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.
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.
Legacy DNA ID: Legacy DNA ID from PAX6/2 database
DNA change: Variation at DNA level.
RNA change: Effect of change on RNA.
- = = RNA change identical to DNA change
- ? = unknown
- (=) = no significant effect expected (but no experimental proof)
- (0) = change expected to abolish transcription
- (ex4ex5del) = probably deletion of exons 4 to 5
- (ex4ex5dup) = probably duplication of exons 4 to 5
- +cry = activation of cryptic splice site (no sequence published)
- spl? = effect on splicing very likely (no experimental proof), examples;
- splice donor site change (nucleotides +1 to +5 affected)
- splice acceptor site change (nucleotides -2 to -1 affected)
- new intronic AG splice acceptor di-nucleotide created close to (within 15 nucleotides) of normal splice acceptor site
- (spl?) = might affect splicing (no experimental proof), examples;
- change affects first or last nucleotide of exon
- change creates strong splice donor or splice acceptor site in exon
Protein change: Predicted effect of change on protein (usually without experimental proof!)
- ? = unknown
- (0) = change expected to abolish translation
- ?fs = frame shift, but observed phenotype does not fit with prediction (for instance less severe phenotype (BMD) observed, more severe phenotype (DMD) expected)
- ?no fs = frame shift, but observed phenotype does not fit with prediction (for instance more severe phenotype (DMD) observed, less severe phenotype (BMD) expected)
- del = causes deletion
- fs = causes frame shift
- fs? = effect on reading frame very likely (no experimental proof)
- (fs?) = might affect the reading frame (no experimental proof)
- no fs = does not cause frame shift
- X = stop codon (nonsense)
RNA information: RNA information
Protein information: Protein Info
MLYCD DB-ID: Database IDentifier; When available, links to OMIM ID's are provided.
Location: Variant location at DNA level.
- 5' Gene flanking
- 5' UTR
- 3' UTR
- 3' Gene flanking
Base number: NucleotideNumber
5' Sequence Context: 5' sequence context
Original Sequence: original sequence
Variant Sequence: Variant Sequence
3' Sequence Context: 3' Sequence context
Type: Type of variant at DNA level.
Domain: Protein Domain
Detection Method: Detection Method
- Amplicon Melting Analysis
- Chemical Cleavage of Mismatch
- Dideoxy Fingerprinting
- Direct Sequencing
- Heteroduplex Analysis
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, like 5/132.
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.
- 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
# 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