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.
Genomic Reference Sequence.
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.
DNA change: Variation at DNA level.
DNA published: What the variant was reported as (e.g. 521delT); listed only when different from "DNA change".
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: 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)
Re-site: Variant creates (+) or destroys (-) a restriction enzyme recognition site.
Frequency: Frequency of non pathogenic variant reported listed as number of variant alleles/number of control alleles tested, like 5/132.
ATRX DB-ID: Database IDentifier; When available, links to OMIM ID's are provided.
Variant remarks: Variant remarks
Disease: Disease phenotype of the patient(s).
Reference: Literature reference with possible link to publication in PubMed, dbSNP entry or other online resource. "Submitted:" indicates that the mutation was submitted directly to this database by the laboratory indicated.
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.
- Amino = Amino Acid Sequence
- BESS = Base Excision Sequence Scanning
- CMC = Chemical Mismatch Cleavage
- 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
- 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
- Microarray = Allele specific hybridization
# Reported: Number of times this case has been reported
Ethnic origin: Ethnic origin of the patient
Disease Mesh ID: Disease Mesh ID
- D017085 = alpha-Thalassemia
- D017086 = beta-Thalassemia
- D006455 = Abnormal Hemoglobins
- D013789 = Thalassemia
Geographic origin: Geographic origin of the patient