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LegendPlease note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.
Effect: The variant's effect on the protein's function, in the format Reported/Curator concluded; '+' indicating the variant affects function, '+?' probably affects function, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect not classified.
DNA change (cDNA): Description of variant at DNA level, based on a coding DNA reference sequence (following HGVS recommendations); e.g. c.123C>T, c.123_145del, c.123_126dup.
RNA change: Description of variant at RNA level (following HGVS recommendations).
- r.? = unknown
- r.(?) = RNA not analysed but probably transcribed copy of DNA variant
- r.spl? = RNA not analysed but variant probably affects splicing
- r.(spl?) = RNA not analysed but variant may affect splicing
- r.0? = change expected to abolish transcription
- p.(Arg345Pro) = change predicted from DNA (RNA not analysed)
- p.Arg345Pro = change derived from RNA analysis
- p.? = unknown effect
- p.0? = probably no protein produced
DB-ID: Database ID of variant, grouping multiple observations of the same variant together, starting with the HGNC gene symbol, followed by an underscore (_) and a six digit number (e.g. DMD_012345). _000000 is used for variants where DNA was not analysed (change predicted from RNA analysis), variants seen in animal models or variants not seen in humans but functionally tested in vitro.
Frequency: Frequency in which the variant was found; e.g 5/760 chromosomes (in 5 of 760 chromosomes tested), 1/33 patients (in 1 of 33 patients analysed in study), 0.05 controls (in 5% of control cases tested).
Freq. EA: Frequency in which the variant was found in the European American population; e.g. 5/760 (in 5 of 760 chromosomes tested).
Freq. AA: Frequency in which the variant was found in the African American population; e.g. 5/760 (in 5 of 760 chromosomes tested).
Template: Template(s) used to detect the sequence variant; DNA = genomic DNA, RNA = RNA (cDNA).
- RNA = RNA (cDNA)
- ? = unknown
- ? = Unknown
- arrayCGH = array for Comparative Genomic Hybridisation
- arraySEQ = array for resequencing
- arraySNP = array for SNP typing
- arrayCNV = array for Copy Number Variation (SNP and CNV probes)
- BESS = Base Excision Sequence Scanning
- CMC = Chemical Mismatch Cleavage
- CSCE = Conformation Sensitive Capillary Electrophoresis
- DGGE = Denaturing-Gradient Gel-Electrophoresis
- DHPLC = Denaturing High-Performance Liquid Chromatography
- DOVAM = Detection Of Virtually All Mutations (SSCA variant)
- ddF = dideoxy Fingerprinting
- DSCA = Double-Strand DNA Conformation Analysis
- EMC = Enzymatic Mismatch Cleavage
- HD = HeteroDuplex analysis
- MCA = high-resolution Melting Curve Analysis (hrMCA)
- IHC = Immuno-Histo-Chemistry
- MAPH = Multiplex Amplifiable Probe Hybridisation
- MLPA = Multiplex Ligation-dependent Probe Amplification
- SEQ-NG = Next-Generation Sequencing
- SEQ-NG-H = Next-Generation Sequencing - Helicos
- SEQ-NG-I = Next-Generation Sequencing - Illumina/Solexa
- SEQ-NG-R = Next-Generation Sequencing - Roche/454
- SEQ-NG-S = Next-Generation Sequencing - SOLiD
- Northern = Northern blotting
- PCR = Polymerase Chain Reaction
- PCRdig = PCR + restriction enzyme digestion
- PCRlr = PCR, long-range
- PCRm = PCR, multiplex
- PCRq = PCR, quantitative
- PAGE = Poly-Acrylamide Gel-Electrophoresis
- PTT = Protein Truncation Test
- PFGE = Pulsed-Field Gel-Electrophoresis (+Southern)
- RT-PCR = Reverse Transcription and PCR
- SEQ = SEQuencing
- SBE = Single Base Extension
- SSCA = Single-Strand DNA Conformation polymorphism Analysis (SSCP)
- SSCAf = SSCA, fluorescent (SSCP)
- Southern = Southern blotting
- TaqMan = TaqMan assay
- Western = Western Blotting
Remarks: Remarks about the individual.