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

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

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

Stature: individual has abnormal stature
All options:

• yes (<3rd centile)
• stature, short (HPO_0004322)
• stature, short, asymmetric (HPO_0008929)
• stature, short, disproportionate (HPO_0003498)
• stature, short, proportionate (HPO_0003508)
• stature, short, mesomelic (HPO_0008845)
• stature, short, mild (HPO_0003502)
• stature, short, moderately (HPO_0008848)
• stature, short, severe (HPO_0003510)
• stature, tall (HPO_0000098)
• stature, tall, proportionate (HPO_0011407)
• stature, tall, disproportionate (HPO_0001519)
• - = no
• ? = unknown
• n/a = not analysed

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

Malformation/Genital: individual has genital malformations (please specify)
All options:

• abnormal = genitourinary abnormalities (HP:0000078)
• clitoral hypertrophy (HP:0008665)
• cryptorchidism (HP:0000028)
• epididymis abnormality (HP:0009714)
• epispadias (HP:0000039)
• hydronephrosis (HP:0000126)
• hypospadias (HP:0000047)
• genital external hypoplasia (HP:0003241)
• genitalia external female hypoplastic (HP:0012815)
• clitoral hypoplasia (HP:0000060)
• labial hypoplasia (HP:0000066)
• labia majora hypoplasia (HP:0000059)
• labia minora hypoplasia (HP:0000064)
• genitalia external male hypoplastic (HP:0000050)
• penis hypoplasia (HP:0008736)
• micropenis (HP:0000054)
• microphallus (HP:0030260)
• penis torsion (HP:0030263)
• scrotal hypoplasia (HP:0000046)
• testicular size decreased (HP:0008734)
• prostate hypoplastic (HP:0008687)
• urethral atresia (HP:0000068)
• urethral atresia female (HP:0000067)
• urethral atresia male (HP:0000052)
• normal = no genitourinary abnormalities (-HP:0000078)
• ? = unknown
• nr = not reported

Thyroid/Dysfunction: individual has abnormal thyroid function (please specify)
All options:

• normal = no thyroid dysfunction (-HP:0002926)
• thyroid dysfunction (HP:0002926)
• hyperthyrodism (HP:0000836)
• hypothyroidism (HP:0000821)
• hypothyroidism, central (HP:0011787)
• hypothyroidism, compensated (HP:0008223)
• hypothyroidism, congenital (HP:0000851)
• hypothyroidism, hypothalamic (HP:0008237)
• hypothyroidism, pituitary (HP:0008245)
• hypothyroidism, primary (HP:0000832)
• thyroid agenesis (HP:0011787, congenital)
• thyroiditis, Hashimoto (HP:0000872)
• ? = unknown
• nr = not reported

Hearing/Loss: individual has hearing loss (hearing defect, hearing impairment), please specify
All options:

• abnormal = hearing abnormality (HP:0000364)
• hearing loss = hearing loss (defect, impairment) (HP:0000365, +)
• aminoglycoside-induced = aminoglycoside-induced hearing loss (HP:0011975)
• conductive = hearing loss, conductive (HP:0000405)
• conductive bilateral = bilateral conductive hearing loss (HP:0008513)
• conductive congenital = congenital conductive hearing loss (HP:0008591)
• conductive mild = mild conductive hearing loss (HP:0008598)
• conductive progressive = progressive conductive hearing loss (HP:0008607)
• high frequency = high frequency hearing loss (progressive) (HP:0005101)
• high frequency sensorineural = high frequency sensorineural hearing loss (HP:0001757)
• low-frequency = low-frequency hearing loss (HP:0008542)
• low-frequency sensorineural = low-frequency sensorineural hearing loss (HP:0008573)
• mixed = hearing loss, mixed (HP:0000410)
• otitis media = otitis media (HP:0000388)
• otitis media acute = acute otitis media (HP:0000371)
• otitis media chronic = chronic otitis media (HP:0000389)
• otitis media recurrent = recurrent otitis media (HP:0000403)
• neurosensory mild = mild neurosensory hearing loss (HP:0008587)
• progressive = hearing loss, progressive (HP:0001730)
• sensorineural = hearing loss, sensorineural (HP:0000407)
• sensorineural bilateral = hearing loss, sensorineural, bilateral (HP:0008619)
• sensorineural congenital = hearing loss, congenital sensorineural (HP:0008527)
• sensorineural childhood onset = childhood onset sensorineural hearing loss (HP:0011474)
• sensorineural infantile = infantile sensorineural hearing loss (HP:0008610)
• sensorineural late = late sensorineural hearing loss (HP:0008615)
• sensorineural moderate = moderate sensorineural hearing loss (HP:0008504)
• sensorineural profound = profound sensorineural hearing loss (HP:0011476)
• sensorineural severe = severe sensorineural hearing loss (HP:0008625)
• sensorineural postlingual = postlingual sensorineural hearing loss (HP:0008596)
• sensorineural prelingual = prelingual sensorineural hearing loss (HP:0000399)
• sensorineural progressive = hearing loss, progressive sensorineural (HP:0000408)
• normal = normal hearing
• ? = unknown
• nr = not reported

