LOVD - Legend for OPA1



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.

OPA1 DB-ID: Database IDentifier; When available, links to OMIM ID's are provided.

DNA change (cDNA): Variation at DNA level.

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

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

Exon: Exon numbering.

Affected domain: Affected domain of the protein.
  • Basic (exons 1-3)
  • GTPase (exons 10-17)
  • Dynamin Central (exons 18-26)
  • Putative GED (exons 29-30)
  • Non-specific domain

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)


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.

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

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

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

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

DNA change/variant 1: Variation at DNA-level described according to the OPA1 transcript variant 1 (exon 4, not 5/4b and 7/5b; RefSeq: NM_015560.2). Variant 1, the original transcript identified, contains 29 exons and encodes an isoform (1) of 960 amino acids (aa). Listed only when different form "DNA change" for reasons of compatibility with the previous naming convention.

Exon/variant 1: Exon numbering described according to the OPA1 transcript variant 1 (exon 4/not 4b and 5b; RefSeq: NM_015560.2). Variant 1, the original transcript identified, contains 29 exons and encodes an isoform (1) of 960 amino acids (aa). Listed only for reasons of compatibility with the previous naming convention.

Protein/isoform 1: Variation at protein level described according to the OPA1 isoform 1 (exon 4, not 5/4b and 7/5b; RefSeq: NP_056375.2). Isoform 1, the original isoform identified, contains 960 amino acids (aa) and is encoded by 29 exons (transcript variant 1). Listed only when different form "Protein" for reasons of compatibility with the previous naming convention.

DNA published: What the variant was reported as (e.g. 521delT); listed only when different from "DNA change".

Variant remarks: Variant remarks

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

Gender: Patient gender
  • Female
  • Male

Disease: Disease phenotype of the patient(s).
  • ADOA = Autosomal Dominant Optic Atrophy
  • ADOAD = Autosomal Dominant Optic Atrophy + Deafness
  • ADOA+ = Autosomal Dominant Optic Atrophy "plus"
  • AR-CMT2 = Charcot-Marie-Tooth Disease, Axonal, Autosomal Recessive
  • CMT2K = Charcot-Marie-Tooth Disease, Axonal, Autosomal Dominant, Type 2K
  • CMT4A = Charcot-Marie-Tooth Disease, Type 4A
  • CMTDI = Charcot-Marie-Tooth Disease, Dominant Intermediate
  • CMTRIA = Charcot-Marie-Tooth Disease, Recessive Intermediate A
  • DSS = Dejerine-Sottas Syndrome

Age of onset: Age of the patient when the first symptoms occurred.
  • Asymptomatic
  • < 1 year
  • 1-5 years
  • 6-10 years
  • 11-20 years
  • 21-30 years
  • 31-40 years
  • 41-50 years
  • > 50 years

Age at last examination: Age of the patient at the last examination.
  • < 1 year
  • 1 year
  • 2 years
  • 3 years
  • 4 years
  • 5 years
  • 6 years
  • 7 years
  • 8 years
  • 9 years
  • 10 years
  • 11 years
  • 12 years
  • 13 years
  • 14 years
  • 15 years
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  • 41 years
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  • 108 years
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  • 110 years
  • 111 years
  • 112 years
  • 113 years
  • 114 years
  • 115 years
  • 116 years
  • 117 years
  • 118 years
  • 119 years
  • 120 years

Duration of disease: Duration of the disease between first symptoms and the age of the last clinical examination.
  • < 11 years
  • 11-20 years
  • 21-30 years
  • 31-40 years
  • 41-50 years
  • > 50 years

Affected relatives: Indicate the presence of affected relatives genetically confirmed.
  • Yes
  • No
  • Unknown

