Legend

Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.

Phenotype details: additional information on the phenotype of the individual, preferably use HPO terms only (http://www.human-phenotype-ontology.org/)

Diagnosis/Initial: initial diagnosis, before molecular testing

Diagnosis/Definite: phenotype individual after molecular testing (OMIM abbreviation)

Inheritance: Indicates the inheritance of the phenotype in the family; unknown, familial (autosomal/X-linked, dominant/ recessive), paternal (Y-linked), maternal (mitochondrial), isolated (sporadic) or complex
All options:

• Unknown
• Familial
• Familial, autosomal dominant
• Familial, autosomal recessive
• Familial, X-linked
• Familial, X-linked dominant
• Familial, X-linked dominant, male sparing
• Familial, X-linked recessive
• Paternal, Y-linked
• Maternal, mitochondrial
• Isolated (sporadic)
• Di-genic
• Complex
• - = Not applicable

Age/Examination: age at which the individual was examined.

• 35y = 35 years
• 04y08m = 4 years and 8 months
• 00y00m01d12h = 1 day and 12 hours
• 18y? = around 18 years
• 30y-40y = between 30 and 40 years
• >54y = older than 54
• ? = unknown

Age/Diagnosis: age diagnosis was confirmed

• 35y = 35 years
• 04y08m = 4 years and 8 months
• 00y00m01d12h = 1 day and 12 hours
• 18y? = around 18 years
• 30y-40y = between 30 and 40 years
• >54y = older than 54
• ? = unknown

Growth: does the individual have abnormal growth (pre- and post-natal)
All options:

• normal = normal growth
• abnormal = growth abnormality (HP:0001507)
• delayed = delayed (HP:00001510)
• overgrowth = overgrowth (HP:0001548)
• overgrowth prenatal = prenatal overgrowth (HP:0001548)
• overgrowth postnatal = postnatal overgrowth (HP:0001548)
• retardation prenatal = prenatal growth retardation (HP:0001511, IUGR)
• no retardation prenatal = no prenatal growth retardation (-HP:0001511)
• retardation prenatal mild = mild prenatal growth retardation (HP:0008883)
• retardation prenatal moderate = moderate prenatal growth retardation (HP:0011408)
• retardation prenatal severe = severe prenatal growth retardation (HP:0008846)
• retardation postnatal = postnatal growth retardation (HP:0008897)
• retardation postnatal mild = mild postnatal growth retardation (HP:0001530)
• retardation postnatal moderate = moderate postnatal growth retardation (HP:0008855)
• retardation postnatal severe = severe postnatal growth retardation (HP:0008850)
• ? = unknown
• n/a = not analysed

Age/Onset: Age first symptoms disease appeared in individual:

• 35y = 35 years
• 04y08m = 4 years and 8 months
• 00y00m01d12h = 1 day and 12 hours
• 18y? = around 18 years
• 30y-40y = between 30 and 40 years
• >54y = older than 54
• ? = unknown

Phenotype/Onset: individual's phenotype at Age/Onset described using HPO

Skin/Wrinkling: does the patient individual have abnormal skin wrinkling
All options:

• face = wrinkling, facial (HP:0009762)
• skin excessive = wrinkling, skin, excessive (HP:0007392, +)
• skin excessive dorum = wrinkling, skin, excessive, on dorum of hands/fingers (HP:0007407)
• skin excessive palmar = wrinkling, skin, excessive, palmar (HP:0007605)
• skin loose = wrinkling, skin, loose, hands/feet (palmoplantar cutis laxa, HPO_0007517)
• skin premature = wrinkling, skin (premature) (HP:0100678)
• skin neonatal = wrinkling, skin, neonatal of hands/feet (HP:0007414)
• periobital = wrinkles, periobital (HP:0000607)
• no = no increased wrinkling (-)
• ? = unknown
• n/a = not analysed

Hypermobility: does the individual have hypermobility/laxity (please specify)
All options:

• cervical spine = cervical spine hypermobility (HP:0003318)
• joint = joint hypermobility (HPO_0001382, +)
• joint finger = finger joint hypermobility (HP:0006094)
• joint interphalangeal = hypermobility interphalangeal joints (HP:0005620)
• joint interphalangeal distal = hypermobility distal interphalangeal joints (HP:0006201)
• joint toe = hypermobility toe joints (HP:0010510)
• no = no hypermobility (-)
• ? = unknown
• n/a = not analysed

Hernia: individual has hernia(s), please specify
All options:

• hernia = hernia (HP:0100790)
• abdominal wall = hernia of the abdominal wall (HP:0004299)
• abdominal recurrent = recurrent abdominal hernia (inclusional) (HP:0004872)
• crural = crural hernia (HP:0100541)
• diaphragmatic = diaphragmatic hernia (HP:0000776)
• diaphragmatic congenital = congenital diaphragmatic hernia (HP:0000776)
• femoral = femoral hernia (HP:0100541)
• genital = genital hernia (HP:0100823)
• hiatal = hiatal hernia (HP:0002036)
• inguinal = inguinal hernia (HP:0000023, +)
• intervertebral nuclei = herniated intervertebral nuclei (HP:0008441)
• omphalocele = omphalocele (HP:0001539)
• umbilical = umbilical hernia (HP:0001537)
• vaginal = vaginal hernia (HP:0100672)
• ventral = ventral hernia (HP:0002933)
• no = no hernia
• ? = unknown
• n/a = not analysed

