LSDB - Controlled vocabulary terms
Note: This is a working document. Final information will be collected into the VarioML wiki pages.
Inheritance pattern (of phenotype, note: look also inheritance ontology. http://www.human-phenotype-ontology.org/index.php/hpo_docu.html)
- 'familial, consanguineous parents'
- 'familial, autosomal dominant'
- 'familial, autosomal recessive'
- 'familial, X-linked'
- 'sporadic, consanguineous parents'
- 'sporadic, consanguineous parents (1st degree)'
- 'sporadic, consanguineous parents (2nd degree)'
- 'sporadic, consanguineous parents (3rd degree)'
- 'sporadic, non-consanguineous parents'
- 'sporadic, consanguinity parents?'
- 'sporadic? (parents not tested)'
- 'de novo'
- 'de novo, maternal chromosome'
- 'de novo, paternal chromosome'
- 'de novo, from either parent'
- 'inherited, maternal chromosome'
- 'inherited, paternal chromosome'
- 'inherited, from either parent
Complex frameshift: Frameshift involving insertions and deletions
Exon deletion: Deletion encompassing a whole exon or exons, frameshift status unknown
Exon duplication: Duplication of one of more exons, frameshift status unknown
Frameshift: Deletion or insertion causing reading frame shift
In-frame deletion: Deletion of a whole codon or codons. Can include deletion of one or more exons
In-frame duplication: A duplication that does not change the reading frame. Can include one or more exons
In-frame insertion: An insertion of a whole codon or codons. Can include one or more exons
Intronic variant: A variant in an intron which has not been shown to affect splicing
Missense: Substitution resulting in a change to a different amino acid
Nonsense: Substitution resulting in a change to a stop codon
Out of frame deletion: Deletion of part of a codon or number of codons resulting in a frameshift. Can include one or more exons
Out of frame duplication: A duplication that changes the reading frame. Can include one or more exons
Out of frame insertion: An insertion of part of a codon or number of codons resulting in a frameshift. Can include one or more exons
Silent: A nucleotide change that does not change the amino acid
Splice site variant: A mutation that affects splicing
Number of independent observations of a DNA variant (Frequency in XML)
Example values from the Data sharing between LSDBs paper
found once (should it be "found at least once" ?. Same with other terms)
over 100 times
Origin (note this field will be replaced by genetic source and inheritance pattern . JM DEC 2010)
in vitro (cloned) familial familial, consanguineous parents familial, autosomal dominant familial, autosomal recessive familial, X-linked sporadic sporadic, consanguineous parents sporadic, consanguineous parents (1st degree) sporadic, consanguineous parents (2nd degree) sporadic, consanguineous parents (3rd degree) sporadic, non-consanguineous parents sporadic, consanguinity parents? sporadic? (parents not tested) uniparental disomy de novo de novo, somatic mosaicism de novo, germline mosaicism de novo, germline and somatic mosaicism de novo, in patient de novo, in patient (maternal allele) de novo, in patient (paternal allele) de novo, in mother de novo, in mother (grandmaternal allele) de novo, in mother (grandpaternal allele) de novo, in father de novo, in father (grandmaternal allele) de novo, in father (grandpaternal allele) uniparental disomy, maternal allele uniparental disomy, paternal allele
Tissue distribution (Note. This will be normalized with other fields JM May 2011)
- mosaic in germline
Parent #1 Parent #2 Paternal (inferred) Paternal (confirmed) Maternal (inferred) Maternal (confirmed) de novo de novo, on paternal allele de novo, maternal allele
See the paper From LOVD:
No known pathogenicity
Probably no pathogenicity
Unknown Probably pathogenic Pathogenic
Probably Not Pathogenic
Not Known Probably Pathogenic Pathogenic Unclassified
Class 1 – Certainly not pathogenic
Class 2 – Unlikely to be pathogenic but cannot be formally proven
Class 3 – Likely to be pathogenic but cannot be formally proven
Class 4 - Certainly pathogenic
Class 5 - Unknown (not in spec)
Not Known implies that a submitter has given no data on pathogenicity. Unclassified implies that the submitter has specifically indicated that they are unable to classify the pathogenicity of the variant.
Source iso5218 (codes 0,1,2,9)
ARMS CF20: CF Common Mutation Test CF29: Analysis of 29 mutations using the Elucigene CF29 kit CSCE: Conformation sensitive capillary electrophoresis DGGE: Denaturing gradient gel electrophoresis dHPLC: Denaturing high performance liquid chromatography Heteroduplex analysis Loss of heterozygosity analysis Meta-PCR MLPA: Multiplex ligation-dependent probe amplification MS-PCR: Mutagenically separated PCR Multiplex PCR Not Known: The information has not been recorded or provided Not Specified: Test information cannot be determined PCR-PAGE PTT: Protein Trucation Test RNA: RNA work performed Sequencing SNPlex: The SNPlex™ Genotyping System from ABI SSCP SSCP/Heteroduplex