Additional features: Indicate the additional features to the classical description of the disease.
  • Age-related macular degeneration
  • Anemia
  • Ataxia
  • Cardiomyopathy
  • Cataract
  • Cerebellar syndrome
  • Cognitive impairment
  • Diabetes
  • Diaphragmatic paralysis
  • Diarrhea
  • Dysautonomia
  • Dysphagia
  • Dysphonia
  • Dystonia
  • Epilepsy
  • Exocrine pancreatic insufficiency
  • Facial paralysis
  • Glaucoma
  • Hand/finger tremor
  • Hearing loss
  • Hepatic failure
  • High blood pressure
  • Hoarse voice
  • Intestinal obstruction
  • Multiple sclerosis-like illness
  • Myopathy
  • Neuropathic pain
  • Neutropenia
  • Nociceptive pain
  • Ocular hypertension
  • Ophthalmoplegia
  • Optic atrophy
  • Other cause of optic neuropathy
  • Parkinsonian syndrome
  • Peripheral neuropathy
  • Ptosis
  • Pyramidal feature
  • Renal failure
  • Retinitis pigmentosa
  • Spastic paraplegia
  • Vestibular signs
  • Vocal cord paresis

Visual acuity: Best corrected visual acuity. OD: oculus dexter (right eye); OS: oculus sinister (left eye).
Excellent vision: Log MAR < 0.1 ⇔ Snellen > 20/25 ⇔ Decimal > 0.9
Moderately impaired vision: Log MAR 0.2–0.1 ⇔ Snellen 20/32–20/25 ⇔ Decimal 0.63–0.9
Severely impaired vision: Log MAR 0.9–0.3 ⇔ Snellen 20/160–20/40 ⇔ Decimal 0.13–0.5
Profound visual loss: Log MAR > 0.9 ⇔ Snellen < 20/160 ⇔ Decimal < 0.13
Snellen in foot.
  • ----------OCULUS DEXTER-----------
  • OD: Excellent vision (Log MAR < 0.1)
  • OD: Moderately impaired vision (Log MAR: 0.2-0.1)
  • OD: Severely impaired vision (Log MAR: 0.9-0.3)
  • OD: Profound visual loss (Log MAR > 0.9)
  • ----------OCULUS SINISTER-----------
  • OS: Excellent vision (Log MAR < 0.1)
  • OS: Moderately impaired vision (Log MAR: 0.2-0.1)
  • OS: Severely impaired vision (Log MAR: 0.9-0.3)
  • OS: Profound visual loss (Log MAR > 0.9)

Evolution of vision loss: Evolution of vision loss since diagnosis. Worsening if loss of two or more decimal lines; improvement if gain of two or more decimal lines.
  • Unknown
  • Worsening = Worsening (loss of 2 or more decimal lines since diagnosis)
  • Stable
  • Improvement = Improvement (gain of 2 or more decimal lines since diagnosis)

Optic disc: Optic disc appearance.
  • ----------OCULUS DEXTER-----------
  • OD: Normal
  • OD: Temporal pallor
  • OD: Diffuse pallor
  • OD: Temporal grey pigmentary crescent
  • OD: Peripapillary atrophy
  • ----------OCULUS SINISTER-----------
  • OS: Normal
  • OS: Temporal pallor
  • OS: Diffuse pallor
  • OS: Temporal grey pigmentary crescent
  • OS: Peripapillary atrophy

Cupping: Cup to disc ratio on fundoscopy.
  • ----------OCULUS DEXTER-----------
  • OD: [0-0.4]
  • OD: [0.5-0.7]
  • OD: [0.8-1]
  • ----------OCULUS SINISTER-----------
  • OS: [0-0.4]
  • OS: [0.5-0.7]
  • OS: [0.8-1]

Color vision: Clinical evaluation of color vision using Ishihara color vision test, desaturated 15 Hue test or Farnsworth 100 Hue test.
  • ----------OCULUS DEXTER-----------
  • OD: Normal
  • OD: Tritanopia (Blue-Yellow)
  • OD: Protanopia (Red-Green)
  • OD: Deuteranopia
  • OD: Generalised non specific dyschromatopsia
  • ----------OCULUS SINISTER-----------
  • OS: Normal
  • OS: Tritanopia (Blue-Yellow)
  • OS: Protanopia (Red-Green)
  • OS: Deuteranopia
  • OS: Generalised non specific dyschromatopsia

