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Aliases for FAM46A Gene

Aliases for FAM46A Gene

  • Family With Sequence Similarity 46 Member A 2 3 5
  • HBV X-Transactivated Gene 11 Protein 3 4
  • HBV XAg-Transactivated Protein 11 3 4
  • C6orf37 3 4
  • XTP11 3 4
  • Family With Sequence Similarity 46, Member A 2
  • Chromosome 6 Open Reading Frame 37 2
  • Retinal Expressed Gene C6orf37 3
  • Protein FAM46A 3

External Ids for FAM46A Gene

Previous HGNC Symbols for FAM46A Gene

  • C6orf37

Previous GeneCards Identifiers for FAM46A Gene

  • GC06M082512
  • GC06M082201
  • GC06M079672

Summaries for FAM46A Gene

GeneCards Summary for FAM46A Gene

FAM46A (Family With Sequence Similarity 46 Member A) is a Protein Coding gene. Diseases associated with FAM46A include Retinitis Pigmentosa 25 and Retinitis Pigmentosa. GO annotations related to this gene include poly(A) RNA binding. An important paralog of this gene is FAM46C.

Gene Wiki entry for FAM46A Gene

Additional gene information for FAM46A Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FAM46A Gene

Genomics for FAM46A Gene

Regulatory Elements for FAM46A Gene

Enhancers for FAM46A 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
GH06H081981 1.1 Ensembl ENCODE dbSUPER 10.4 -229.2 -229247 1.3 JUND ZNF341 TARDBP JUN PRDM10 ZNF398 EP300 FAM46A TPBG GC06M081988 ENSG00000260574
GH06H081787 1 Ensembl ENCODE 11 -34.8 -34755 1.1 IRF2 FOXA2 RARA FOS NR2F6 CREM MIXL1 GATAD2A TEAD1 FOXA3 ENSG00000206886 ENSG00000219702 FAM46A LINC02542 LOC105377873 LINC01526
GH06H081812 0.8 FANTOM5 Ensembl 13.5 -60.1 -60127 1.4 POLR2A MAFK RARA FAM46A ENSG00000206886 ENSG00000219702 LINC02542 LINC01526 LOC105377873
GH06H081893 1 Ensembl ENCODE 10.7 -142.6 -142552 2.8 SOX13 MXI1 SAP130 MAX RAD21 ZNF7 YY1 CTBP1 GATA3 HNF4G FAM46A ENSG00000260574 LINC01526
GH06H081833 0.9 Ensembl ENCODE 11.7 -81.7 -81715 1.4 ZNF146 JUN CEBPB EP300 RAD21 RFX5 JUND NFYB ZNF580 RCOR1 FAM46A ENSG00000206886 ENSG00000219702 LINC02542 LINC01526 ENSG00000260574
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around FAM46A on UCSC Golden Path with GeneCards custom track

Promoters for FAM46A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000321694 574 4401 HDGF PKNOX1 MLX ARID4B SIN3A FEZF1 ZNF2 YY1 ZNF143 SP3

Genomic Locations for FAM46A Gene

Genomic Locations for FAM46A Gene
261,336 bases
Minus strand

Genomic View for FAM46A Gene

Genes around FAM46A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FAM46A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FAM46A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FAM46A Gene

Proteins for FAM46A Gene

  • Protein details for FAM46A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein FAM46A
    Protein Accession:
    Secondary Accessions:
    • A8K7U4
    • Q5TF86
    • Q8NFZ9
    • Q9BW32
    • Q9NXV5

    Protein attributes for FAM46A Gene

    442 amino acids
    Molecular mass:
    49666 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAH00683.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for FAM46A Gene


neXtProt entry for FAM46A Gene

Post-translational modifications for FAM46A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for FAM46A Gene

No data available for DME Specific Peptides for FAM46A Gene

Domains & Families for FAM46A Gene

Gene Families for FAM46A Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for FAM46A Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the FAM46 family.
  • Belongs to the FAM46 family.
genes like me logo Genes that share domains with FAM46A: view

Function for FAM46A Gene

Phenotypes From GWAS Catalog for FAM46A Gene

Gene Ontology (GO) - Molecular Function for FAM46A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22658674
GO:0005515 protein binding IPI 25814554
genes like me logo Genes that share ontologies with FAM46A: view
genes like me logo Genes that share phenotypes with FAM46A: view

Animal Model Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for FAM46A Gene

Localization for FAM46A Gene

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 FAM46A gene
Compartment Confidence
nucleus 3
cytosol 3
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for FAM46A Gene

Pathways & Interactions for FAM46A Gene

SuperPathways for FAM46A Gene

No Data Available

Gene Ontology (GO) - Biological Process for FAM46A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010468 regulation of gene expression IMP 21810271
GO:0030193 regulation of blood coagulation IMP 21810271
genes like me logo Genes that share ontologies with FAM46A: view

No data available for Pathways by source and SIGNOR curated interactions for FAM46A Gene

