Human Gene BARD1 (uc021vwf.1)
  Description: Homo sapiens BRCA1 associated RING domain 1 (BARD1), mRNA.
RefSeq Summary (NM_000465): This gene encodes a protein which interacts with the N-terminal region of BRCA1. In addition to its ability to bind BRCA1 in vivo and in vitro, it shares homology with the 2 most conserved regions of BRCA1: the N-terminal RING motif and the C-terminal BRCT domain. The RING motif is a cysteine-rich sequence found in a variety of proteins that regulate cell growth, including the products of tumor suppressor genes and dominant protooncogenes. This protein also contains 3 tandem ankyrin repeats. The BARD1/BRCA1 interaction is disrupted by tumorigenic amino acid substitutions in BRCA1, implying that the formation of a stable complex between these proteins may be an essential aspect of BRCA1 tumor suppression. This protein may be the target of oncogenic mutations in breast or ovarian cancer. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013].
Transcript (Including UTRs)
   Position: hg19 chr2:215,593,275-215,674,428 Size: 81,154 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr2:215,593,400-215,674,208 Size: 80,809 Coding Exon Count: 9 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:215,593,275-215,674,428)mRNA (may differ from genome)Protein (680 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblExonPrimerGeneCardsGeneNetwork
HGNCLynxMalacardsMGIPubMedTreefam
UniProtKBWikipedia

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): BARD1
CDC HuGE Published Literature: BARD1
Positive Disease Associations: breast cancer , breast cancer breast cancer, male colorectal cancer ovarian cancer prostate cancer , Coronary Artery Disease , Neuroblastoma , neuroblastoma (high-risk)
Related Studies:
  1. breast cancer
    Stacey, S. N. et al. 2006, The BARD1 Cys557Ser Variant and Breast Cancer Risk in Iceland, PLoS Med 2006 3(7) e217. [PubMed 16768547]
    Our findings suggest that BARD1 Cys557Ser is an ancient variant that confers risk of single and multiple primary breast cancers, and this risk extends to carriers of the BRCA2 999del5 mutation.
  2. breast cancer
    Huo, X. et al. 2006, Common non-synonymous polymorphisms in the BRCA1 Associated RING Domain (BARD1) gene are associated with breast cancer susceptibility, Breast Cancer Res Treat 2006. [PubMed 17028982]
  3. breast cancer breast cancer, male colorectal cancer ovarian cancer prostate cancer
    Karppinen, S. M. et al. 2006, Nordic collaborative study of the BARD1 Cys557Ser allele in 3956 cancer cases, J Med Genet 2006. [PubMed 16825437]
    These results provide further evidence that BARD1 Cys557Ser confers a slightly increased risk of breast cancer in women.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: BARD1
Diseases sorted by gene-association score: breast cancer* (341), brca1 hereditary breast and ovarian cancer syndrome* (121), brca2 hereditary breast and ovarian cancer syndrome* (115), breast cancer susceptibility, bard1-related* (100), neuroblastoma, susceptibility (12), hereditary breast ovarian cancer* (8), sporadic breast cancer (6), ovarian cancer, somatic (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 6.72 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 76.01 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -109.40220-0.497 Picture PostScript Text
3' UTR -20.39125-0.163 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR002110 - Ankyrin_rpt
IPR020683 - Ankyrin_rpt-contain_dom
IPR001357 - BRCT_dom

Pfam Domains:
PF00023 - Ankyrin repeat
PF12796 - Ankyrin repeats (3 copies)
PF13606 - Ankyrin repeat
PF13637 - Ankyrin repeats (many copies)
PF13857 - Ankyrin repeats (many copies)
PF16589 - BRCT domain, a BRCA1 C-terminus domain

SCOP Domains:
52113 - BRCT domain
48403 - Ankyrin repeat

ModBase Predicted Comparative 3D Structure on F6MDH8
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Descriptions from all associated GenBank mRNAs
  LF213837 - JP 2014500723-A/21340: Polycomb-Associated Non-Coding RNAs.
AX794378 - Sequence 1 from Patent WO03051920.
JF790280 - Homo sapiens BRCA1 associated RING domain 1 isoform alfa (BARD1) mRNA, complete cds.
JF790281 - Homo sapiens BRCA1 associated RING domain 1 isoform beta (BARD1) mRNA, complete cds.
U76638 - Human BRCA1-associated RING domain protein (BARD1) mRNA, complete cds.
JF790284 - Homo sapiens BRCA1 associated RING domain 1 isoform delta (BARD1) mRNA, complete cds.
AK223409 - Homo sapiens mRNA for BRCA1 associated RING domain 1 variant, clone: FCC109A11.
BC126426 - Homo sapiens BRCA1 associated RING domain 1, mRNA (cDNA clone MGC:161704 IMAGE:8992142), complete cds.
BC126428 - Homo sapiens BRCA1 associated RING domain 1, mRNA (cDNA clone MGC:161706 IMAGE:8992144), complete cds.
JF790283 - Homo sapiens BRCA1 associated RING domain 1 isoform phi (BARD1) mRNA, complete cds.
AK314260 - Homo sapiens cDNA, FLJ95007, highly similar to Homo sapiens BRCA1 associated RING domain 1 (BARD1), mRNA.
JF790286 - Homo sapiens BRCA1 associated RING domain 1 isoform eta (BARD1) mRNA, complete cds.
JF790282 - Homo sapiens BRCA1 associated RING domain 1 isoform gamma (BARD1) mRNA, complete cds.
KJ905697 - Synthetic construct Homo sapiens clone ccsbBroadEn_15367 BARD1 gene, encodes complete protein.
AB590656 - Synthetic construct DNA, clone: pFN21AB5790, Homo sapiens BARD1 gene for BRCA1 associated RING domain 1, without stop codon, in Flexi system.
AK301843 - Homo sapiens cDNA FLJ51596 complete cds, highly similar to BRCA1-associated RING domain protein 1.
JF790285 - Homo sapiens BRCA1 associated RING domain 1 isoform epsilon (BARD1) mRNA, partial cds.
MA449414 - JP 2018138019-A/21340: Polycomb-Associated Non-Coding RNAs.
AK310759 - Homo sapiens cDNA, FLJ17801.
JD299355 - Sequence 280379 from Patent EP1572962.
JD236219 - Sequence 217243 from Patent EP1572962.
KX257619 - Homo sapiens BRCA1-associated RING domain 1 lncRNA (BARD1), partial sequence.
JF790287 - Homo sapiens BRCA1 associated RING domain 1 isoform pi (BARD1) mRNA, partial cds.
JD537772 - Sequence 518796 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_bard1Pathway - BRCA1-dependent Ub-ligase activity

-  Other Names for This Gene
  Alternate Gene Symbols: F6MDH8, F6MDH8_HUMAN, JF790281
UCSC ID: uc021vwf.1
RefSeq Accession: NM_000465
Protein: F6MDH8

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: JF790281.1
exon count: 9CDS single in 3' UTR: no RNA size: 2324
ORF size: 2043CDS single in intron: no Alignment % ID: 99.87
txCdsPredict score: 4201.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.