Foot/Abnormality: individual has abnormality foot (please specify)
All options:

• abnormality = abnormality foot (HP:0001760, +)
• absent = absent foot (HP:0011301)
• abnormality musculature = abnormality foot musculature (HP:0001436)
• asymmetry = foot asymmetry (HP:0010507)
• bone ossification = abnormal foot bone ossification (HP:0010675)
• brachydactyly = brachydactyly foot (HP:0001831)
• broad = broad foot (HP:0001769)
• calcaneovalgus = calcaneovalgus foot (HP:0001848)
• club (talipes equinovarus) = club foot (talipes equinovarus) (HP:0001762)
• contractures congenital = congenital foot contractures (HP:0005745)
• contraction deformities congenital = congenital foot contraction deformities (HP:0005853)
• deformities positional = positional foot deformities (HP:0005656)
• deformity structural = structural foot deformity (HP:0010219)
• deformities talipes = talipes foot deformities (HP:0001883)
• deformity valgus = valgus foot deformity (HP:0008081)
• drop foot (extensor/dorsiflexor weakness) = foot drop (extensor/dorsiflexor weakness) (HP:0009027)
• medial deviation = medial deviation foot (HP:0008082)
• narrow = narrow foot (HP:0001786)
• polydactyly postaxial = posterior (postaxial) polydactyly of foot (HP:0001830)
• polydactyly preaxial = preaxial polydactyly of foot (HP:0001841)
• polysyndactyly postaxial = postaxial polysyndactyly of foot (HP:0005817)
• short = short foot (HP:0001773)
• skin plantar = abnormality plantar skin of foot (HP:0100872)
• split (lobster-claw deformity) = split foot (lobster-claw deformity) (HP:0001839)
• ulcers penetrating = penetrating foot ulcers (HP:0001026)
• no = no abnormality
• ? = unknown
• n/a = not analysed

Scoliosis: does the individual have scoliosis or kyphoscoliosis (please specify)
All options:

• kyphoscoliosis = kyphoscoliosis (HP:0002751)
• kyphoscoliosis congenital = kyphoscoliosis, congenital (HP:0008453)
• kyphoscoliosis lumbar = kyphoscoliosis, lumbar (HP:0004626)
• kyphoscoliosis thoracic = kyphoscoliosis, thoracic (HP:0005659)
• kyphoscoliosis thoracolumbar = kyphoscoliosis, thoracolumbar (HP:0003423)
• scoliosis = scoliosis (HP:0002650, +)
• scoliosis compensatory = scoliosis, compensatory (HP:0100884)
• scoliosis congenital progressive = scoliosis, congenital, progressive (HP:0008458)
• scoliosis lumbar = scoliosis, lumbar (HP:0004626)
• scoliosis thoracic = scoliosis, thoracic (HP:0002943)
• scoliosis thoracolumbar = scoliosis, thoracolumbar (HP:0002944)
• no = no (kypho)scoliosis
• ? = unknown
• n/a = not analysed

Head/Fontanel: individual has abnormality fontanel (please specify)
All options:

• abnormal = abnormality of fontanelles(HP:0011328)
• abnormal fontanel/sutures = abnormality fontanelles and cranial sutures(HP:0000235)
• abnormal anterior = abnormality anterior fontanelle(HP:0000236)
• abnormal anterior small = small anterior fontanel(HP:0000237)
• anterior large open = large open anterior fontanel(HP:0000260)
• closure delayed = delayed closure of fontanel(HP:0000270)
• closure delayed (persistent) anterior = delayed closure (persistent) anterior fontanel(HP:0001476)
• closure delayed large = large, late-closing fontanelle(HP:0000239)
• closure premature fontanel = premature fontanel closure(HP:0001363)
• closure premature fontanelles = premature closure of fontanelles(HP:0005458)
• closure premature anterior = premature anterior fontanel closure(HP:0008491)
• closure premature posterior = premature posterior fontanelle closure(HP:0005494)
• extra = extra fontanelles(HP:0012367)
• midline skin dimples over = midline skin dimples over anterior/posterior fontanelles(HP:0005498)
• persistent anterior open = persistent open anterior fontanelle(HP:0004474)
• persistent wide = persistent wide fontanel(HP:0010537)
• posterior large = large posterior fontanel(HP:0004491)
• small = small fontanelles(HP:0005486)
• widely patents = widely patent fontanels and sutures(HP:0004492)
• no = normal fontanel
• ? = unknown
• n/a = not analysed

Head/Size: individual has abnormal size of the head
All options:

• macrocephaly = macrocephaly (HP:0000256)
• no macrocephaly = no macrocephaly (-HP:0000256)
• macrocephaly congenital = congenital macrocephaly (HP:0004488)
• no macrocephaly congenital = no congenital macrocephaly (-HP:0004488)
• macrocephaly postnatal = postnatal macrocephaly (HP:0005490)
• macrocephaly progressive = progressive macrocephaly (HP:0004481)
• macrocephaly relative = relative macrocephaly (HPO_0004482)
• microcephaly = microcephaly (yes <3rd centile, HP:0000252)
• no = no microcephaly (-HP:0000252, -)
• congenital = congenital microcephaly (HP:0011451)
• microcephaly mild = mild microcephaly (HP:0040196)
• postnatal = postnatal microcephaly (HP:0005484)
• progressive = postnatal progressive microcephaly (HP:0000253)
• ? = unknown
• nr = not reported
• n/a = not applicable