Nose/Bridge: shape nasal bridge (please specify)
All options:

• abnormal = abnormality nasal bridge (HP:0000422)
• absent = absent nasal bridge (HP:0005285)
• broad = broad (wide) nasal bridge (HP:0000431)
• flat = flat (depressed/low) nasal bridge (HP:0005280)
• high = high (prominent/elevated) nasal bridge (HP:0000426)
• hypoplastic = hypoplastic nasal bridge (HP:0005281)
• short = short nasal bridge (HP:0003194)
• thin = thin (narrow) nasal bridge (HP:0000446)
• normal = normal nasal bridge
• ? = unknown
• nr = not reported

Nose/Alae: individual has abnormal nasal alae (please specify)
All options:

• abnormal = abnormal nasal alae (HP:0000429)
• normal = normal alae (-HP:0000463)
• aplasia = aplastic alae
• anteverted = anteverted nares (HP:0000463)
• anteverted thin = thin anteverted nares (HP:0004495)
• broad = broad nasal tip (HP:0000455)
• cartilaginous = cartilaginous ossification nose (HP:0005275)
• cleft = cleft alae (HP:0003191)
• flared = flared alae (HP:0000454)
• flat = flat alae (HP:0010649)
• hypoplasia = hypoplastic alae (HP:0000430)
• thick = thick alae (HP:0009928)
• ? = unknown
• nr = not reported

Teeth/Anomalies: individual has anomalies teeth, please specify
All options:

• amelogenesis imperfecta = amelogenesis imperfecta (HP:0000705)
• cylindric = cylindric shape teeth
• delayed = delayed eruption teeth (HP:0000684)
• delayed permanent = delayed permanent teeth (HP:0000696)
• delayed primary = delayed primary teeth (HP:0000680)
• delayed loss = delayed loss primary teeth (HP:0006335)
• hypoplasia = hypoplasia teeth (HP:0000685)
• hypoplasia enamel = hypoplasia dental enamel (HP:0006297)
• hypoplasia enamel general = generalized hypoplasia dental enamel (HP:0006282)
• hypoplasia enamel local = localized hypoplasia dental enamel (HP:0011074)
• hypoplasia teeth primary = hypoplasia primary teeth (HP:0006334)
• hypoplasia tooth germ = hypoplasia tooth germ (HP:0006353)
• irregular = irregular teeth (HP:0040079)
• small = small teeth (HP:0000691)
• spaced abnormal = abnormal spacing teeth (HP:0000692)
• spaced variable = variabe spacing teeth (HP:0006316)
• spaced wide = widely spaced teeth (HP:0000687)
• spaced wide primary = widely spaced primary teeth (HP:0006313)
• spaced wide front = widely spaced front teeth (HP:0006304)
• yellow-brown = yellow-brown discoloration (HP:0006286)
• - = normal teeth
• ? = unknown
• nr = not reported

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

Brachydactyly: individual has brachydactyly, please specify
All options:

• brachydactyly = brachydactyly (HP:000156)
• brachytelomesophalangy = brachytelomesophalangy (HP:0005872)
• short thumb = short thumb (HP:0009778)
• short 5th finger = short 5th finger (HP:0009237)
• short toe = short toe (HP:0001831)
• short 3rd toe = short 3rd toe (HP:0005643)
• brachydactyly-A = brachydactyly, type A (HP:0009370)
• brachydactyly-A1 = brachydactyly, type A1 (HP:0009371)
• brachydactyly-A2 = brachydactyly, type A2 (HP:0009372)
• brachydactyly-B = brachydactyly, type B (HP:0005831
• brachydactyly-C = brachydactyly, type C (HP:0009373)
• brachydactyly-D = brachydactyly, type D (HP:0005627)
• brachydactyly-E = brachydactyly, type E (HP:0005863)
• brachydactyly unilateral = brachydactyly, unilateral (HP:0006008)
• - = no brachydactyly
• ? = unknown
• n/a = not analysed

Bone/Age: does the patient have an abnormal bone age (please specify)
All options:

• accelerated = accelerated bone age (HP:0002805)
• delayed = markedly delayed bone age (HP:0003799, +)
• dysharmonic = dysharmonic bone age (HP:0200000)
• dysharmonic accelerated = dysharmonic accelerated bone age (HP:0200001)
• dysharmonic delayed = dysharmonic delayed bone age (HP:0005832)
• maturation accelerated = accelerated skeletal maturation (HP:0005616)
• maturation delayed = delayed skeletal maturation (HP:0002750)
• - = normal bone age
• ? = unknown
• n/a = not analysed

Teeth/Number: abnormal number of teeth
All options:

• no = no abnormal number teeth (-HP:0006483)
• abnormal = abnormal number teeth (HP:0006483)
• number incisors = abnormal number incisors (HP:0011064)
• number permanent teeth = abnormal number permanent teeth (HP:0011044)
• increased = increased number teeth (HP:0011069)
• mesiodens = mesiodens (HP:0011067)
• supernumerary maxillary incisor = supernumerary maxillary incisor (HP:0006332)
• reduced = reduced number teeth (HP:0009804)
• single incisor = single median maxillary incisor (HP:0006315)
• ageneis tooth selective = selective tooth agenesis (HP:0001592)
• agenesis permanent = agenesis permanent teeth (HP:0006349)
• agenesis canine = agenesis canine (HP:0012738)
• agenesis incisor = agenesis of incisor (HP:0006485)
• agenesis molar = agenesis molar (HP:0011051)
• agenesis premolar = agenesis premolar (HP:0011054)
• hypodontia = hypodontia (HP:0000668)
• anodontia = anodontia (HP:0000674)
• oligodontia = oligodontia (HP:0000677)
• oligodontia primary = oligodontia primary teeth (HP:0012225)
• ? = unknown

Eye/Orbital: individual has abnormality orbital region (specify)
All options:

• coloboma = coloboma (HP:0000589)
• choroidal = choroidal coloboma (HP:0000611)
• choroid bilateral = bilateral choroid coloboma (HP:0007956)
• choroidoretinal = choroidoretinal coloboma (HP:0000567)
• eyelid = eyelid coloboma (HP:0000625)
• lower eyelid = lower eyelid coloboma (HP:0000652)
• upper eyelid = upper eyelid coloboma (HP:0000636)
• irido-fundal = irido-fundal coloboma (HP:0007748)
• iris = iris coloboma (HP:0000612)
• iris and retina = coloboma of iris and retina (HP:0007744)
• lens = lens coloboma (HP:0100719)
• macular = macular coloboma (HP:0001116)
• ocular = ocular coloboma (HP:0000589)
• optic disk (nerve) = optic disk (nerve) coloboma (HP:0000588)
• retina = retinal coloboma (HP:0000480)
• retinal bilateral = bilateral retinal coloboma (HP:0007808)
• globe abnormality (HP:0100886)
• cyclopia (HP:0009914)
• deeply set eyes (HP:0000490)
• hypertelorism (HP:0000316)
• hypotelorism (HP:0000601)
• proptosis (HP:0000520)
• shallow orbits (HP:0000586)
• vertical orbital dystopia (HP:0030867)
• no = no abnormality
• ? = unknown
• nr = not reported

