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 function of the gene/protein, displayed in the format 'R/C'. R is the value reported by the source (publication, submitter) and this classification may vary between records. C is the value concluded by the curator. Note that in some database the curator uses Summary records to give details on the classification of the variant.Values used: '+' indicating the variant affects function, '+?' probably affects function, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect was not classified.

IDbase Accession Number: IDbase Accession Number

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)

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)
• missing protein (VariO:0240)
• sequence retaining amino acid indel (VariO:0029)
• alternatively initiated protein (VariO:0443)
• artificial protein variation (VariO:0246)
• mistranslated protein (VariO:0330)
• protein structural inheritance (VariO:0026)
• epigenetic protein variation (VariO:0025)
• post translational modification (VariO:0028)
• proteinaceous infection (VariO:0027)

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)
• RNA splicing change (VariO:0334)
• exon loss (VariO:0381)
• missing RNA (VariO:0245)
• unsense variation (VariO:0514)

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. For deletions/duplications extending beyond the reference transcript resp. {0}/{2} is used to replace del/dup. Extent of the deletion/duplication should be specified using the genomic description (g.). "-" indicates the variant described on genomic level does not affect the coding DNA reference sequence.

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

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

P-domain: region/domain protein affected

CpG: Variation occurs in CpG dinucleotide; number is the position in the codon

Enzyme activity: activity variant enzym

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.

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.

How to query this table

All list views have search fields which can be used to search data. You can search for a complete word or you can search for a part of a search term. If you enclose two or more words in double quotes, LOVD will search for the combination of those words only exactly in the order you specify. Note that search terms are case-insensitive and that wildcards such as * are treated as normal text! For all options, like "and", "or", and "not" searches, or searching for prefixes or suffixes, see the table below.

Operator	Column type	Example	Matches
	Text	Arg	all entries containing 'Arg'
space	Text	Arg Ser	all entries containing 'Arg' and 'Ser'
|	Text	Arg|Ser	all entries containing 'Arg' or 'Ser'
!	Text	!fs	all entries not containing 'fs'
^	Text	^p.(Arg	all entries beginning with 'p.(Arg'
$	Text	Ser)$	all entries ending with 'Ser)'
=""	Text	=""	all entries with this field empty
=""	Text	="p.0"	all entries exactly matching 'p.0'
!=""	Text	!=""	all entries with this field not empty
!=""	Text	!="p.0"	all entries not exactly matching 'p.0?'
combination	Text	*|Ter !fs	all entries containing '*' or 'Ter' but not containing 'fs'
	Date	2020	all entries matching the year 2020
|	Date	2020-03|2020-04	all entries matching March or April, 2020
!	Date	!2020-03	all entries not matching March, 2020
<	Date	<2020	all entries before the year 2020
<=	Date	<=2020-06	all entries in or before June, 2020
>	Date	>2020-06	all entries after June, 2020
>=	Date	>=2020-06-15	all entries on or after June 15th, 2020
combination	Date	2019|2020 <2020-03	all entries in 2019 or 2020, and before March, 2020
	Numeric	23	all entries exactly matching 23
|	Numeric	23|24	all entries exactly matching 23 or 24
!	Numeric	!23	all entries not exactly matching 23
<	Numeric	<23	all entries lower than 23
<=	Numeric	<=23	all entries lower than, or equal to, 23
>	Numeric	>23	all entries higher than 23
>=	Numeric	>=23	all entries higher than, or equal to, 23
combination	Numeric	>=20 <30 !23	all entries with values from 20 to 29, but not equal to 23

Some more advanced examples:

Example	Matches
Asian	all entries containing 'Asian', 'asian', including 'Caucasian', 'caucasian', etc.
Asian !Caucasian	all entries containing 'Asian' but not containing 'Caucasian'
Asian|African !Caucasian	all entries containing 'Asian' or 'African', but not containing 'Caucasian'
"South Asian"	all entries containing 'South Asian', but not containing 'South East Asian'

To sort on a certain column, click on the column header or on the arrows. If that column is already selected to sort on, the sort order will be swapped. The column currently sorted on has a darker blue background color than the other columns. The up and down arrows next to the column name indicate the current sorting direction. When sorting on any field other than the default, LOVD will sort secondarily on the default sort column.