Development: individual has developmental (psychomotor) delay; please specify (global, cognitive, language/speech, mental, motor, social/emotional)
All options:

• global = global developmental delay (+, HP:0001263)
• global mild = mild global developmental delay (HP:0011342)
• global moderate = moderate global developmental delay (HP:0011343)
• global profound = profound global developmental delay (HP:0012736)
• global severe = severe global developmental delay (HP:0011344)
• motor = motor delay (HP:0001270)
• no motor = no motor delay (HP:0001270)
• motor fine = delay fine motor development (HP:0010862)
• motor gross = delay gross motor development (HP:0002194)
• neurodevelopmental = neurodevelopmental delay (HP:0012758)
• regression = developmental regression (HP:0002376)
• stagnation = developmental stagnation (HP:0007281)
• stagnation seizures = developmental stagnation at onset seizures (HP:0006834)
• social = delayed social development (HP:0012434)
• speech/language = delayed speech/language development (HP:0000750)
• no = no developmental delay (-)
• ? = unknown
• n/a = not analysed

Abdominal/Symptoms: individual has abdominal symptoms (please specify)
All options:

• abdominal = abdominal symptoms (HP:0011458)
• anorexia = anorexia (HP:0002039)
• appetite poor = appetite poor (HP:0004396)
• feeding problems = feeding problems (HP:0011968, +)
• no feeding problems = feeding problems (-HP:0011968)
• feeding delayed = delayed self-feeding toddler years (HP:0012381)
• feeding infancy = feeding problems infancy (HP:0008872)
• feeding nasal regurgitation = nasal regurgitation (HP:0011469)
• feeding poor suck = poor suck (HP:0002033)
• feeding tube gastrostomy = gastrostomy tube feeding infancy (HP:0011471)
• feeding tube nasogastric = nasogastric tube feeding infancy (HP:0011470)
• malnutrition = malnutrition (HP:0004395)
• protein avoidance = protein avoidance (HP:0002038)
• constipation = constipation (HP:0002019)
• distention = abdominal distention (HP:0003270)
• protuberant = protuberant abdomen (HP:0001538
• diarrhea = diarrhea (HP:0002014)
• diarrhea chronic = chronic diarrhea (HP:0002028)
• diarrhea intermittent = intermittent diarrhea (HP:0002254)
• diarrhea intractable = intractable diarrhea (HP:0002041)
• diarrhea protracted = protracted diarrhea (HP:0004385)
• diarrhea secretory = secretory diarrhea (HP:0005208)
• nausea/vomitting = nausea and vomitting (HP:0002017)
• nausea = nausea (HP:0002018)
• vomitting = vomitting (HP:0002013)
• vomitting episodic = episodic vomitting (HP:0002572)
• vomitting projectile = projectile vomitting (HP:0002587)
• pain = abdominal pain (HP:0002027)
• colic = abdominal colic (HP:0011848)
• pain epidosic = episodic abdominal pain (HP:0002574)
• normal = no abdominal symptoms
• ? = unknown
• nr = not reported
• n/a = not analysed

Hypotonia: does the individual have hypotonia (please specify)
All options:

• appendicular = appendicular hypotonia (HP:0012389)
• central = central hypotonia (HP:0011398)
• facial = facial hypotonia (HP:0000297)
• episodic generalized = episodic generalized hypotonia (HP:0006852)
• generalized = generalized hypotonia (HP:0001290, +)
• generalized defect NMJ = generalized hypotonia due to defect at neuromuscular junction (HP:0003397)
• infantile axial = infantile axial hypotonia (HP:0009062)
• infantile muscular = infantile muscular hypotonia (HP:0008947)
• muscular = muscular hypotonia (HP:0001252)
• muscular severe = severe muscular hypotonia (HP:0006829)
• muscular trunk = muscular hypotonia trunk (HP:0008936)
• neonatal = neonatal hypotonia (HP:0001319)
• neonatal generalized = generalized neonatal hypotonia (HP:0008935)
• neonatal severe males = severe neonatal hypotonia in males (HP:0006830)
• oral motor = oral motor hypotonia (HP:0030190)
• no = no hypotonia (-)
• ? = unknown
• n/a = not analysed

Eye/Lens/Cataract: individual has cataract (please specify)
All options:

