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Aliases for FAM53A Gene

Aliases for FAM53A Gene

  • Family With Sequence Similarity 53 Member A 2 3 5
  • Dorsal Neural-Tube Nuclear Protein 3 4
  • Protein FAM53A 3 4
  • Family With Sequence Similarity 53, Member A 2
  • Dorsal Neural Tube Nuclear Protein 2
  • DNTNP 3

External Ids for FAM53A Gene

Summaries for FAM53A Gene

GeneCards Summary for FAM53A Gene

FAM53A (Family With Sequence Similarity 53 Member A) is a Protein Coding gene. An important paralog of this gene is FAM53C.

UniProtKB/Swiss-Prot for FAM53A Gene

  • May play an important role in neural development; the dorsomedial roof of the third ventricle.

Additional gene information for FAM53A Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FAM53A Gene

Genomics for FAM53A Gene

GeneHancer (GH) Regulatory Elements for FAM53A Gene

Promoters and enhancers for FAM53A 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
GH04J001682 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 584.5 -0.1 -113 3.1 ZFX MLLT1 ZNF687 L3MBTL2 TRIM24 MYC NCOA6 ZNF148 GLIS2 POLR2A FAM53A ENSG00000207009 GC04M001683 PIR55509 ENSG00000270195 SLBP TMEM129 GC04P001691
GH04J001710 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 30.4 -29.1 -29110 5.7 DACH1 HDGF SP1 MNT ZFX IRF5 MLLT1 ZNF687 SIX5 L3MBTL2 ENSG00000270195 SLBP HAUS3 RNF4 FAM53A FAM193A CRIPAK NELFA MAEA ENSG00000272588
GH04J001719 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 30.3 -38.0 -37958 5.4 SPI1 SP1 MNT ZFX HCFC1 GTF2F1 ZNF687 SIX5 L3MBTL2 TRIM24 TMEM129 TACC3 ENSG00000270195 FAM53A SLBP ENSG00000233799 PIR44595 GC04P001740
GH04J001745 Enhancer 1.3 Ensembl ENCODE dbSUPER 26.9 -63.7 -63749 5.1 DACH1 RAD21 NR2F6 SP1 MNT L3MBTL2 KLF14 ZBTB7A MYC MAX ENSG00000270195 FAM53A TMEM129 TACC3 SLBP GC04M001751 GC04P001740
GH04J001751 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 24.2 -68.2 -68151 2.8 NR2F6 SPI1 ZBTB7A MYC GLIS2 ZIC2 REST ZNF24 PATZ1 MBD1 GC04M001751 ENSG00000270195 FAM53A TACC3 FGFR3 GC04P001740
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around FAM53A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the FAM53A gene promoter:
  • CUTL1
  • FOXO4
  • GATA-1
  • LCR-F1
  • Lhx3a
  • LHX3b
  • Nkx2-2
  • RP58
  • SRY
  • STAT5B

Genomic Locations for FAM53A Gene

Genomic Locations for FAM53A Gene
110,252 bases
Minus strand
66,388 bases
Minus strand

Genomic View for FAM53A Gene

Genes around FAM53A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FAM53A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FAM53A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FAM53A Gene

Proteins for FAM53A Gene

  • Protein details for FAM53A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein FAM53A
    Protein Accession:
    Secondary Accessions:
    • Q6ZUL5

    Protein attributes for FAM53A Gene

    398 amino acids
    Molecular mass:
    42585 Da
    Quaternary structure:
    No Data Available

neXtProt entry for FAM53A Gene

Post-translational modifications for FAM53A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for FAM53A Gene

Domains & Families for FAM53A Gene

Gene Families for FAM53A Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for FAM53A Gene


Suggested Antigen Peptide Sequences for FAM53A Gene

GenScript: Design optimal peptide antigens:
  • Dorsal neural-tube nuclear protein (FA53A_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the FAM53 family.
  • Belongs to the FAM53 family.
genes like me logo Genes that share domains with FAM53A: view

Function for FAM53A Gene

Molecular function for FAM53A Gene

UniProtKB/Swiss-Prot Function:
May play an important role in neural development; the dorsomedial roof of the third ventricle.

Phenotypes From GWAS Catalog for FAM53A Gene

genes like me logo Genes that share phenotypes with FAM53A: view

Animal Model Products

CRISPR Products

Clone Products

  • Applied Biological Materials (abm): Clones for FAM53A - Now 50% OFF >
  • * FAM53A as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * FAM53A tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for FAM53A Gene

Localization for FAM53A Gene

Subcellular locations from UniProtKB/Swiss-Prot for FAM53A Gene

Nucleus. Note=Subnuclear distribution. {ECO:0000250 UniProtKB:Q5ZKN5}.

