Sequence variations are described basically as recommended by the Ad-Hoc Nomenclature Committee of the Human Genome Variation Society (HGVS). For the most recent recommendations see the HGVS "Nomenclature for the description of sequence variants" web page. The most recent publication on the subject is by den Dunnen JT & Antonarakis SE (2000), Hum.Mut. 15: 7-12.
Coding DNA Reference Sequence, with the first base of the Met-codon counted as position 1.
NOTE: in all cases, unless indicated otherwise, all data of an entry are as reported by the author(s)/submitter.
Path.: Variant pathogenicity, in the format Reported/Concluded; '+' indicating the variant is pathogenic, '+?' probably pathogenic, '-' no known pathogenicity, '-?' probably no pathogenicity, '?' effect unknown.
Exon: Exon numbering (01, 02, 03 .... 13). Each number includes the coding exon and the following intron (ie '06' covers exon 6 and intron 6). '05' covers exon 5, exon 5a, the intron between exon 5 and exon 5a (intron 5-1) and the intron between exon 5a and exon 6 (intron 5-2). In the reference cDNA sequence NM_000280.3 the exons numbered 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14 and 15 correspond to exons 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 and 13 in this database.
Location: Location of the genomic change:
Legacy DNA ID: 'Legacy' mutation nomenclature using the original PAX6 cDNA numbering from the MuStaR PAX6 database.
DNA change: Variation at DNA level based on reference cDNA sequence NM_000280.3. In this database, base 1 is the first nucleotide of the initiation codon (base 534 of NM_000280.3). Base -1 is immediately 5' of base 1. Base *1 is immediately 3' of the stop codon.
All intronic changes are numbered relative to the nearest exonic base. The last base of exon 8 is 682, so the first base of intron 8 is 682+1. The first base of exon 9 is 683, so the last base of intron 8 is 683-1.
RNA change: Effect of change on RNA. In this database the RNA entry is left blank (-) if the change is predicted to be identical to the DNA change.
Protein change: Predicted effect of change on protein (usually without experimental proof).
RNA information: Additional information about RNA change (including experimental evidence where available).
Protein information: Additional information about protein change - unless otherwise stated this is predicted from the genomic mutation and is not based on experimental evidence.
PAX6 DB-ID: DataBase IDentifier; unique identifier for each mutation.
Base number: Position of change within cDNA. For mutations that change more than one base, the most 5' affected nucleotide is given. For intronic mutations, the nearest exonic nucleotide is given.
5' Sequence Context: Bases immediately 5' of the sequence change.
Original Sequence: The original (wild type) sequence.
Variant Sequence: The new (mutant or variant) sequence.
3' Sequence Context: Bases immediately 3' of the sequence change.
Type: Type of variant at DNA level.
Domain: PAX6 protein domain (PD, paired domain; LNK, linker region; HD, homeodomain; PST, proline-serine-threonine-rich domain).
Detection Method: Technique used to detect the mutation.
RE Site: Variant creates (+) or destroys (-) a restriction enzyme recognition site.
Frequency: Frequency of polymorphism reported listed as number of variant alleles/number of control alleles tested, eg 5/132.
Remarks: Other information.
Patient ID: Internal reference to the patient, such as an hospital patient id.
Disease: Disease phenotype of the patient(s).
Reference/Submitter: Literature reference with links to publication in PubMed, dbSNP entry or other online resource (if available). There is also a link to the Submitter ID
Template: Variant detected in DNA, RNA and/or 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.
# Reported: Number of times this case has been reported
Population: Additional information on patient population
Gender: Patient gender
Sequence Inheritance: Sequence Inheritance
Phenotype Inheritance: Phenotype Inheritance
Second PCR: Second PCR
CIS: Other Mutation in Cis
Conserved residue: Variation affects conserved base or amino acid
Related Phenotype: Related Phenotype
Unrelated Phenotype: Unrelated Phenotype