• cataract = cataract (HP:0000518)
• age-related = age-related cataract (HP:0011141)
• age-related second/third decade = cataracts develop in second or third decade (HP:0007825)
• age-related cortical = age-related cortical cataract (HP:0011143)
• age-related nuclear = age-related nuclear cataract (HP:0011142)
• age-related posterior subcapsular = age-related posterior subcapsular cataract (HP:0011144)
• early = early cataracts (HP:0001113)
• juvenile = juvenile cataract (HP:0001118)
• juvenile cortical = juvenile cortical cataract (HP:0007876)
• juvenile zonulars = juvenile zonular cataracts (HP:0007713)
• presenile = presenile cataract (HP:0007819)
• progressive = cataract, progressive (HP:0007834)
• anterior cortical = anterior cortical cataract (HP:0007795)
• anterior polar = anterior polar cataract (HP:0001134)
• anterior subcapsular = anterior subcapsular cataract (HP:0010923)
• capsular = capsular cataract (HP:0100017)
• capsular posterior = posterior capsular cataract (HP:0100020)
• cortical pulverulen = cataracts, cortical pulverulen (HP:0007780)
• posterior subcapsular iridescent = cataracts, posterior, subcapsular, iridescent (HP:0007889)
• cerulean (congenital) = cerulean (congenital) cataract (HP:0007976)
• congenital/lenticular (bilateral) = cataract congenital/lenticular (bilateral) (HP:0000519)
• coralliform = coralliform cataract (HP:0010921)
• cortical = cortical cataract (HP:0100019)
• cortical dense posterior = dense posterior cortical cataract (HP:0007948)
• cortical posterior = posterior cortical cataract (HP:0010924)
• fasciculiform = fasciculiform cataract (frosted, needle-shaped, aculeiform) (HP:0010926)
• lamellar (congenital) = lamellar cataract (congenital) (HP:0007971)
• lamellar pulverulent = lamellar pulverulent cataract (HP:0010694)
• membranous = membranous cataract (HP:0010922)
• nonnuclear polymorphic congenital = nonnuclear polymorphic congenital cataract (HP:0007692)
• nuclear = nuclear cataract (HP:0100018)
• nuclear congenital = congenital nuclear cataract (HP:0008024)
• nuclear diffuse = diffuse nuclear cataract (HP:0007657)
• nuclear pulverulent = pulverulent nuclear (central) cataract (HP:0010698)
• pulverulent = pulverulent cataract (HP:0010693)
• nuclear punctate = nuclear punctate cataract (HP:0010925)
• nuclear triangular = triangular nuclear cataract (HP:0010699)
• polar = polar cataract (HP:0010696)
• polar posterior = posterior polar cataract (HP:0001115)
• punctate = punctate cataract (HP:0007648)
• pyramidal (anterior) = pyramidal (anterior) cataract (HP:0010697)
• subcapsula (lenticular) = cataract subcapsula (lenticular) (HP:0000523)
• subcapsular posterior = posterior subcapsular cataract (HP:0007787)
• sutural = sutural cataract (HP:0010695)
• total = total cataract (HP:0010700)
• y-sutural posterior = posterior y-sutural cataract (HP:0008031)
• zonular = zonular cataract (HP:0010920)
• no = no cataract
• ? = unknown
• n/a = not analysed

Protein: result from protein staining

Eye/Movement: individual has abnormality in eye movement (please specify)
All options:

• abnormal = abnormal eye movement (HP:0000496)
• abduction ocular = abnormality of ocular abduction
• adduction impaired = impaired ocular adduction
• apraxiao culomotor = oculomotor apraxia
• fixation = abnormal visual fixation
• movement conjugate = abnormal conjugate eye movement
• supranuclear gaze palsy = supranuclear gaze palsy
• convergence impaired = impaired convergence
• cyclodeviation
• esodeviation
• exodeviation
• heterophoria
• heterotropia
• hypodeviation
• hyperdeviation
• strabismus = strabismus (HP:0000486)
• strabismus alternating = alternating strabismus (HP:0031717)
• strabismus congenital = congenital strabismus (HP:0000487)
• strabismus comitant = comitant strabismus
• strabismus convergent = convergent strabismus (HP:0020054)
• strabismus divergent = divergent strabismus (HP:0020045)
• strabismus incomitant = incomitant strabismus
• strabismus incomitant horizontal = incomitant strabismus horizontal (HP:0020044)
• strabismus incomitant vertical = incomitant strabismus vertical (HP:0020043)
• strabismus monocular = monocular strabismus (HP:0010877)
• strabismus neurogenic = neurogenic strabismus (HP:0032775)
• strabismus unilateral = unilateral strabismus (HP:0010877)
• esophoria = esophoria
• esotropia = esotropia (HP:0000565)
• esotropia alternating = alternating esotropia (HP:0001137)
• exophoria = exophoria
• exotropia = exotropia (HP:0000577)
• exotropia congenital = congenital exotropia (HP:0008033)
• movements extraocular = limited extraocular movements
• movements involuntary = abnormal involuntary eye movements
• movements conjugate chaotic = chaotic rapid conjugate ocular movements (HP:0007295)
• movements eye paroxysmal = paroxysmal involuntary eye movements (HP:0007704)
• movements eye uncontrolled = uncontrolled eye movements (HP:0007738)
• opsoclonus = opsoclonus (HP:0010543)
• nystagmus = nystagmus (HP:0000639)
• nystagmus-induced head nodding = nystagmus-induced head nodding (HP:0001361)
• nystagmus congenital = congenital nystagmus (HP:0006934)
• nystagmus congenital horizontal = congenital horizontal nystagmus (HP:0007859)
• nystagmus divergence = divergence nystagmus (HP:0030691)
• nystagmus downbeat = downbeat nystagmus (HP:0010545)
• nystagmus gaze-evoked = gaze-evoked nystagmus (HP:0000640)
• nystagmus gaze-evoked horizontal = gaze-evoked horizontal nystagmus (HP:0007979)
• nystagmus horizontal = horizontal nystagmus (HP:0000666)
• nystagmus horizontal jerk = horizontal jerk nystagmus (HP:0007286)
• nystagmus horizontal monocular = horizontal monocular nystagmus (HP:0007747)
• nystagmus horizontal opticokinetic = horizontal opticokinetic nystagmus (HP:0008026)
• nystagmus horizontal pendular = horizontal pendular nystagmus (HP:0007811)
• nystagmus pendular = pendular nystagmus (HP:0012043)
• nystagmus physiologic = physiologic nystagmus (HP:0012044)
• nystagmus rotary = rotary nystagmus (HP:0001583)
• nystagmus upbeat = upbeat nystagmus (HP:0011477)
• nystagmus vertical = vertical nystagmus (HP:0010544)
• nystagmus vestibular = vestibular nystagmus (HP:0010542)
• movements saccadic = abnormality of saccadic eye movements
• ophthalmoparesis = ophthalmoparesis
• pursuit smooth = abnormality of ocular smooth pursuit
• compensatory chin elevation
• Duane anomaly = Duane anomaly
• Marcus Gunn = Marcus Gunn jaw winking synkinesis
• visual gaze preference = visual gaze preference
• normal = normal eye movement (-HP:0000496)
• ? = unknown