Drugs & Compounds for FAM46A Gene

No Compound Related Data Available

Transcripts for FAM46A Gene

Unigene Clusters for FAM46A Gene

Family with sequence similarity 46, member A:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for FAM46A Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4
SP1: - -
SP2: -

Relevant External Links for FAM46A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for FAM46A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FAM46A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for FAM46A Gene

This gene is overexpressed in Placenta (28.3), Salivary gland (20.9), and Skin (19.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for FAM46A Gene

Protein tissue co-expression partners for FAM46A Gene

NURSA nuclear receptor signaling pathways regulating expression of FAM46A Gene:


SOURCE GeneReport for Unigene cluster for FAM46A Gene:


mRNA Expression by UniProt/SwissProt for FAM46A Gene:

Tissue specificity: Widely expressed, with preferential expression observed in the retina compared to other ocular tissues.

Evidence on tissue expression from TISSUES for FAM46A Gene

  • Skin(4.2)
  • Intestine(4.1)
  • Eye(4)
genes like me logo Genes that share expression patterns with FAM46A: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for FAM46A Gene

Orthologs for FAM46A Gene

This gene was present in the common ancestor of animals.

Orthologs for FAM46A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia FAM46A 33 34
  • 99.55 (n)
(Ornithorhynchus anatinus)
Mammalia FAM46A 34
  • 96 (a)
(Canis familiaris)
Mammalia FAM46A 33 34
  • 94.9 (n)
(Bos Taurus)
Mammalia FAM46A 33 34
  • 94.24 (n)
(Mus musculus)
Mammalia Fam46a 33 16 34
  • 91.36 (n)
(Rattus norvegicus)
Mammalia Fam46a 33
  • 91.02 (n)
(Monodelphis domestica)
Mammalia FAM46A 34
  • 89 (a)
(Gallus gallus)
Aves FAM46A 33 34
  • 85.54 (n)
(Anolis carolinensis)
Reptilia FAM46A 34
  • 82 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia fam46a 33
  • 83.38 (n)
Str.1648 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.13086 33
(Danio rerio)
Actinopterygii fam46a 34
  • 83 (a)
FAM46A (1 of 2) 34
  • 83 (a)
LOC100330676 33
  • 76.71 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG30497 34
  • 26 (a)
(Caenorhabditis elegans)
Secernentea pqn-44 34
  • 35 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 50 (a)
Species where no ortholog for FAM46A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • 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)

Evolution for FAM46A Gene

Gene Tree for FAM46A (if available)
Gene Tree for FAM46A (if available)

Paralogs for FAM46A Gene

Paralogs for FAM46A Gene

(4) SIMAP similar genes for FAM46A Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with FAM46A: view

Variants for FAM46A Gene

Sequence variations from dbSNP and Humsavar for FAM46A Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000090701 -- 81,746,497(+) CCAAA(C/G)TGAGC utr-variant-3-prime
rs1001210075 -- 81,752,299(+) ACCCC(A/G)GGCCT intron-variant
rs1001353149 -- 81,745,701(+) AGTCA(A/G)TACAG downstream-variant-500B
rs1001769585 -- 81,753,797(+) AGCTC(A/G)CTGCC upstream-variant-2KB
rs1001829436 -- 81,752,490(+) CGGCA(A/G)CACTT utr-variant-5-prime

Variation tolerance for FAM46A Gene

Residual Variation Intolerance Score: 37.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.14; 38.93% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for FAM46A 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 and Structural Variations from Database of Genomic Variants (DGV) for FAM46A Gene

Disorders for FAM46A Gene

MalaCards: The human disease database

(2) MalaCards diseases for FAM46A Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
retinitis pigmentosa 25
  • rp25
retinitis pigmentosa
  • retinitis pigmentosa 1
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for FAM46A

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with FAM46A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for FAM46A Gene

Publications for FAM46A Gene

  1. Identification of a novel VNTR polymorphism in C6orf37 and its association with colorectal cancer risk in Chinese population. (PMID: 16545789) Cui J … Yao C (Clinica chimica acta; international journal of clinical chemistry 2006) 3 4 45 60
  2. Identification and characterization of C6orf37, a novel candidate human retinal disease gene on chromosome 6q14. (PMID: 12054608) Lagali PS … Ayyagari R (Biochemical and biophysical research communications 2002) 2 3 4 60
  3. FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases. (PMID: 27060136) Kuchta K … Ginalski K (Nucleic acids research 2016) 2 3 60
  4. A large-scale candidate gene association study of age at menarche and age at natural menopause. (PMID: 20734064) He C … Hunter DJ (Human genetics 2010) 3 45 60
  5. Genetic analysis of FAM46A in Spanish families with autosomal recessive retinitis pigmentosa: characterisation of novel VNTRs. (PMID: 17803723) Barragán I … Antiñolo G (Annals of human genetics 2008) 2 3 60

Products for FAM46A Gene

Sources for FAM46A Gene

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