Protein: result from protein staining

Head/Skull: individual has abnormal skull (specify)
All options:

• abnormal skull (HP:0000929)
• calvaria abnormal (HP:0002683)
• calcaria thickened (HP:0002684)
• calvaria thin (HP:0010539)
• calvarial morphology abnormal
• frontal region abnormal shape
• frontal bone hypoplasia (HP:0005466)
• frontal bossing (HP:0002007)
• malar bones abnormal (HP:0012369)
• malar flattening (HP:0000272)
• malar prominence (HP:0010620)
• normal skull (-HP:0000929)
• ? = unknown
• nr = not reported

Calcification: individual has calcification(s), please specify
All options:

• aorta = calcification aorta (HP:0004963)
• basal ganglia = calcification basal ganglia (HP:0002135)
• brain = brain/intracerebral/intracranial calcification (HP:0002514)
• cartilage = calcification cartilage (HP:0100593)
• choroid plexus = calcification choroid plexus calcification (HP:0006960)
• liver = liver calcification (HP:0006559)
• muscle = calcification muscles (HP:0100249)
• pancreatic = pancreatic calcification (HP:0005213)
• - = no calcifications
• ? = unknown
• n/a = not analysed

Face/Cheeks: individual has abnormal cheeks (please specify)
All options:

• abnormal = abnormality cheeks (HP:0004426)
• full = full (chubby/puffy) cheeks (HP:0000293)
• prominent = cheekbone prominence (HP:0012370)
• sunken = sunken cheeks (HP:0009938)
• underdeveloped = cheekbone underdevelopment (HP:0010669)
• normal = normal cheeks
• ? = unknown
• nr = not reported

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

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

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

Face/Shape: individual's shape of the face
All options:

• asymmetric = asymmetric face (HP:0000324)
• asymmetric crying = asymmetric crying face (HP:0011333)
• broad = broad face (HP:0000283)
• dysmorphic = dysmorphic face (HP:0001999)
• flat = flat face (HP:0012368)
• hypomimic = hypomimic face (HP:0000338)
• large = large face (HP:0100729)
• long = long face (HP:0000276)
• myopatic = myopatic face (HP:0002058)
• midface retrusion = midface retrusion (HP:0011800)
• narrow = narrow face (HP:0000275)
• oval = oval face (HP:0000300)
• progeroid = progeroid face (HP:0005328)
• prominent forehead = prominent forehead (HP:0011220)
• no prominent forehead = no prominent forehead (-HP:0011220)
• round = round face (HP:0000311)
• short = short face (HP:0011219)
• small = small face (HP:0000274
• square = square face (HP:0000321)
• triangular = triangular face (+ HP:0000325)
• normal = normal face
• ? = unknown
• nr = not reported
• n/a = not analysed

Facial/Nose: abnormalities nose, shape (specify)
All options:

• abnormality = abnormality nose (+, HP:0000366)
• abnormality external = abnormality external nose (+, HP:00010938)
• aplasia = aplasia nose (HP:0009927)
• aplasia/hypoplasia = aplasia/hypoplasia nose (HP:0009924)
• bifid = bifid nose (HP:0011803)
• broad tip = broad nasal tip (HP:0000455)
• bulbous = bulbous nose (HP:0000414)
• large beaked = large beaked nose (HP:0003683)
• long = long nose (HP:0003189)
• midline defect = midline defect nose (HP:0004122)
• narrow = narrow nose (HP:0000460)
• normal = normal nose (-)
• pear-shaped = pear-shaperd nose (HP:0000447)
• prominent = prominent nose (HP:0000448)
• short = short nose (HP:0003196)
• slender = slender nose (HP:0000417)
• wide = wide nose (HP:0000445)
• ? = unknown
• nr = not reported

Hand_Feet/Abnormal: individual has abnormal hand or feet (specify)
All options:

• finger long = long finger
• finger long thumb = long thumb
• finger long 2nd = long 2nd finger
• finger long 3rd = long 3rd finger
• finger long 4rd = long 4rd finger
• finger long 5th = long 5th finger
• finger small = small finger
• finger short = short finger (HP:0009381)
• finger short thumb = short thumb
• finger short 2nd = short 2nd finger
• finger short 3rd = short 3rd finger
• finger short 4rd = short 4rd finger
• finger short 5th = short 5th finger
• metacapal short = short metacapal (HP:0010049)
• metacapal short 1st = short 1st metacapal
• metacapal short 2nd = short 2nd metacapal
• metacapal short 3rd = short 3rd metacapal
• metacapal short 4rd = short 4rd metacapal
• metacapal short 5th = short 5th metacapal
• metatarsal short = short metatarsal (HP:0010743)
• metatarsal short 1st = short 1st metatarsal
• metatarsal short 2nd = short 2nd metatarsal
• metatarsal short 3rd = short 3rd metatarsal
• metatarsal short 4rd = short 4rd metatarsal
• metatarsal short 5th = short 5th metatarsal
• toe absent = ansent toe (HP:0010760)
• toe long hallux = long hallux (HP:0001847)
• toe long 2nd = long 2nd toe
• toe long 3rd = long 3rd toe
• toe long 4rd = long 4rd toe
• toe long 5th = long 5th toe
• toe short = short toe (HP:0001831)
• toe short hallux = short hallux
• toe short 2nd = short 2nd toe
• toe short 3rd = short 3rd toe
• toe short 4rd = short 4rd toe
• toe short 5th = short 5th toe
• toe small = small toe (HP:0030031)
• normal hand/feet
• nr = not reported

Hair/Pigmentation: individual has abnormal pigmentation hair
All options:

• normal = normal pigmentation hair (-HP:0009887)
• abnormal = abnormal pigmentation hair (HP:0009887)
• albinism = albinism (HP:0001022)
• fair = fair hair (HP:0002286)
• hypopigmentation = hypopigmentation (HP:0005599)
• hypopigmentation general = general hypopigmentation (HP:0011358)
• hypopigmentation patchy = patchy hypopigmentation (HP:0011365)
• poliosis = poliosis (HP:0002290)
• graying = premature graying (HP:0002216)
• red = red hair (HP:0002297)
• silver-gray = silver-gray hair (HP:0002218)
• white = white hair (HP:0011364)
• white forlock = white forlock (HP:0002211)
• ? = unknown
• nr = not reported

Hormone: individual has hormone abnormality (specify)
All options:

• ACTH+ = adrenocorticotropic hormone excess (HP:0011749)
• ACTH- = adrenocorticotropic hormone deficiency (HP:0011748)
• CRH- = corticotropin-releasing hormone deficiency (HP:0011737)
• FSH+ = high follicle stimulating hormone (HP:0008232)
• FSH- = low follicle stimulating hormone (HP:0030341)
• GH+ = growth hormone excess (HP:0000845)
• GH- = growth hormone deficiency (HP:0000824)
• GNRH = hypothalamic gonadotropin-releasing hormone deficiency (HP:0003164)
• LH+ = high luteinizing hormone (HP:0011969)
• LH- = low luteinizing hormone (HP:0030344)
• PTH+c = high circulating parathyroid hormone (HP:0003165)
• PTH+ = high parathyroid hormone, hyperparathyroidism (HP:0000843)
• PTH- = low parathyroid hormone, hypoparathyroidism (HP:0000829)
• PTHp = pseudohypoparathyroidism (HP:0000852)
• TSH+ = thyroid-stimulating hormone excess (HP:0002925)
• TSH- = TSH deficiency, pituitary hypothyroidism (HP:0008245)
• TH resistance = pituitary resistance to thyroid hormone (HP:0008227)
• - = normal
• ? = unknown
• n/a = not analysed

Calcium: individual has abnormal calcium homeostasis (blood and/or urine)
All options:

• hypercalcemia = hypercalcemia (HP:0003072)
• hypercalcemia infantile = infantile hypercalcemia (HP:0008250)
• hypercalciuria = hypercalciuria (HP:0002150)
• hypercalcemia = hypercalcemia (HP:0003072)
• hypocalcemia = hypocalcemia (HP:0002901)
• hypocalcemic seizures = hypocalcemic seizures (HP:0002199)
• hypocalcemic tetany = hypocalcemic tetany (HP:0003472)
• hypocalciuria = hypocalciuria (HP:0003127)
• reduced calcium/creatinine clearance = reduced ratio renal calcium/creatinine clearance (HP:0003513)
• wasting = renal calcium wasting (HP:0012637)
• - = normal calcium homeostasis
• ? = unknown
• n/a = not analysed

Intellectual_dis: individual has intellectual disability (intellectual disability (mental retardation), HP:0001249,mental retardation); please specify
All options:

• yes = intellectual disability (HP:0001249, IQ below 70)
• borderline = intellectual disability, borderline (HP:0006889, IQ 70-79)
• mild = intellectual disability, mild (HP:0001256, IQ 50-69)
• moderate = intellectual disability, moderate (HP:0002342, IQ 35-49)
• profound = intellectual disability, profound (HP:0002187, IQ below 20)
• severe = intellectual disability, severe (HP:0010864, IQ 20-34)
• progressive = intellectual disability, progressive (HP:0006887)
• no = no intellectual disability (IQ above 79, -)
• ? = unknown
• n/a = not analysed

Ion_Homeostasis: individual has abnormal ion homeostasis, please specify
All options:

• cation = abnormal cation homeostasis (HP:0010929)
• chloride = abnormal chloride homeostasis (HP:0011422)
• hyperchloremia = hyperchloremia (HP:0011423)
• hypochloremia = hypochloremia (HP:0003113)
• sweat chloride = elevated sweat chloride (HP:0012236)
• phosphate = abnormal phosphate homeostasis (HP:0100529)
• hyperphosphatemia = hyperphosphatemia (HP:0002905)
• hypophosphatemia = hypophosphatemia (HP:0002148)
• hypophosphatemia renal= renal hypophosphatemia (HP:0008732)
• hypophosphatemic rickets = hypophosphatemic rickets (HP:0004912)
• hypophosphatemia transient= transient hypophosphatemia (HP:0008285)
• plasma pyrophosphate = elevated plasma pyrophosphate (HP:0011864)
• - = normal calcium homeostasis
• ? = unknown
• n/a = not analysed

Neck: individual has abnormality neck
All options:

• abnormality = abnormality neck (HP:0000464)
• broad = broad neck (HP:0000475)
• long = long neck (HP:0000472)
• short = short neck (HP:0000470)
• webbed = webbed neck (HP:0000465)
• redundant skin = redundant neck skin (HP:0005989)
• abnormality musculature = abnormality musculature neck (HP:0011006)
• flexion limited = limited neck flexion (HP:0005991)
• flexor weakness = flexor muscle weakness (HP:0003722)
• limited range of motion = limited neck range of motion (HP:0000466)
• motion limited = limitation of neck motion (HP:0005986)
• muscle hypoplasia = neck muscle hypoplasia (HP:0008984)
• muscle weakness = neck muscle weakness (HP:0000467)
• adipose tissue decreased = decreased adipose tissue around neck (HP:0005995)
• adipose tissue increased = increased adipose tissue around neck (HP:0000468)
• normal = normal neck
• ? = unknown
• n/a = not analysed

Weight: individual has abnormal weight (specify)
All options:

• abnormal = abnormal body weight (HP:0004323)
• decreased = decreased body weight (HP:0004325)
• increased = increased body weight (HP:0004324)
• BMI abnormal = abnormal BMI (HP:0045081)
• BMI decreased = decreased BMI (HP:0045082)
• BMI increased = increased BMI (HP:0031418)
• obesity = obesity (HP:0001513)
• abdominal = obesity, abdominal (HP:0012743)
• truncal = obesity, truncal (HP:0001956)
• truncal childhood = obesity, truncal, childhood-onset (HP:0008915)
• overweight = overweight (HP:0025502)
• - = no obesity (-HP:0001513)
• ? = unknown
• nr = not reported

Ossification/Ectopic: individual has ossification, please specify
All options:

• ectopic = ectopic ossification (HP:0011986)
• ectopic ligament = ectopic ossification, ligament tissue (HP:0011989)
• ectopic muscle = ectopic ossification, muscle tissue (HP:0011987)
• ectopic tendon = ectopic ossification, tendon tissue (HP:0011988)
• - = absent
• ? = unknown
• n/a = not analysed

Bone/Density: individual has abnormal bone density, please specify
All options:

• normal = normal bone mineral density
• abnormal = abnormal bone mineral density (HP:0004348)
• reduced = reduced bone mineral density (HP:0004349)
• generalized demineralization = generalized bone demineralization (HP:0006462)
• osteomalacia = osteomalacia (HP:0002749)
• osteopenia = osteopenia (HP:0000938)
• osteoporosis = osteoporosis (HP:0000939)
• patchy reduced = patchy reduction bone mineral density (HP:0010657)
• patchy variation = patchy variation bone mineral density (HP:0010659)
• rickets = rickets (HP:0002748)
• hypophosphatemic rickets = hypophosphatemic rickets (HP:0004912)
• rickets lower limbs = rickets lower limbs (HP:0006463)
• ? = unknown
• nr = not reported

Puberty: individual has precocious (early) or delayed puberty
All options:

• + = puberty, precocious (HP:0000826)
• menstrual irregularities (HP:0000858)
• abnormality menstrual cycle (HP:0000140)
• amenorrhea (HP:0000141)
• amenorrhea, primary (HP:0000786)
• amenorrhea, secondary (HP:0000869)
• delayed menarche (HP:0012569)
• menometrorrhagia (HP:0400008)
• menorrhagia (HP:0000132)
• metrorrhagia (HP:0100608)
• oligomenorrhea (HP:0000876)
• polymenorrhea (HP:0400007)
• dysmenorrhea (HP:0100607)
• puberty, delayed (HP:0000823)
• puberty, precocious (HP:0000826)
• puberty, precocious, female (HP:0010456)
• puberty, precocious, male (HP:0008185)
• puberty, precocious, isosexual (HP:0008236)
• puberty, precocious, with Sertoli cell tumor (HP:0008204)
• - = normal onset puberty
• ? = unknown
• nr = not reported

Reproduction/Abnormal/Physiology: individual has abnormality reproductive system physiology (please specify)
All options:

• abnormal = abnormality reproductive system physiology (HP:0000080)
• abnormality female = abnormality female reproductive system physiology (HP:0030012)
• dysfunction sexual female = female sexual dysfunction (HP:0030014)
• anorgasmia female = female anorgasmia (HP:0030015)
• dyspareunia = dyspareunia (HP:0030016)
• vaginismus = vaginismus (HP:0030017)
• libido decreased female = decreased female libido (HP:0030018)
• libido increased female = increased female libido (HP:0030019)
• endometriosis = endometriosis (HP:0030127)
• endometriosis cervical= cervical endometriosis (HP:0012889)
• abnormality male = abnormality male reproductive system physiology (HP:0012874)
• abnormality genitalia internal male = abnormality male internal genitalia (HP:0000025
• dysfunction = male sexual dysfunction (HP:0040307)
• libido decreased male = decreased male libido (HP:0040306)
• libido increased male = increased male libido (HP:0040305)
• anorgasmia male = male anorgasmia (HP:0040308)
• ejaculation abnormal = abnormal ejaculation (HP:0012875)
• ejaculation premature = premature ejaculation (HP:0012876)
• ejaculation retrograde = retrograde ejaculation (HP:0012877)
• ejaculation retarded = retarded ejaculation (HP:0012878)
• anejaculation = anejaculation (HP:0012879)
• impotence = impotence (HP:0000802)
• fertility decreased = decreased fertility (HP:0000144)
• fertility decreased female = decreased female fertility (HP:0000868)
• fertility decreased male = decreased male fertility (HP:0012041)
• infertility = infertility (HP:0000789)
• infertility female = female infertility (HP:0008222)
• infertility male = male infertility (HP:0003251)
• hypogonadism = hypogonadism (HP:0000135)
• hypogonadism male = male hypogonadism (HP:0000026)
• hypogonadism hypogonadotrophic = hypogonadotrophic hypogonadism (HP:0000044)
• hypogonadism female = female hypogonadism (HP:0000134)
• hypogonadism hypergonadotropic = hypergonadotropic hypogonadism (HP:0000815)
• normal = no abnormality (-HP:0000080)
• ? = unknown
• nr = not reported