How to query this table

All list views have search fields which can be used to search data. You can search for a complete word or you can search for a part of a search term. If you enclose two or more words in double quotes, LOVD will search for the combination of those words only exactly in the order you specify. Note that search terms are case-insensitive and that wildcards such as * are treated as normal text! For all options, like "and", "or", and "not" searches, or searching for prefixes or suffixes, see the table below.

Operator	Column type	Example	Matches
	Text	Arg	all entries containing 'Arg'
space	Text	Arg Ser	all entries containing 'Arg' and 'Ser'
|	Text	Arg|Ser	all entries containing 'Arg' or 'Ser'
!	Text	!fs	all entries not containing 'fs'
^	Text	^p.(Arg	all entries beginning with 'p.(Arg'
$	Text	Ser)$	all entries ending with 'Ser)'
=""	Text	=""	all entries with this field empty
=""	Text	="p.0"	all entries exactly matching 'p.0'
!=""	Text	!=""	all entries with this field not empty
!=""	Text	!="p.0"	all entries not exactly matching 'p.0?'
combination	Text	*|Ter !fs	all entries containing '*' or 'Ter' but not containing 'fs'
	Date	2020	all entries matching the year 2020
|	Date	2020-03|2020-04	all entries matching March or April, 2020
!	Date	!2020-03	all entries not matching March, 2020
<	Date	<2020	all entries before the year 2020
<=	Date	<=2020-06	all entries in or before June, 2020
>	Date	>2020-06	all entries after June, 2020
>=	Date	>=2020-06-15	all entries on or after June 15th, 2020
combination	Date	2019|2020 <2020-03	all entries in 2019 or 2020, and before March, 2020
	Numeric	23	all entries exactly matching 23
|	Numeric	23|24	all entries exactly matching 23 or 24
!	Numeric	!23	all entries not exactly matching 23
<	Numeric	<23	all entries lower than 23
<=	Numeric	<=23	all entries lower than, or equal to, 23
>	Numeric	>23	all entries higher than 23
>=	Numeric	>=23	all entries higher than, or equal to, 23
combination	Numeric	>=20 <30 !23	all entries with values from 20 to 29, but not equal to 23

Some more advanced examples:

Example	Matches
Asian	all entries containing 'Asian', 'asian', including 'Caucasian', 'caucasian', etc.
Asian !Caucasian	all entries containing 'Asian' but not containing 'Caucasian'
Asian|African !Caucasian	all entries containing 'Asian' or 'African', but not containing 'Caucasian'
"South Asian"	all entries containing 'South Asian', but not containing 'South East Asian'

To sort on a certain column, click on the column header or on the arrows. If that column is already selected to sort on, the sort order will be swapped. The column currently sorted on has a darker blue background color than the other columns. The up and down arrows next to the column name indicate the current sorting direction. When sorting on any field other than the default, LOVD will sort secondarily on the default sort column.

Legend

Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.

Template: Template(s) used to detect the sequence variant; DNA (genomic DNA), RNA (cDNA) or protein
All options:

• DNA
• RNA = RNA (cDNA)
• protein
• ? = unknown

Technique: technique(s) used to identify the sequence variant.
All options:

