


    ENSEMBL Gene Tree for FAM46D (if available)
    TreeFam Gene Tree for FAM46D (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for FAM46D gene
    FAM46B2  FAM46C2  FAM46A2  
    4 SIMAP similar genes for FAM46D using alignment to 2 protein entries:     FA46D_HUMAN (see all proteins):
    FAM46A    XTP11    FAM46C    FAM46B

    Find genes that share paralogs with FAM46D           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for FAM46D (see all 1319)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1384302551,2
    --79589033(+) TGAGTA/CCATAT 1 -- us2k10--------
    rs1884017171,2
    --79589066(+) CAAGAA/GAAAGG 1 -- us2k10--------
    rs66220161,2
    C--79589139(+) GTCAAA/GTTAAA 1 -- us2k1 tfbs31Minor allele frequency- G:0.00CSA 1
    rs1418970161,2
    --79589295(+) AGTTAC/TCTTGT 1 -- us2k10--------
    rs1859736891,2
    --79589589(+) CTTAAA/GATAAA 1 -- us2k10--------
    rs59132511,2
    C,F,A,H--79589699(+) AGTAGG/ACCTTT 1 -- us2k117Minor allele frequency- A:0.24NS EA NA WA CSA 1980
    rs1904850261,2
    --79589864(+) ACAAAC/TGAATG 1 -- us2k10--------
    rs1385981481,2
    C--79589916(+) TTACTC/TACATT 1 -- us2k10--------
    rs1492937981,2
    C--79589967(+) GCTATG/TCTATT 1 -- us2k10--------
    rs1840605871,2
    --79590795(+) GCCCAC/GAGTCC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for FAM46D (79591003 - 79700810 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for FAM46D:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv6972CNV Insertion18451855
    esv1341044CNV Insertion17803354

    Locus Specific Mutation Databases (LSDB): FAM46D

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing FAM46D
    DNA2.0 Custom Variant and Variant Library Synthesis for FAM46D

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    1 disease for FAM46D:    
    About MalaCards
    recurrent corneal erosion

    2 diseases from the University of Copenhagen DISEASES database for FAM46D:
    Keratopathy     Recurrent corneal erosion

    Find genes that share disorders with FAM46D           About GenesLikeMe

    Genetic Association Database (GAD): FAM46D

    Export disorders for FAM46D gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for FAM46D gene integrated from 10 sources:
    (articles sorted by number of sources associating them with FAM46D)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    4. A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. (PubMed id 19377476)1 Tarpey P.S.... Stratton M.R. (Nat. Genet. 2009)
    5. Identification of FAM46D as a novel cancer/testis antigen using EST data and serological analysis. (PubMed id 19540335)1 Bettoni F....Camargo A.A. (Genomics 2009)
    6. Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project. (PubMed id 17903300)4 Fox C.S....Atwood L.D. (BMC Med. Genet. 2007)
    7. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
    8. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (Nature 2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 169966 HGNC: 28399 AceView: FAM46D Ensembl:ENSG00000174016 euGenes: HUgn169966
    ECgene: FAM46D H-InvDB: FAM46D

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for FAM46D Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for FAM46D gene:
    Search GeneIP for patents involving FAM46D

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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