Visual field: Type, value of mean deviation and results of visual field.
  • ----------OCULUS DEXTER - TYPE-----------
  • OD: Type: Goldmann visual field
  • OD: Type: Humphrey/Octopus automated perimetry
  • ----------OCULUS DEXTER - MEAN DEVIATION-----------
  • OD: MD: > 0
  • OD: MD: [0 to -4]
  • OD: MD: [-4.01 to -12]
  • OD: MD: [-12.01 to -20]
  • OD: MD: < -20
  • ----------OCULUS DEXTER - RESULT-----------
  • OD: Result: Normal
  • OD: Result: Centrocecal scotoma
  • OD: Result: Central scotoma
  • OD: Result: Paracentral scotoma
  • OD: Result: Defect in the superotemporal visual field
  • OD: Result: Undefined central defect
  • ----------OCULUS SINISTER - TYPE-----------
  • OS: Type: Goldman visual field
  • OS: Type: Humphrey/Octopus automated perimetry
  • ----------OCULUS SINISTER - MEAN DEVIATION-----------
  • OS: MD: > 0
  • OS: MD: [0 to -4]
  • OS: MD: [-4.01 to -12]
  • OS: MD: [-12.01 to -20]
  • OS: MD: < -20
  • ----------OCULUS SINISTER - RESULT-----------
  • OS: Result: Normal
  • OS: Result: Centrocecal scotoma
  • OS: Result: Central scotoma
  • OS: Result: Paracentral scotoma
  • OS: Result: Defect in the superotemporal visual field
  • OS: Result: Undefined central defect

OCT: Mean retinal nerve fiber layer (RNFL) thickness and mean ganglion cell layer (GCL) thickness by optical coherence tomography (OCT).
  • ----------OCULUS DEXTER - RETINAL NERVE FIBER LAYER-----------
  • OD: Mean RNFL: Not known
  • OD: Mean RNFL: Normal
  • OD: Mean RNFL: Thinning only in the temporal quadrant
  • OD: Mean RNFL: Thinning only in the superior quadrant
  • OD: Mean RNFL: Thinning only in the inferior quadrant
  • OD: Mean RNFL: Thinning only in the nasal quadrant
  • OD: Mean RNFL: Thinning in 2 or more quadrants
  • ----------OCULUS DEXTER - GANGLION CELL LAYER-----------
  • OD: Mean GCL: Not known
  • OD: Mean GCL: Normal
  • OD: Mean GCL: Mean average GCL thickness thinner
  • ----------OCULUS SINISTER - RETINAL NERVE FIBER LAYER-----------
  • OS: Mean RNFL: Not known
  • OS: Mean RNFL: Normal
  • OS: Mean RNFL: Thinning only in the temporal quadrant
  • OS: Mean RNFL: Thinning only in the superior quadrant
  • OS: Mean RNFL: Thinning only in the inferior quadrant
  • OS: Mean RNFL: Thinning only in the nasal quadrant
  • OS: Mean RNFL: Thinning in 2 or more quadrants
  • ----------OCULUS SINISTER - GANGLION CELL LAYER-----------
  • OS: Mean GCL: Not known
  • OS: Mean GCL: Normal
  • OS: Mean GCL: Mean average GCL thickness thinner
  • ----------DEVICE-----------
  • Device: Cirrus
  • Device: Stratus
  • Device: Heidelberg
  • Device: Other

Visual handicap: Indicate the eventual handicap of the patient, at the last clinical examination, ONLY due to visual loss. D:driving; F: feeding; SL: social life; W: working.
  • ----------DRIVING-----------
  • D: Able to drive
  • D: Was never allowed to drive
  • D: Stopped driving
  • ----------FEEDING-----------
  • F: Able to eat, cook and buy food without help
  • F: Able to eat and cook, but needs help to buy food
  • F: Able to eat, but needs help to cook and buy food
  • F: Needs help to eat, cook and buy food
  • ----------SOCIAL LIFE-----------
  • SL: No difficulty at all
  • SL: Reduced
  • SL: Severely reduced

Hearing loss: Presence of hearing loss due to a genetic cause, i.e. excluding other possible causes (infection, medication, trauma...), and age of onset.
  • ----------PRESENCE-----------
  • Yes
  • No
  • ----------ONSET-----------
  • Age of onset < 5 years
  • Age of onset 5-10 years
  • Age of onset 11-20 years
  • Age of onset 21-30 years
  • Age of onset 31-40 years
  • Age of onset > 40 years