• ? = unknown
• ARMS = amplification refractory mutation system
• arrayCGH = array for Comparative Genomic Hybridisation
• arrayMET = array for methylation analysis
• arraySEQ = array for resequencing
• arraySNP = array for SNP typing
• arrayCNV = array for Copy Number Variation (SNP and CNV probes)
• ASO = allele-specific oligo hybridisation
• BESS = Base Excision Sequence Scanning
• CMC = Chemical Mismatch Cleavage
• COBRA = Combined Bisulfite Restriction Analysis
• CSCE = Conformation Sensitive Capillary Electrophoresis
• CSGE = Conformation Sensitive Gel Electrophoresis
• ddF = dideoxy Fingerprinting
• 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
• DSDI = Detection Small Deletions and Insertions
• EMC = Enzymatic Mismatch Cleavage
• expr = expression analysis
• FISH = Fluorescent In-Situ Hybridisation
• FISHf = fiberFISH
• HD = HeteroDuplex analysis
• HPLC = High-Performance Liquid Chromatography
• IEF = IsoElectric Focussing
• IHC = Immuno-Histo-Chemistry
• Invader = Invader assay
• MAPH = Multiplex Amplifiable Probe Hybridisation
• MAQ = Multiplex Amplicon Quantification
• MCA = Melting Curve Analysis, high-resolution (HRMA)
• microscope = microscopic analysis (karyotype)
• microsat = microsatellite genotyping
• minigene = expression minigene construct
• MIP = Molecular Inversion Probe amplification
• MIPsm = single molecule Molecular Inversion Probe amplification
• MLPA = Multiplex Ligation-dependent Probe Amplification
• MLPA-ms = Multiplex Ligation-dependent Probe Amplification, methylation specific
• MS = mass spectrometry
• Northern = Northern blotting
• NUC = nuclease digestion (RNAseT1, S1)
• OM = optical mapping
• PAGE = Poly-Acrylamide Gel-Electrophoresis
• PCR = Polymerase Chain Reaction
• PCRdd = PCR, digital droplet
• PCRdig = PCR + restriction enzyme digestion
• PCRh = PCR, haloplex
• PCRlr = PCR, long-range
• PCRm = PCR, multiplex
• PCRms = PCR, methylation sensitive
• PCRq = PCR, quantitative (qPCR)
• PCRrp = PCR, repeat-primed (RP-PCR)
• PCRsqd = PCR, semi-quantitative duplex
• PE = primer extension (APEX, SNaPshot)
• PEms = primer extension, methylation-sensitive single-nucleotide
• PFGE = Pulsed-Field Gel-Electrophoresis (+Southern)
• PTT = Protein Truncation Test
• RFLP = Restriction Fragment Length Polymorphisms
• RT-PCR = Reverse Transcription and PCR
• RT-PCRq = Reverse Transcription and PCR, quantitative
• SBE = Single Base Extension
• SEQ = SEQuencing (Sanger)
• SEQb = bisulfite SEQuencing
• SEQp = pyroSequencing
• SEQms = sequencing, methylation specific
• SEQ-ON = next-generation sequencing - Oxford Nanopore
• SEQ-NG = next-generation sequencing
• SEQ-NG-RNA = next-generation sequencing RNA
• SEQ-NG-H = next-generation sequencing - Helicos
• SEQ-NG-I = next-generation sequencing - Illumina/Solexa
• SEQ-NG-IT = next-generation sequencing - Ion Torrent
• SEQ-NG-R = next-generation sequencing - Roche/454
• SEQ-NG-S = next-generation sequencing - SOLiD
• SEQ-PB = next-generation sequencing - Pacific Biosciences
• SNPlex = SNPlex
• Southern = Southern blotting
• SSCA = Single-Strand DNA Conformation polymorphism Analysis (SSCP)
• SSCAf = fluorescent SSCA (SSCP)
• STR = Short Tandem Repeat
• TaqMan = TaqMan assay
• Western = Western blotting
• - = not applicable

Tissue: tissue type used for analysis

Remarks: remarks regarding the screening like WGS (whole genome sequencing), WES (whole exome sequencing, gene panel (incl. a list of genes analysed), etc.

Legend

Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.

Allele: On which allele is the variant located? Does not necessarily imply inheritance! 'Paternal' (confirmed or inferred), 'Maternal' (confirmed or inferred), 'Parent #1' or #2 for compound heterozygosity without having screened the parents, 'Unknown' for heterozygosity without having screened the parents, 'Both' for homozygozity.

Effect: The variant's effect on the function of the gene/protein, displayed in the format 'R/C'. R is the value reported by the source (publication, submitter) and this classification may vary between records. C is the value concluded by the curator. Note that in some database the curator uses Summary records to give details on the classification of the variant.Values used: '+' indicating the variant affects function, '+?' probably affects function, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect was not classified.

Classification method: The method used for the clinical classification of this variant.
All options:

• ACMG
• ACGS
• EAHAD-CFDB
• ENIGMA
• IARC
• InSiGHT
• kConFab
• other

Clinical classification: Clinical classification of variant, preferably based on standardised criteria (e.g. ACMG), directed on the clinical consequences as published/submitted, indicated using an enriched system including inheritance: e.g. pathogenic, pathogenic (dominant), pathogenic (recessive), pathogenic (!), pathogenic (maternal), pathogenic (paternal). Standard inheritance is covered by dominant/recessive, imprinting by maternal/paternal. A '!' warns for exceptional circumstances to be explained in the 'Remarks' field (low penetrance, variants pathogenic in heterozygous state only, hypomorphic/hypermorphic variants, protective variants, etc.). Non-disease consequences (e.g. drug metabolism (pharmacogenetics), risk factor, blood group, tasting bitter) are indicated using additions to the benign classification; benign (dominant), benign (recessive), benign (!), etc. The value 'association' is used for variants associated with a phenotype and 'NA' for variants from in vitro/in silico records. NOTE: classification may differ from the opinion of the curator as given in a variant SUMMARY-record or the 'Functional effect concluded'). NOTE: pathogenic/likely pathogenic should go together with "variant (probably) affects function" In ClassFunctional.
All options:

