LOVD - Legend for RB1

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.

g-position: Variation at DNA level according to GenBank accession number L11910 (NCBI Genbank)

cDNA change: Variation at DNA level.

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

Exon: Exon numbering.

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)

RBWiki: RBWiki

expected consequence type: expected consequence type at protein level, e.g. frameshift, missense
  • unknown
  • missense
  • nonsense
  • silent
  • frameshift
  • in-frame
  • splice
  • variant
  • promoter

RB1 DB-ID: Database IDentifier; When available, links to OMIM ID's are provided.

originated_in: data on the cell of origin, either germline or somatic (mosaic mutations are of somatic origin)
  • germline
  • somatic
  • unknown

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

Phenotype: Disease phenotype of the patient(s). rb = retinoblastoma
  • retinoblastoma
  • unilateral rb
  • bilateral rb
  • no cancer
  • other cancer

Mut. origin: Origin of mutation
  • unknown
  • germline
  • somatic
  • mosaicism

Tissue: Tissue type in which the sequence variant was detected.

Template: Variant detected in DNA, RNA and/or Protein.
  • DNA
  • RNA
  • Protein

tumor-genotype: Genotype of the tumor cells like homozygous, heterozygous, LOH
  • heterozygous
  • hemi/homozygous
  • LOH
  • unknown

family history: Occurrence of the tumor in the family: familial= another family member suffers from the tumor, low penetrance= unaffected carriers with the same mutation, sporadic= first occurence of the tumor (de novo or somatic)
  • familial
  • isolated
  • familial low penetrance
  • unknown

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

Published: Patient data is published in a paper
  • published
  • unpublished