Pure tone audiometry: Indicate the pure tone audiometry results
  • N/A = Not available
  • Normal hearing (loss of 0-20dB)
  • Mild loss (loss of 21-40dB)
  • Moderate loss (loss of 41-60dB)
  • Severe loss (loss of 61-90dB)
  • Profound loss (loss exceeding 90dB)

Auditory brainstem responses: Indicate the auditory brainstem responses
  • N/A = Not available
  • Normal
  • Absent
  • Delayed

Otoacoustic emission: Otoacoustic emission
  • N/A = Not available
  • Present
  • Absent

Functional disability: Indicate the functional disability of the patient at the last clinical examination for lower and upper limbs (respectively LL and UL). The disease duration before the need of the technical assistance mentioned at last examination is noted in brackets.
  • No technical assistance
  • ----------LOWER LIMBS - BRACES/ORTHESIS-----------
  • LL: walking with braces/orthesis (disease duration unknown)
  • LL: walking with braces/orthesis (disease duration < 10 years)
  • LL: walking with braces/orthesis (disease duration 10-20 years)
  • LL: walking with braces/orthesis (disease duration 21-30 years)
  • LL: walking with braces/orthesis (disease duration > 30 years)
  • ----------LOWER LIMBS - SUPPORT-CANE/CRUTCH-----------
  • LL: walking with support-cane/crutch (disease duration unknown)
  • LL: walking with support-cane/crutch (disease duration < 10 years)
  • LL: walking with support-cane/crutch (disease duration 10-20 years)
  • LL: walking with support-cane/crutch (disease duration 21-30 years)
  • LL: walking with support-cane/crutch (disease duration > 30 years)
  • ----------LOWER LIMBS - WHEELCHAIR BOUND-----------
  • LL: wheelchair bound (disease duration unknown)
  • LL: wheelchair bound (disease duration < 10 years)
  • LL: wheelchair bound (disease duration 10-20 years)
  • LL: wheelchair bound (disease duration 21-30 years)
  • LL: wheelchair bound (disease duration > 30 years)
  • ----------UPPER LIMBS - BUTTONS/ZIP-----------
  • UL: difficulty with buttons/zip (disease duration unknown)
  • UL: difficulty with buttons/zip (disease duration < 10 years)
  • UL: difficulty with buttons/zip (disease duration 10-20 years)
  • UL: difficulty with buttons/zip (disease duration 21-30 years)
  • UL: difficulty with buttons/zip (disease duration >30 years)
  • ----------UPPER LIMBS - WRITE-----------
  • UL: difficulty to write (disease duration unknown)
  • UL: difficulty to write (disease duration < 10 years)
  • UL: difficulty to write (disease duration 10-20 years)
  • UL: difficulty to write (disease duration 21-30 years)
  • UL: difficulty to write (disease duration >3 0 years)
  • ----------UPPER LIMBS - ARM WEAKNESS-----------
  • UL: proximal arm weakness (disease duration unknown)
  • UL: proximal arm weakness (disease duration < 10 years)
  • UL: proximal arm weakness (disease duration 10-20 years)
  • UL: proximal arm weakness (disease duration 21-30 years)
  • UL: proximal arm weakness (disease duration > 30 years)

Clinical score: Clinical score. For CMT disease: CMTNS (Charcot-Marie-Tooth Neuropathy Score).
  • CMTNS 0
  • CMTNS < 10
  • CMTNS 10-21
  • CMTNS > 21

