LOVD - Legend for CLRN1



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.

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

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)


Protein Domain: Protein Domain
  • Transmembrane 1 (8-28)
  • Transmembrane 2 (101-121)
  • Transmembrane 3 (135-155)
  • Transmembrane 4 (186-206)

Inheritance: Type of inheritance (Heterozygous, Homozygous or Hemizygous))
  • Heterozygous
  • Homozygous
  • Hemizygous

Variant remarks: Integrates Classification:
  • Neutral
  • UV1 : certainly neutral
  • UV2 : likely neutral
  • UV3 : likely pathogenic
  • UV4 : certainly pathogenic
  • Pathogenic

Except for CHM where annotations concerning the effect of the variant are mentioned instead.



dbSNP/RFC: Accession number (rs) in dbSNP or link to reading frame checker for large rearrangements

Reference: Literature reference with possible link to publication in PubMed, dbSNP entry or other online resource.

Reported effect / publication: Original classification reported by the authors. Can differ from the classification in the database depending on additionnal information.

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

Missense: Create a link for USMA: format is {USMA[1]:[2]} with [1] being the gene and [2] being the variant in one-letter-code (no p.). Create a link for MSV3d: format is {MSV3d[1]:[2]} with [1] being the protein UNIPROT id and [2] being the variant in three-letter-code (but no parenthesis).

HSF: Direct link to HSF [1] is Ensembl transcript and [2] is variant/DNA

Re-site: Variant creates (+) or destroys (-) a restriction enzyme recognition site.

CLRN1 DB-ID: Database IDentifier; When available, links to OMIM ID's are provided.

Genomic DNA change: Genomic DNA change following hg19

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

Disease: Disease phenotype of the patient(s).
  • Usher type I (USH1)
  • Usher type II (USH2)
  • Usher type III (USH3)
  • Atypical Usher
  • Choroideremia (CHM)
  • X-linked Retinitis pigmentosa (XLRP)
  • Usher + contiguous gene syndrome
  • Autosomal recessive retinitis pigmentosa (ARRP)
  • Autosomal dominant deafness 11 (DFNA11)
  • Autosomal dominant deafness 8/12 (DFNA8/12)
  • Autosomal dominant deafness 22 (DFNA22)
  • Autosomal dominant deafness 36 (DFNA36)
  • Autosomal recessive deafness 2 (DFNB2)
  • Autosomal recessive deafness 3 (DFNB3)
  • Autosomal recessive deafness 4 (DFNB4)
  • Autosomal recessive deafness 7 (DFNB7)
  • Autosomal recessive deafness 9 (DFNB9)
  • Autosomal recessive deafness 12 (DFNB12)
  • Autosomal recessive deafness 18 (DFNB18)
  • Autosomal recessive deafness 21 (DFNB21)
  • Autosomal recessive deafness 23 (DFNB23)
  • Autosomal recessive deafness 31 (DFNB31)
  • Autosomal recessive deafness 37 (DFNB37)
  • Sector RP + HL
  • Healthy
  • Smith-Magenis Syndrome (SMS)
  • Nonsyndromic recessive auditory neuropathy 1 (NSRAN1)
  • Autosomal Recessive Retinitis Pigmentosa with Late-Onset Hearing Loss (ARRP + LOHL)
  • Non-syndromic Deafness (DFN)
  • Pendred Syndrome (PDS)
  • Thyro├»d disease

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

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.
  • APEX = Arrayed Primer EXtension
  • aCGH = array Comparative Genomics Hybridization
  • 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
  • Minigene = Minigene
  • MLPA = Multiplex Ligation-dependent Probe Amplification
  • PAGE = Poly-Acrylamide Gel-Electrophoresis
  • PCR = Polymerase Chain Reaction
  • PCR-Digest
  • PTT = Protein Truncation Test
  • QPCR = Quantitative PCR
  • RT-PCR = Reverse Transcription and PCR
  • SEQ = SEQuencing
  • SEQ-NG-S = Next Generation Sequencing
  • Southern = Southern Blotting
  • SSCA = Single-Strand DNA Conformation Analysis (SSCP)
  • Western = Western Blotting

Remarks: remarks on patient.

# Reported: Number of times this case has been reported

Gender: Patient gender
  • Female
  • Male

Geographic origin: Geographic origin of the patient