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.
Type: Type of variant at DNA level.
Mutation Effect: Mutation effect at protein or RNA level.
- Exon deletion
- Exon skip
- In-frame deletion
- In-frame insertion
- In-frame deletion/insertion
- Initiating methionine
- Multi-exon deletion
- Splice site
- Stop codon mutated
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)
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
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.
PLOD3 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).
- AAD = Aortic Aneurysm and/or Dissection
- Acrogeria = Acrogeria
- ALGAZ = Al-Gazali syndrome
- Aortic aneurysms = Aortic aneurysms
- Artery dissections = Artery dissections
- CAH = Congenital adrenal hyperplasia
- CCM = Cobblestone-like Cortical Malformation
- Cervical artery dissection = Cervical artery dissection
- Classical EDS = Classical EDS
- Classical-like EDS = Classical-like EDS
- DAD = Distal Aneurysms and Dissections
- Dental Anomalies = Dental Anomalies
- Dermatosparaxis EDS = Dermatosparaxis Ehlers Danlos Syndrome
- EDS = Ehlers Danlos Syndrome type not defined
- EDS AR= EDS autosomal recessive
- EDS I = Ehlers Danlos Syndrome type I
- EDS II = Ehlers Danlos Syndrome type II
- EDS III = Ehlers Danlos Syndrome type III
- EDS IV = Ehlers Danlos Syndrome type IV
- EDS IV (mild) = Mild Ehlers Danlos Syndrome type IV
- EDS IV (severe) = Severe Ehlers Danlos Syndrome type IV
- EDS VI = Ehlers Danlos Syndrome type VI
- EDS VIA = Ehlers Danlos Syndrome type VIA
- EDS VIB = Ehlers Danlos Syndrome type VIB
- EDS B3GALT6 = EDS Beta3GalT6 deficient type
- EDS FKBP22 = EDS FKBP22
- Fibromuscular dysplasia = Fibromuscular dysplasia
- FKBP14 kEDS = FKBP14-kyphoscoliotic EDS
- Gastroschisis = Gastroschisis
- H-TAD = Heritable Thoracic Aorta Disorder
- Intellectual disability = Intellectual disability
- Kyphoscoliotic EDS = Kyphoscoliotic EDS
- Low BMD = Low Bone Mineral Density
- LRS = Larson of Reunion Island Syndrome
- Musculocontractural EDS = Musculocontractural EDS
- Myopia = Myopia
- Progeroid EDS = Progeroid EDS
- SCAD = Spontaneous Coronary Artery Dissection
- Scoliosis = Scoliosis
- SEMDJL = Spondyloepimetaphyseal dysplasia with joint laxity
- spEDS = Spondylodysplastic EDS
- TAAD = Thoracic Aortic Aneurysm and Dissection
- TNXB EDS = TNXB-deficient Ehlers Danlos Syndrome
- TNXB deficiency = TNXB deficiency
- Vascular EDS = Vascular Ehlers Danlos Syndrome
- VCD EDS = Vascular Contractural Deafness Ehlers Danlos Syndrome
- VUR = primary vesicoureteral reflux
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.
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.
- array CGH = Array Comparative Genomic Hybridization
- BESS = Base Excision Sequence Scanning
- CD = Circular Dichroism
- CMC = Chemical Mismatch Cleavage
- CNGP = Custom NGS Gene Panel
- CEP = Custom Exome Panel
- 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
- HRM = High Resolution Melting
- HTS = High Throughput Sequencing
- 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
- SeqArray = Sequencing Array
- SNP Array = SNP Array
- Southern = Southern Blotting
- SSCA = Single-Strand DNA Conformation Analysis (SSCP)
- Western = Western Blotting
- WES = Whole Exome Sequencing
- WGS = Whole Genome Sequencing
- Unknown = Unknown
Ethnic origin: Ethnic origin of the patient