LOVD:Checklist

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Contents 1 Submitter 2 Variant 3 Patient 4 Gene

Submitter

Variable	Description	Example
firstname	Submitter's first name.	Ivo
lastname	Submitter's last name.	Fokkema
institute	Submitter's institute.	Leiden University Medical Center
department	Institute department (optional).	Human Genetics
address	Institutional full address.
city	City the institute is located in. Although this information is also in the address field, this field's value is used for sorting purposes.
country	Submitter's country, chosen from a list.
email	Submitter's email address(es), possibly including those of co-workers.
telephone	Optional telephone number.
reference	The reference text the submitter wishes to be referenced by. Defaults to "Country:City"	Netherlands:Leiden
username..created..	audit and login information

Variant

Variable	Description	Example
Exon	Exon numbering.	32
DNA	Change on DNA level.	c.4406A>T
RNA	Change on RNA level.	r.4406a>u
Protein	Change on protein level.	p.Gln1469Leu
DBID	Identifier unique for this DNA variant. So several database entries on one DNA variant share the same DBID.	DMD_00762
Frequency	Frequency of polymorphism reported listed as number of variant alleles/number of control alleles tested.	29/38
Restriction_site	Variant creates (+) or destroys (-) a restriction enzyme recognition site.	+AluI
pathogenic	How pathogenic is this variant regarded (actually in patient2variant table)	No known pathogenicity
symbol	Gene symbol (actually in patient2variant table)	DMD
allele	Parent from which the variant was inherited (actually in patient2variant table)	Maternal (confirmed)

Patient

Variable	Description	Example
Patient/Patient_ID	Reference to the patient given by the submitter, such as an hospital patient id.
Patient/Phenotype/Disease	Disease phenotype of the patient(s).	DMD
Patient/Detection/Template	Template used to detect the variant(s).	DNA
Patient/Detection/Technique	Technique(s) used to identify the variant(s).	DHPLC, SEQ (selected from a list)
Patient/Reference	Reference to paper, database or submitter.	(e.g. link to pubmed)
Patient/Times_reported	Number of times this case has been reported.	1
Patient/Remarks	Optional public remarks.
Patient/Remarks_Non_Public	Optional non-public remarks.
audit info...

Gene

Variable	Description	Example
symbol	Official HGNC gene symbol.	DMD
gene	Official gene name.	Duchenne Muscular Dystrophy
chrom_location	Chromosome location.	Xp21.2
reference	Optional citation references.	(Links to pubmed)
id_entrez	The gene's Entrez Gene ID.	1756
id_omim_gene	The gene's OMIM Gene ID.	300377
id_omim_disease	The gene's OMIM Disease ID(s) including the disease name(s).	310200 Duchenne Muscular Dystrophy (DMD); 300376 Becker Muscular Dystrophy (BMD)
show_hgmd	Provide link to HGMD?
show_genetests	Provide link to GeneTests.org?
note_index	Optional notes on the index (home) page.
note_listing	Optional notes on the variant listings page.
genbank	Whether or not this gene has a GenBank file in the system (No/local/remote).
genbank_uri	If local, this contains the file name. If remote, this contains the GenBank ID.
refseq	Whether or not this gene has a reference sequence file in the system (No/coding/genomic).
refseq_url	If yes, contains the URL to the reference sequence file.
disclaimer	Whether or not this gene has a disclaimer in the system (No/LOVD standard/custom).
disclaimer_text	If custom, contains the text of the disclaimer.
created_by.. audit etc info