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 FAM53A gene
Compartment Confidence
nucleus 5
cytoskeleton 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for FAM53A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with FAM53A: view

Pathways & Interactions for FAM53A Gene

SuperPathways for FAM53A Gene

No Data Available

Interacting Proteins for FAM53A Gene

Selected Interacting proteins: Q6NSI3-FA53A_HUMAN for FAM53A Gene via IID

Symbol External ID(s) Details

Gene Ontology (GO) - Biological Process for FAM53A Gene


No data available for Pathways by source and SIGNOR curated interactions for FAM53A Gene

Drugs & Compounds for FAM53A Gene

No Compound Related Data Available

Transcripts for FAM53A Gene

mRNA/cDNA for FAM53A Gene

Unigene Clusters for FAM53A Gene

Family with sequence similarity 53, member A:
Representative Sequences:

CRISPR Products

Clone Products

  • Applied Biological Materials (abm): Clones for FAM53A - Now 50% OFF >
  • * FAM53A as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * FAM53A tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

Alternative Splicing Database (ASD) splice patterns (SP) for FAM53A Gene

No ASD Table

Relevant External Links for FAM53A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for FAM53A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FAM53A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for FAM53A Gene

This gene is overexpressed in Testis (x12.0).

Protein differential expression in normal tissues from HIPED for FAM53A Gene

This gene is overexpressed in Fetal testis (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for FAM53A Gene

Protein tissue co-expression partners for FAM53A Gene

NURSA nuclear receptor signaling pathways regulating expression of FAM53A Gene:


SOURCE GeneReport for Unigene cluster for FAM53A Gene:

genes like me logo Genes that share expression patterns with FAM53A: view

No data available for mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for FAM53A Gene

Orthologs for FAM53A Gene

This gene was present in the common ancestor of chordates.

Orthologs for FAM53A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia FAM53A 35 34
  • 97.74 (n)
(Mus musculus)
Mammalia Fam53a 17 35 34
  • 75.49 (n)
(Rattus norvegicus)
Mammalia Fam53a 34
  • 75.24 (n)
(Canis familiaris)
Mammalia FAM53A 35
  • 57 (a)
(Ornithorhynchus anatinus)
Mammalia FAM53A 35
  • 52 (a)
(Monodelphis domestica)
Mammalia FAM53A 35
  • 51 (a)
(Gallus gallus)
Aves FAM53A 35 34
  • 62.53 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia fam53a 34
  • 60.6 (n)
Species where no ortholog for FAM53A 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)
  • cow (Bos Taurus)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • zebrafish (Danio rerio)

Evolution for FAM53A Gene

Gene Tree for FAM53A (if available)
Gene Tree for FAM53A (if available)
Evolutionary constrained regions (ECRs) for FAM53A: view image

Paralogs for FAM53A Gene

Paralogs for FAM53A Gene

genes like me logo Genes that share paralogs with FAM53A: view

Variants for FAM53A Gene

Sequence variations from dbSNP and Humsavar for FAM53A Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1000003136 -- 1,677,118(-) G/C intron_variant
rs1000071735 -- 1,640,016(-) C/A 3_prime_UTR_variant, downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant
rs1000084510 -- 1,665,340(-) T/C intron_variant
rs1000131468 -- 1,659,113(-) C/T intron_variant
rs1000142259 -- 1,606,447(-) G/A/C genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for FAM53A Gene

Variant ID Type Subtype PubMed ID
dgv5081n100 CNV gain 25217958
dgv8901n54 CNV loss 21841781
esv1210969 CNV insertion 17803354
esv1444353 CNV insertion 17803354
esv1465412 CNV insertion 17803354
esv1776644 CNV insertion 17803354
esv23460 CNV loss 19812545
esv2726825 CNV deletion 23290073
esv2726826 CNV deletion 23290073
esv2726827 CNV deletion 23290073
esv2726828 CNV deletion 23290073
esv2726830 CNV deletion 23290073
esv2726831 CNV deletion 23290073
esv2759218 CNV gain 17122850
esv3396266 CNV duplication 20981092
esv3563245 CNV deletion 23714750
esv3563246 CNV deletion 23714750
esv3575670 CNV gain 25503493
nsv1074668 CNV deletion 25765185
nsv1117052 CNV deletion 24896259
nsv1118993 CNV deletion 24896259
nsv1123739 CNV deletion 24896259
nsv1129711 CNV tandem duplication 24896259
nsv1142598 CNV deletion 24896259
nsv428434 CNV gain 18775914
nsv470000 CNV loss 18288195
nsv508989 CNV insertion 20534489
nsv593316 CNV gain 21841781
nsv593320 CNV loss 21841781
nsv593334 CNV loss 21841781
nsv949754 CNV deletion 24416366
nsv949755 CNV deletion 24416366

Variation tolerance for FAM53A Gene

Residual Variation Intolerance Score: 96.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.87; 79.44% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for FAM53A Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FAM53A Gene

Disorders for FAM53A Gene

Additional Disease Information for FAM53A

No disorders were found for FAM53A Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for FAM53A Gene

Publications for FAM53A Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  3. TP53-based interaction analysis identifies cis-eQTL variants for TP53BP2, FBXO28, and FAM53A that associate with survival and treatment outcome in breast cancer. (PMID: 28179588) Fagerholm R … Nevanlinna H (Oncotarget 2017) 3 58
  4. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. (PMID: 28611215) Fei T … Brown M (Proceedings of the National Academy of Sciences of the United States of America 2017) 3 58
  5. Toward a comprehensive characterization of a human cancer cell phosphoproteome. (PMID: 23186163) Zhou H … Mohammed S (Journal of proteome research 2013) 4 58

Products for FAM53A Gene

Sources for FAM53A Gene

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