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.

Template: Template(s) used to detect the sequence variant; DNA (genomic DNA), RNA (cDNA) or protein
All options:

• DNA
• RNA = RNA (cDNA)
• protein
• ? = unknown

Technique: technique(s) used to identify the sequence variant.
All options:

• ? = unknown
• ARMS = amplification refractory mutation system
• 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)
• ASO = allele-specific oligo hybridisation
• BESS = Base Excision Sequence Scanning
• CMC = Chemical Mismatch Cleavage
• COBRA = Combined Bisulfite Restriction Analysis
• CSCE = Conformation Sensitive Capillary Electrophoresis
• CSGE = Conformation Sensitive Gel Electrophoresis
• ddF = dideoxy Fingerprinting
• 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
• DSDI = Detection Small Deletions and Insertions
• EMC = Enzymatic Mismatch Cleavage
• expr = expression analysis
• FISH = Fluorescent In-Situ Hybridisation
• FISHf = fiberFISH
• HD = HeteroDuplex analysis
• HPLC = High-Performance Liquid Chromatography
• IEF = IsoElectric Focussing
• IHC = Immuno-Histo-Chemistry
• Invader = Invader assay
• MAPH = Multiplex Amplifiable Probe Hybridisation
• MAQ = Multiplex Amplicon Quantification
• MCA = Melting Curve Analysis, high-resolution (HRMA)
• microscope = microscopic analysis (karyotype)
• microsat = microsatellite genotyping
• minigene = expression minigene construct
• MIP = Molecular Inversion Probe amplification
• MIPsm = singele molecule Molecular Inversion Probe amplification
• MLPA = Multiplex Ligation-dependent Probe Amplification
• MLPA-ms = Multiplex Ligation-dependent Probe Amplification, methylation specific
• MS = mass spectrometry
• Northern = Northern blotting
• NUC = nuclease digestion (RNAseT1, S1)
• OM = optical mapping
• PAGE = Poly-Acrylamide Gel-Electrophoresis
• PCR = Polymerase Chain Reaction
• PCRdd = PCR, digital droplet
• PCRdig = PCR + restriction enzyme digestion
• PCRh = PCR, haloplex
• PCRlr = PCR, long-range
• PCRm = PCR, multiplex
• PCRms = PCR, methylation sensitive
• PCRq = PCR, quantitative (qPCR)
• PCRrp = PCR, repeat-primed (RP-PCR)
• PCRsqd = PCR, semi-quantitative duplex
• PE = primer extension (APEX, SNaPshot)
• PEms = primer extension, methylation-sensitive single-nucleotide
• PFGE = Pulsed-Field Gel-Electrophoresis (+Southern)
• PTT = Protein Truncation Test
• RFLP = Restriction Fragment Length Polymorphisms
• RT-PCR = Reverse Transcription and PCR
• RT-PCRq = Reverse Transcription and PCR, quantitative
• SBE = Single Base Extension
• SEQ = SEQuencing (Sanger)
• SEQb = bisulfite SEQuencing
• SEQp = pyroSequencing
• SEQms = sequencing, methylation specific
• SEQ-ON = next-generation sequencing - Oxford Nanopore
• SEQ-NG = next-generation sequencing
• SEQ-NG-RNA = next-generation sequencing RNA
• SEQ-NG-H = next-generation sequencing - Helicos
• SEQ-NG-I = next-generation sequencing - Illumina/Solexa
• SEQ-NG-IT = next-generation sequencing - Ion Torrent
• SEQ-NG-R = next-generation sequencing - Roche/454
• SEQ-NG-S = next-generation sequencing - SOLiD
• SEQ-PB = next-generation sequencing - Pacific Biosciences
• SNPlex = SNPlex
• Southern = Southern blotting
• SSCA = Single-Strand DNA Conformation polymorphism Analysis (SSCP)
• SSCAf = fluorescent SSCA (SSCP)
• STR = Short Tandem Repeat
• TaqMan = TaqMan assay
• Western = Western blotting
• - = not applicable

Tissue: tissue type used for analysis

Remarks: remarks regarding the screening like WGS (whole genome sequencing), WES (whole exome sequencing, gene panel (incl. a list of genes analysed), etc.