Legend
Please 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.
Affects function: The variant's effect on the protein's function, in the format 'R/C' where R is the value reported by the source and C is the value concluded by the curator; '+' indicating the variant affects function, '+?' probably affects function, '+*' affects function, not associated with individual's disease phenotype, '#' affects function, not associated with any known disease phenotype, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect not classified.
Exon: number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = from intron 2 to intron 7, 8i_9 = intron 8/exon 9 boundary, _1 = 5' to exon 1, 18_ = 3' of exon 18, _1_18_ = encompassing the entire 18-exon gene
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.123c>u
- 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
ClassClinical: classification of variant based on clinical consequences, preferably using standardised criteria; e.g. ACMG: 5, pathogenic (dominant) (= disease associated, dominant inheritance), pathogenic (recessive) (= disease associated, recessive inheritance), pathogenic (dominant, reduced risk) (= disease associated, dominant inheritance, incomplete penetrance), likely pathogenic (recessive) (= likely disease associated, recessive inheritance), VUS (= variant of unknown significance), likely benign (= likely not disease-associated), benign (= not disease-associated), non-disease phenotype, drug response, risk factor, associated with, etc. NOTE: pathogenic/likely pathogenic should go together with "variant affects function" In ClassFunctional
Protein: description of variant at protein level (following HGVS recommendations).
- 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
VariO/DNA: variation ontology annotation at DNA level
All options:
- DNA substitution (VariO:0136)
- transition (VariO:0313)
- pyrimidine transition (VariO:0314)
- purine transition (VariO:0315)
- not changed (VariO:0140)
- DNA deletion (VariO:0141)
- DNA insertion (VariO:0142)
- DNA indel (VariO:0143)
- DNA inversion (VariO:0145)
- DNA translocation (VariO:0144)
- transversion (VariO:0316)
- DNA modified (VariO:0337)
VariO/RNA: variation ontology annotation at RNA level
All options:
- RNA substitution (VariO:0312)
- transition (VariO:0313)
- pyrimidine transition (VariO:0314)
- purine transition (VariO:0315)
- transversion (VariO:0316)
- missense variation (VariO:0308)
- initiation codon change (VariO:0317)
- termination codon change (VariO:0309)
- nonsense variation (VariO:0310)
- silent variation (VariO:0318)
- RNA deletion (VariO:0319)
- in-frame deletion (VariO:0320)
- out-of-frame deletion (VariO:0321)
- RNA insertion (VariO:0326)
- in-frame insertion (VariO:0332)
- out-of-frame insertion (VariO:0327)
- RNA indel (VariO:0311)
- in-frame indel (VariO:0030)
- out-of-frame indel (VariO:0031)
- effect on RNA splicing (VariO:0362)
- intron gain (VariO:0364)
- variation at five prime cis splice site (VariO:0367)
- variation at canonical five prime splice site (VariO:0368)
- variation at three prime cis splice site (VariO:0370)
- variation at canonical three prime splice site (VariO:0372)
- cryptic splice site activation (VariO:0373)
- cryptic splice donor activation (VariO:0374)
- cryptic splice acceptor activation (VariO:0375)
- exon loss (VariO:0381)
VariO/Protein: variation ontology annotation at protein level
All options:
- protein truncation (VariO:0015)
- sequence retaining amino acid deletion (VariO:0016)
- nonsynonymous variation (VariO:0017)
- amino acid insertion (VariO:0018)
- amphigoric amino acid insertion (VariO:0019)
- sequence retaining amino acid insertion (VariO:0020)
- amino acid substitution (VariO:0021)
- amino acid indel (VariO:0022)
- amphigoric amino acid indel (VariO:0023)
- sequence retaining amino acid indel (VariO:0029)
- post translational modification (VariO:0028)
P-domain: region/domain protein affected
Protein level: Level of translated protein in peripheral blood mononuclear cells. The level is indicated in relative terms as normal/(much) increased/(much) reduced/absent.
mRNA level: Level of transcribed mRNA present in peripheral blood mononuclear cells. The level is indicated in relative terms as normal/(much) increased/(much) reduced/absent.
Enzyme activity: activity variant enzym
CpG: Variation occurs in CpG dinucleotide; number is the position in the codon
Codon change: Codon change
