LOVD - Legend for PAX6

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:
  • 5' flanking
  • 5' UTR
  • Exon
  • Intron
  • 3' UTR
  • 3' flanking
  • Whole gene

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.
  • c.50A>G = the A at position 50 is changed to a G
  • c.33delC = The C at position 33 is deleted
  • c.44_45delTT = T45 and T46 are deleted
  • c.65_79del15 = bases 65-79 (inclusive) are deleted
  • c.215dupG = the G at position 215 is duplicated (ie a G is inserted)
  • c.115_116dupCC = C115 and C116 are duplicated (ie CC is inserted)
  • c.80_110dup31 = bases 80-110 (inclusive) are duplicated (ie 31 bases are inserted)
  • c.65_66insT = a T is inserted between bases 65 and 66
  • c.72_73ins11 = 11 bases are inserted between bases 72 and 73
  • c.112_123del12insGA = bases 112-123 are deleted and two bases (GA) are inserted (10 bases are deleted in total)
  • c.113delAinsCAT = base 113 is deleted and 3 bases (CAT) are inserted (2 bases are inserted in total)
NB for insertions, deletions and duplications up to 4 bases in length, the full sequence of the inserted, deleted or duplicated bases are given (eg insCAGT). For longer changes, the number of bases is given (eg del5, dup11).
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.
  • c.682+2T>A = the T at position 2 of intron 8 is changed to A
  • c.683-5_-4delTTinsAAC = the TT dinucleotide at positions -5 and -4 of intron 8 are deleted and replaced by AAC
  • c.683-1G>A = the last base of intron 8 (G) is replaced by A
  • c.-52+1G>A = the first base of intron 3 (G) is replaced by T

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.
  • r.? = a change different to the DNA change is expected, but the details are unknown
  • r.spl? = probable splice error (no experimental proof), eg:
    • splice donor site change (nucleotides +1 to +5 affected)
    • splice acceptor site change (nucleotides -2 to -1 affected)
    • new intronic AG splice acceptor created within 15 nucleotides of normal splice acceptor site
  • r.(spl?) = possible splice error (no experimental proof), eg:
    • change affects first or last nucleotide of exon
    • change affects less highly conserved bases within the splice donor or acceptor
    • change creates strong splice donor or splice acceptor site in exon
  • r.250_357del = deletion of bases 250-357 inclusive (eg for a splice error confirmed by RT-PCR)

Protein change: Predicted effect of change on protein (usually without experimental proof).
  • p.? = change likely, effect unknown
  • p.= = no change expected
  • p.Met1? = initiation codon altered, effect unknown
  • p.Ala33Pro = the alanine codon at posititon 33 is replaced by a proline codon
  • p.Cys40* = the alanine codon at position 40 is replaced by a stop codon (*)
  • p.84_119del = deletion of amino acids 84-119 inclusive
  • p.Asn150Lysfs*57 = a frameshift (fs) causes replacement of the asparagine codon at position 150 by a lysine codon; termination occurs after 57 codons
  • p.Asp413Glufsext*46 = a frameshift (fs) causes replacement of the aspartate codon at position 413 by glutamate; the protein is extended beyond the normal stop codon (ext) and termination (*) occurs in the 3'UTR after 46 codons
  • p.*423Leufsext*108 = a frameshift (fs) causes replacement of the stop codon (*) at position 423 by leucine; termination of the extended protein (ext*) occurs in the 3'UTR after 108 codons

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.
  • Substitution
  • Deletion
  • Duplication
  • Insertion
  • Inversion
  • Insertion/Deletion
  • Translocation
  • Other/Complex

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.
  • Amplicon Melting Analysis
  • CGH
  • Chemical Cleavage of Mismatch
  • Dideoxy Fingerprinting
  • Direct Sequencing
  • FISH
  • Heteroduplex Analysis
  • MLPA
  • SSCP
  • Other

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.
  • DNA
  • RNA
  • 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.
  • AMA = Amplicon Melting Analysis
  • BESS = Base Excision Sequence Scanning
  • CMC = Chemical Mismatch Cleavage
  • CGH = Comparative Genome Hybridisation
  • 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
  • FISH=Fluorescent in situ hybridization
  • HD = HeteroDuplex analysis
  • IHC = Immuno-Histo-Chemistry
  • mPCR = multiplex PCR
  • MAPH = Multiplex Amplifiable Probe Hybridisation
  • MLPA = Multiplex Ligation-dependent Probe Amplification
  • PAGE = Poly-Acrylamide Gel-Electrophoresis
  • PCR = Polymerase Chain Reaction
  • PTT = Protein Truncation Test
  • RT-PCR = Reverse Transcription and PCR
  • SEQ = SEQuencing
  • Southern = Southern Blotting
  • SSCA = Single-Strand DNA Conformation Analysis (SSCP)
  • Western = Western Blotting
  • Other=other

# Reported: Number of times this case has been reported

Population: Additional information on patient population

Gender: Patient gender
  • female
  • male
  • unknown

Sequence Inheritance: Sequence Inheritance

Phenotype Inheritance: Phenotype Inheritance
  • Familial
  • Sporadic
  • -

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