LOVD - Legend for TNFRSF10B

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.

External ID: Link(s) to variation databases.

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

Mutation effect: Mutation effect at protein or RNA level.
  • Duplication
  • Exon deletion
  • Frameshift
  • In-frame deletion
  • In-frame insertion
  • In-frame deletion/insertion
  • Initiating methionine
  • Missense
  • Multi-exon deletion
  • Nonsense
  • Other
  • Silent
  • Splice site
  • Stop codon mutated
  • UTR variant

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)

PolyPhen 2: PolyPhen 2 prediction of variant effect
  • Not determined
  • Benign
  • Possibly damaging
  • Probably damaging
  • Unknown

Frequency: Frequency of non pathogenic variant reported listed as number of variant alleles/number of control alleles tested, like 5/132.

TNFRSF10B DB-ID: Database IDentifier; When available, links to OMIM ID's are provided.

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.

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

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

Frequency: Frequency of polymorphism reported listed as number of variant alleles/number of control alleles tested, like 5/132.