• pathogenic
• pathogenic (dominant)
• pathogenic (recessive)
• pathogenic (!)
• pathogenic (maternal)
• pathogenic (paternal)
• likely pathogenic
• likely pathogenic (dominant)
• likely pathogenic (recessive)
• likely pathogenic (!)
• likely pathogenic (maternal)
• likely pathogenic (paternal)
• VUS
• VUS (!)
• likely benign
• likely benign (dominant)
• likely benign (recessive)
• likely benign (!)
• likely benign (maternal)
• likely benign (paternal)
• benign
• benign (dominant)
• benign (recessive)
• benign (!)
• benign (maternal)
• benign (paternal)
• conflicting
• association
• NA

DNA change (genomic) (hg19): HGVS description of variant at DNA level, based on the genomic (chromosomal) DNA reference sequence; e.g. g.12345678C>T, g.12345679del, g.12345678_12345890dup

DNA change (hg38): HGVS description of variant at DNA level, based on the hg38 genomic (chromosomal) eference sequence; e.g. g.12345678C>T, g.12345679del, g.12345678_12345890dup

Published as: listed only when different from "DNA change"; variant as reported originally (e.g. 521delT). Variants seen in animal models, tested in vitro, predicted from RNA analysis, etc. are described between brackets like c.(456C>G)

ISCN: description of the variant according to ISCN nomenclature

DB-ID: database ID of variant, grouping multiple observations of the same variant together, starting with the HGNC gene symbol, followed by an underscore (_) and a six digit number (e.g. DMD_012345). _000000 is used for variants where DNA was not analysed (change predicted from RNA analysis), variants seen in animal models or variants not seen in humans but functionally tested in vitro

Variant remarks: remarks regarding variant described, e.g. germline mosaicism in mother, 345 kb deletion, muscle RNA analysed, not in 200 control chromosomes tested, on founder haplotype, etc.

Reference: publication describing the variant submitted, incl. links to OMIM, PubMed or other source, e.g. "den Dunnen ASHG2003 P2346"

ClinVar ID: ID of variant in ClinVar database

dbSNP ID: the dbSNP ID

Origin: Origin of variant/record: Germline = in all cells, De novo = in all cells, but not in either parent, Germline/De novo (untested) = in all cells, parents not tested (use only when De novo is likely, e.g. isolated/sporadic cases with dominant disease), Somatic = present in a subset of cells, but not in either parent, Uniparental disomy = from parental disomy (maternal or paternal), CLASSIFICATION record = submitter only sharing variant classification (note another report may share Individual data), SUMMARY record = master summary record from curator (may link to another database), In vitro (cloned) = data resulting from in vitro functional assays, animal model = data from animal model, Artefact = false positive variant call, DUPLICATE record = variant already described on another chromosome (e.g. unbalanced translocation, duplicating transposition, 2nd fusion transcript, etc.)
All options:

• Germline
• De novo
• Germline/De novo (untested)
• Somatic
• Uniparental disomy
• Uniparental disomy, maternal allele
• Uniparental disomy, paternal allele
• CLASSIFICATION record
• SUMMARY record
• In vitro (cloned)
• In silico
• animal model
• Artefact
• DUPLICATE record
• Unknown
• Not applicable

Segregation: Indicates whether the variant segregates with the phenotype (yes), does not segregate with the phenotype (no) or segregation is unknown (?)
All options:

• ? = unknown
• yes = segregates with phenotype
• no = does not segregate with phenotype
• - = not applicable

Frequency: frequency in which the variant was found; e.g 5/760 chromosomes (in 5 of 760 chromosomes tested), 1/33 patients (in 1 of 33 patients analysed in study), 0.05 controls (in 5% of control cases tested)

Re-site: restriction enzyme recognition site created (+) or destroyed (-); e.g. BglII+;BamHI-

VIP: variant VIP-status was requested for matchmaking - need collaboration(s) to crack the case - please contact the submitter/curator. NOTE: to get VIP status ask the curator.

Methylation: result of methylation test; GOM (gain of methylation), LOM (loss of methylation), 30% (30% methylated). NOTE: when several tests were done mention the method as well (e.g. MS-PCR 75%)

IDbase Accession Number: IDbase Accession Number

VariO/DNA: variation ontology annotation at DNA level
All options:

• DNA substitution (VariO:0136)
• transition (VariO:0313)
• pyrimidine transition (VariO:0314)
• purine transition (VariO:0315)
• not changed (VariO:0140)
• DNA deletion (VariO:0141)
• DNA insertion (VariO:0142)
• DNA indel (VariO:0143)
• DNA inversion (VariO:0145)
• DNA translocation (VariO:0144)
• transversion (VariO:0316)

VariO/Protein: variation ontology annotation at protein level
All options:

