LOVD - Legend for SOX2

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.

Exon: Exon numbering (all SOX2 mutations are in exon 1 since it is a single exon gene)

Legacy DNA ID: This column is not used in the SOX2 database

DNA change: Variation at DNA level. Bases are numbered according to the reference cDNA sequence. Base 1 is the first nucleotide of the initiation codon. Base -1 is immediately 5' of base 1. Base *1 is immediately 3’ of the stop codon.
  • c.138T>G = the T at position 138 of the coding region is changed to a G
  • c.*22G>A = the G at position 22 of the 3’UTR is changed to A
  • c.387delC = the C at position 387 is deleted
  • c.943_944delTC = T943 and C944 are deleted
  • c.70_89del20 = bases 70-89 (inclusive) are deleted
  • c.285dupG = the G at position 285 is duplicated (ie a G is inserted)
  • c.89_90dupCC = C89 and C90 are duplicated (ie CC is inserted)
  • c.180_210dup31 = bases 180-210 (inclusive) are duplicated (ie 31 bases are inserted)
  • c.95_96insT = a T is inserted between bases 95 and 96
  • c.72_73ins11 = 11 bases are inserted between bases 72 and 73
  • c.112_123del12insGA = bases 112-123 are deleted and two bases (GA) are inserted (10 bases are deleted in total)
NB for insertions, deletions and duplications up to 4 bases in length, the full sequence of the inserted, deleted or duplicated bases are given (eg insCAGT). For longer changes, the number of bases is given (eg del8, dup11).

RNA change: Effect of change on RNA. The field is left blank if the change is predicted to be identical to the DNA change.
  • r.? = effect predicted, details unknown
  • r.0 = transcription abolished

Protein change: Predicted effect of change on protein (usually without experimental proof).
  • p.? = change likely, effect unknown
  • p.= = no change expected
  • p.Met1? = initiation codon altered, effect unknown
  • p.Asn46Lys = the asparagine codon at position 46 is replaced by a lysine codon
  • p.Glu93* = the glutamate codon at position 93 is replaced by a stop codon (*)
  • p.84_119del = deletion of amino acids 84-119 inclusive
  • p.Gly23Argfs*65 = a frameshift (fs) causes replacement of the glycine codon at position 23 by an arginine codon; termination occurs after 65 codons
  • p.Ser315ThrfsextX*112 = a frameshift (fs) causes replacement of the serine codon at position 315 by threonine; the protein is extended beyond the normal stop codon (ext) and termination (*) occurs in the 3'UTR after 112 codons

RNA information: Additional information about RNA change

Protein information: Additional information about protein change

SOX2 DB-ID: Database IDentifier; unique identifier for each sequence variant

Location: Variant location within the gene
  • 5' flanking
  • 5' UTR exon
  • 5' UTR intron
  • ORF exon
  • ORF intron
  • 3' UTR
  • 3' flanking
  • Whole gene
  • Part gene
  • Other

Base number: Position of change within cDNA. If the mutation involves more than one base, the most 5' affected base is given

5' Sequence Context: Six bases (or more, if required) immediately 5' of the change

Original Sequence: The original (wild type) sequence

Variant Sequence: The new (mutant or variant) sequence

3' Sequence Context: Six bases (or more. if required) immediately 3' of the change

Type: Type of variant at DNA level (choose from drop-down menu)
  • Substitution
  • Deletion
  • Duplication
  • Insertion
  • Inversion
  • Insertion/Deletion
  • Translocation
  • Other/Complex

Domain: SOX2 protein domain: NTD (N-terminal domain), HMG (HMG box) or CTD (C-terminal domain)

Detection Method: Technique used to detect the mutation
  • Amplicon Melting Analysis
  • CGH
  • Chemical Cleavage of Mismatch
  • Dideoxy Fingerprinting
  • Direct Sequencing
  • FISH
  • Heteroduplex Analysis
  • MLPA
  • SSCP
  • Other

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 (chromosomes) tested, e.g. 5/132.

Remarks: Any other comments

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.
  • 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.
  • 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
  • Other=other

# Reported: Number of times this case has been reported

Population: Additional information on patient population

Gender: Patient gender
  • female
  • male
  • unknown

Sequence Inheritance: Sequence Inheritance

Phenotype Inheritance: Phenotype Inheritance
  • Familial
  • Sporadic
  • -

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