Electroneuromyography: Indicate the type of neuropathy, and the values of the electrophysiological parameters. MNCV: Motor Nerve Conduction Velocity (in m/s); CMAP: Compound Muscle Action Potential (in mV); SNAP: Sensory Nerve Action Potential (in ÁV).
  • ----------TYPE OF NEUROPATHY-----------
  • Sensori-motor neuropathy
  • Sensory neuropathy
  • Motor neuropathy
  • Axonal
  • Demyelinating
  • Intermediate
  • ----------PARAMETERS VALUES-----------
  • Median or ulnar nerves: not recordable
  • Median or ulnar nerves: MNCV < 10 m/s
  • Median or ulnar nerves: MNCV 10-20 m/s
  • Median or ulnar nerves: MNCV 21-30 m/s
  • Median or ulnar nerves: MNCV 31-40 m/s
  • Median or ulnar nerves: MNCV > 40 m/s
  • Median or ulnar nerves: CMAP < 0.5 mV
  • Median or ulnar nerves: CMAP 0.5-1 mV
  • Median or ulnar nerves: CMAP 1.1-6 mV
  • Median or ulnar nerves: CMAP > 6 mV
  • Median or ulnar nerves: SNAP < 1 ÁV
  • Median or ulnar nerves: SNAP 1.1-6 ÁV
  • Median or ulnar nerves: SNAP 6.1-12 ÁV
  • Median or ulnar nerves: SNAP > 12 ÁV
  • Common fibular nerve: not recordable
  • Common fibular nerve: CMAP < 0.5 mV
  • Common fibular nerve: CMAP 0.5-1 mV
  • Common fibular nerve: CMAP 1.1-2 mV
  • Common fibular nerve: CMAP > 2 mV
  • Common fibular nerve: MNCV < 10 m/s
  • Common fibular nerve: MNCV 10-20 m/s
  • Common fibular nerve: MNCV 21-30 m/s
  • Common fibular nerve: MNCV 31-40 m/s
  • Common fibular nerve: MNCV > 40 m/s
  • Sural nerve: not recordable
  • Sural nerve: SNAP < 1 ÁV
  • Sural nerve: SNAP 1-5 ÁV
  • Sural nerve: SNAP 5.1-10 ÁV
  • Sural nerve: SNAP > 10 ÁV

Histology: Histological findings.
  • ----------MUSCLE BIOPSY-----------
  • Muscle biopsy: Not performed
  • Muscle biopsy: Normal
  • Muscle biopsy: Ragged-red-fibers
  • Muscle biopsy: Cox-fibers
  • Muscle biopsy: Lipids accumulation
  • ----------NERVE BIOPSY-----------
  • Nerve biopsy: Not performed
  • Nerve biopsy: Normal
  • Nerve biopsy: Axonal
  • Nerve biopsy: Demyelinating
  • Nerve biopsy: Predominantly axonal with mild demyelinating features
  • Nerve biopsy: Predominanly demyelinating with mild axonal features
  • Nerve biopsy: Mixed axonal-demyelinating features

Brain imaging: Brain imaging. MRI: magnetic resonance imaging; MR-spectroscopy: magnetic resonance spectroscopy.
  • ----------MAGNETIC RESONANCE IMAGING-----------
  • MRI: Not performed
  • MRI: Normal
  • MRI: Basal ganglia calcifications
  • MRI: Basal ganglia lesions
  • MRI: Brainstem lesions
  • MRI: Cerebellar atrophy
  • MRI: Corpus callosum abnormalities
  • MRI: Cortical atrophy
  • MRI: Grey matter abnormal signal
  • MRI: Leukodystrophy
  • MRI: Optic atrophy
  • MRI: Optic nerve chiasmal lesions
  • MRI: Optic nerve lesions
  • MRI: Posterior cortical lesions
  • MRI: Stroke-like lesions
  • MRI: White matter abnormal signal
  • ----------MAGNETIC RESONANCE SPECTROSCOPY-----------
  • MR-spectroscopy: Lactate peak

Habits: Habits of the patient. Active or quitting smoking, tabagism in pack year; alcohol consumption in drinks per week.
  • ----------TOBACCO-----------
  • Tobacco: None
  • Tobacco: Occasionally
  • Tobacco: 1-5 packs/year
  • Tobacco: 6-10 packs/year
  • Tobacco: 11-15 packs/year
  • Tobacco: 16-20 packs/year
  • Tobacco: > 20 packs/year
  • ----------ALCOHOL-----------
  • Alcohol: None
  • Alcohol: Occasionally
  • Alcohol: 1-7 drinks/week
  • Alcohol: 8-14 drinks/week
  • Alcohol: 15-21 drinks/week
  • Alcohol: > 21 drinks/week

Geographic origin: Geographic origin of the patient

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