• protein truncation (VariO:0015)
• sequence retaining amino acid deletion (VariO:0016)
• nonsynonymous variation (VariO:0017)
• amino acid insertion (VariO:0018)
• amphigoric amino acid insertion (VariO:0019)
• sequence retaining amino acid insertion (VariO:0020)
• amino acid substitution (VariO:0021)
• amino acid indel (VariO:0022)
• amphigoric amino acid indel (VariO:0023)
• missing protein (VariO:0240)
• sequence retaining amino acid indel (VariO:0029)
• alternatively initiated protein (VariO:0443)
• artificial protein variation (VariO:0246)
• mistranslated protein (VariO:0330)
• protein structural inheritance (VariO:0026)
• epigenetic protein variation (VariO:0025)
• post translational modification (VariO:0028)
• proteinaceous infection (VariO:0027)

VariO/RNA: variation ontology annotation at RNA level
All options:

• RNA substitution (VariO:0312)
• transition (VariO:0313)
• pyrimidine transition (VariO:0314)
• purine transition (VariO:0315)
• transversion (VariO:0316)
• missense variation (VariO:0308)
• initiation codon change (VariO:0317)
• termination codon change (VariO:0309)
• nonsense variation (VariO:0310)
• silent variation (VariO:0318)
• RNA deletion (VariO:0319)
• in-frame deletion (VariO:0320)
• out-of-frame deletion (VariO:0321)
• RNA insertion (VariO:0326)
• in-frame insertion (VariO:0332)
• out-of-frame insertion (VariO:0327)
• RNA indel (VariO:0311)
• in-frame indel (VariO:0030)
• out-of-frame indel (VariO:0031)
• effect on RNA splicing (VariO:0362)
• intron gain (VariO:0364)
• RNA splicing change (VariO:0334)
• exon loss (VariO:0381)
• missing RNA (VariO:0245)
• unsense variation (VariO:0514)

Exon: number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = from intron 2 to intron 7, 8i_9 = intron 8/exon 9 boundary, _1 = 5' to exon 1, 18_ = 3' of exon 18, _1_18_ = encompassing the entire 18-exon gene

DNA change (cDNA): description of variant at DNA level, based on a coding DNA reference sequence (following HGVS recommendations); e.g. c.123C>T, c.123_145del, c.123_126dup. For deletions/duplications extending beyond the reference transcript resp. {0}/{2} is used to replace del/dup. Extent of the deletion/duplication should be specified using the genomic description (g.). "-" indicates the variant described on genomic level does not affect the coding DNA reference sequence.

Haplotype: haplotype on which variant was found

RNA change: description of variant at RNA level (following HGVS recommendations).

• r.123c>u
• r.? = unknown
• r.(?) = RNA not analysed but probably transcribed copy of DNA variant
• r.spl? = RNA not analysed but variant probably affects splicing
• r.(spl?) = RNA not analysed but variant may affect splicing
• r.0? = change expected to abolish transcription

Protein: description of variant at protein level (following HGVS recommendations).

• p.(Arg345Pro) = change predicted from DNA (RNA not analysed)
• p.Arg345Pro = change derived from RNA analysis
• p.? = unknown effect
• p.0? = probably no protein produced

P-domain: region/domain protein affected

Exon_old: exon number according to older numbering

Function/GVS: functional annotation of position based on the Genome Variation Server
All options:

• intergenic
• 5 flank = near gene 5
• 5'UTR
• coding
• coding near splice
• coding synonymous
• coding synonymous near splice
• codingComplex
• codingComplex near splice
• frameshift
• frameshift near splice
• missense
• missense near splice
• 5' splice
• intron
• 3' splice
• stop gained
• stop gained near splice
• stop lost
• stop lost near splice
• 3'UTR
• 3 flank = near gene 3

Predict/AGVGD: Align GVGD score; C0, C15, C25, C35, C45, C55 or C65

Predict/MutationTaster: Mutation Taster prediction variant; disease causing, polymorphism

Predict/SIFT: SIFT predicted effect of variant

Predicted: predicted consequence of variant (RNA/protein level)
All options:

• missense
• nonsense
• frameshift
• no-stop
• silent
• splicing affected
• splicing affected, exon skipped
• splicing affected?
• deletion
• deletion, small
• deletion, large
• deletion, exon
• deletion, multi exon
• duplication
• duplication, small
• duplication, large
• insertion
• insertion, small
• insertion, large
• delins = insertion/deletion
• conversion
• other/complex

Type/DNA: type of variant at DNA level. NOTE: can be derived automatically from the variant description (for all levels)
All options:

• substitution
• deletion
• deletion, small
• deletion, large
• duplication
• duplication, small
• duplication, large
• insertion
• insertion, small
• insertion, large
• delins = insertion/deletion
• inversion
• conversion
• transposition
• translocation
• other/complex

CpG: Variation occurs in CpG dinucleotide; number is the position in the codon

Enzyme activity: activity variant enzym

mRNA level: Level of transcribed mRNA present in peripheral blood mononuclear cells. The level is indicated in relative terms as normal/(much) increased/(much) reduced/absent.

Predict-BioInf: predicted effect of variant using bioinformatic analysis tools (e.g. AGVGD, CADD, conservation, Grantham, MutationTaster, PolyPhen, REVEL, SIFT, splicing, etc.)

Legacy protein change: description of variant at protein level using a traditional (legacy) numbering system.

Protein level: Level of translated protein in peripheral blood mononuclear cells. The level is indicated in relative terms as normal/(much) increased/(much) reduced/absent.