Testis/Abnormal: individual has abnormality testis, please specify
All options:

• abnormal = abnormality testis (HP:0000035)
• aplasia = aplasia testes (HP:0010469)
• aplasia/hypoplasia = aplasia/hypoplasia testes (HP:0010468)
• atrophy = testicular atrophy (HP:0000029)
• cryptorchidism = cryptorchidism (HP:0000028)
• cryptorchidism bilateral = bilateral cryptorchidism (HP:0008689)
• cryptorchidism unilateral = unilateral cryptorchidism (HP:0012741)
• dysgenesis = testicular dysgenesis (HP:0008715)
• dysplastic = dysplastic testes (HP:0008733)
• failure primary = primary testicular failure (HP:0008720)
• hydrocele = hydrocele testis (HP:0000034)
• Leydig cells abnormal = Leydig cells (HP:0010789)
• Leydig cells hyperplasia = Leydig cells (HP:0010791)
• Leydig cells hypoplasia = Leydig cells (HP:0010790)
• macroorchidism = macroorchidism (HP:0000053)
• macroorchidism congenital = congenital macroorchidism (HP:0008640)
• macroorchidism postpubertal = postpubertal macroorchidism (HP:0002050)
• microlithiasis = testicular microlithiasis (HP:0012215)
• orchitis = orchitis (HP:0100796)
• size decreased = decreased testicular size (HP:0008734)
• supernumerary = supernumerary testes (HP:0010470)
• torsion = testicular torsion (HP:0100813)
• normal = normal testis
• ? = unknown
• nr = not reported

Vitamin: individual has vitamin abnormality, please specify
All options:

• vitamin metabolism = abnormal vitamin metabolism
• vitamin A = vitamin A deficiency (HP:0004905)
• vitamin A metabolism = abnormal vitamin A metabolism
• vitamin B metabolism = abnormal vitamin-B metabolism
• vitamin B1 = vitamin B1 deficiency (HP:0100503)
• vitamin B12 = vitamin B12 deficiency (HP:0100502)
• vitamin B12 metabolism = abnormal vitamin B12 metabolism
• vitamin B2 = vitamin B2 deficiency (HP:0100504)
• vitamin B3 = vitamin B3 deficiency (HP:0100497)
• vitamin B3 metabolism = abnormal vitamin B3 metabolism
• vitamin B5 = vitamin B5 deficiency (HP:0100505)
• vitamin B6 = vitamin B6 deficiency (HP:0008326)
• vitamin B8 = vitamin B8 deficiency (HP:0100506)
• vitamin C = vitamin C deficiency (HP:0100510)
• vitamin C metabolism = abnormal vitamin C metabolism
• vitamin D = vitamin D deficiency (HP:0100512)
• vitamin D metabolism = abnormal vitamin D metabolism
• vitamin E = vitamin E deficiency (HP:0100513)
• vitamin E metabolism = abnormal vitamin E metabolism
• vitamin K = vitamin K deficiency (HP:0011892)
• vitamin K metabolism = abnormal vitamin K metabolism
• - = normal vitamin
• ? = unknown
• n/a = not analysed

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
• 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 = singele 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-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
• 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, sex-linked and 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)
• association
• unclassified
• 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%)

Codon change: Codon change

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)

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

DNA/Legacy: original description (specify reference sequence)

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/Grantham: Grantham score

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

Predict/PolyPhen: PolyPhen predicted effect of variant; benign, possibly damaging, probably damaging, unknown (no prediction)

Predict/PolyPhenScore: score PolyPhen prediction (format 0.690)

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

Conservation: conservation, conservation score, (species)

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/CADD: CADD score (Combined Annotation–Dependent Depletion) from cadd.gs.washington.edu

Predict/Splice: splice prediction

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.