Sequence variations are described basically as recommended by the Ad-Hoc Committee for Mutation Nomenclature of the Human Genome Variation Society (HGVS). For the most recent recommendations see the HGVS' Nomenclature for the description of sequence variations page. The most recent publication on the subject is by den Dunnen JT & Antonarakis SE (2000), Hum.Mut. 15:7-12.
Exon: exon numbering (see also the Genomic Reference Sequence).
DNA / DNA allele 1: mutation at DNA level. Nucleotide numbering is according to the Genomic Reference Sequence.
DNA allele 2: mutation at DNA level (see DNA allele 1)
- ? = unknown
- (Xi) = second X-chromosome, carrying a normal gene (for instance DMD), which is expected to be inactivated
- 0 = no second allele (e.g. for second X-chromosome in males)
RE-site: the mutation creates (+) or destroys (-) a restriction enzyme recognition site
RNA: effect of change on RNA
- = = RNA change identical to DNA change
- ? = unknown
- (=) = no significant effect expected (but no experimental proof)
- (0) = change expected to abolish transcription
- (ex4ex5del) = probably deletion of exons 4 to 5
- (ex4ex5dup) = probably duplication of exons 4 to 5
- +cry = activation of cryptic splice site (no sequence published)
- spl? = effect on splicing very likely (no experimental proof), examples;
- splice donor site change (nucleotides +1 to +5 affected)
- splice acceptor site change (nucleotides -2 to -1 affected)
- new intronic AG splice acceptor di-nucleotide created close to (within 15 nucleotides) of normal splice acceptor site
- (spl?) = might affect splicing (no experimental proof), examples;
- change affects first or last nucleotide of exon
- change creates strond splice donor or splice acceptor site in exon
Protein: predicted effect of change on protein (usually without experimental proof !)
- ? = unknown
- (0) = change expected to abolish translation
- ?fs = frame shift, but observed phenotype does not fit with prediction (for instance less severe phenotype (BMD) observed, more severe phenotype (DMD) expected)
- ?no fs = frame shift, but observed phenotype does not fit with prediction (for instance more severe phenotype (DMD) observed, less severe phenotype (BMD) expected)
- del = causes deletion
- fs = causes frame shift
- fs? = effect on reading frame very likely (no experimental proof)
- (fs?) = might affect the reading frame (no experimental proof)
- no fs = does not cause frame shift
- X = stop codon (nonsense)
Phenotype: phenotype of the patient(s)
- ? = phenotypic effect of allelic variant uncertain (questionable)
(examples; ?DMD, ?LGMD, etc.)
Freq.: frequency reported listed as number of variant alleles/number of control alleles tested like 5/132
Reference: literature reference with possible link to publication in PubMed, dbSNP entry or other online resource. "DB:" indicates that the mutation was submitted directly to this database by the laboratory indicated.
When submitting a sequence variant, selecting the reference type and filling in the reference ID (Pubmed ID, dbSNP) is sufficient. If you would like to use a different reference, please use the reference ID field.
DNA/RNA: mutation detected in;
- DNA = DNA
- RNA = RNA and DNA
- protein = protein
Technique: technique used to reveal the change reported. For all methods, confirmation by sequencing (SEQ) is included. Select SEQ only when none of other techniques was used.
- BESS = Base Excision Sequence Scanning
- CMC = Chemical Mismatch Cleavage
- DGGE = Denaturing-Gradient Gel-Electrophoresis
- DHPLC = Denaturing High-Performance Liquid Chromatography
- DOVAM = Detection Of Virtually All Mutations (SSCA variant)
- DSCA = Double-Strand DNA Conformation Analysis
- HD = HeteroDuplex analysis
- IHC = Immuno-Histo-Chemistry
- mPCR = multiplex PCR
- MAPH = Multiplex Amplifiable Probe Hybridisation
- MLPA = Multiplex Ligation-dependent Probe Amplification
- PAGE = Poly-Acrylamide Gel-Electrophoresis
- PCR = Polymerase Chain Reaction
- PTT = Protein Truncation Test
- RT-PCR = Reverse Transcription and PCR
- SEQ = SEQuencing
- Southern = Southern Blotting
- SSCA = Single-Strand DNA Conformation Analysis (SSCP)
- Western = Western Blotting
FOXL2db-ID: FOXL2 database IDentifier. When available, links to OMIM ID's are provided
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