LOVD - Legend for HGD



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.

HGD DB-ID: Database IDentifier; When available, links to OMIM ID's are provided.

Exon: Exon numbering.

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: 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)


Original description: Variant_original_description

Variant remarks: Variant remarks

Predicted Mutation Effect**: The effects of the novel missense variants on stability and protein-protein afinity was assessed in the context of the molecular interactions of the wild-type residue using mCSM and DUET.

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.

Mutation HOT-SPOT: mutation_HOT_SPOT

Allele code: Indicates individual alleles of the patients (i.e. patient with the Patient_ID (AKU_AQR_11) has alleles AKU_AQR_11a and AKU_AQR_11b)

Type: Type of variant at DNA level.
  • Substitution
  • Deletion
  • Duplication
  • Insertion
  • Inversion
  • Insertion/Deletion
  • Translocation
  • Other/Complex

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.

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.
  • 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

Location: Variant location at DNA level.
  • 5' Gene flanking
  • 5' UTR
  • Exon
  • Intron
  • 3' UTR
  • 3' Gene flanking
  • unknown

Patient ID: Internal reference to the patient, such as an hospital patient id.

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.

# Reported: Number of times this case has been reported

Geographic origin: Geographic origin of the patient

Patient/Affected_per_Family: Number of patients per family

Families Patients: test