Legend

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Birth_Details: birth details individual: gestational age (weeks), premature birth (HP:0001622, <37w); birth weight (in g/SD); birth length (in cm/SD); OFC at birth (in cm/SD)

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

Birth/Weight: weight at birth (in kg, with SD)

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

OFC at birth (SDS): OFC at birth in SDS

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

Height-Weight-OFC: Height-Weight-OFC last visit (SDS)

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

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

Feeding_Problems/Start: when did the feeding problems start; birth = at birth, 3m = at 3 months, 2y = at 2 years

Feeding_Problems/Duration: what was the duration of the feeding problems (in y); 2 = 2 years, ongoing, brief,

Eczema: does the individual have eczema (HPO_0000964); present (+), perioral eczema (perioral, HPO_0011127), seborrheic dermatitis (seborrheic, HPO_0001051), eczematoid dermatitis (ecz.derm., HPO_0000976), absent (-), unknown (?), not analysed (n/a)
All options:

• + = present
• perioral = perioral eczema (HPO_0011127)
• seborrheic = seborrheic dermatitis (HPO_0001051)
• ecz.derm. = eczematoid dermatitis (HPO_0000976)
• - = absent
• ? = unknown
• n/a = not analysed

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

Skin/Vascular: individual has vascular skin abnormality, please specify
All options:

• abnormal vascular = vascular skin abnormality (HP:0011276)
• angioedema = angioedema (HP:0100665)
• angiokeratoma = angiokeratoma (HP:0001014)
• angiokeratoma corporis diffusum = angiokeratoma corporis diffusum (HP:0001071)
• cutis marmorata = cutis marmorata (HP:0000965, +)
• erythema = erythema (HP:0010783)
• erythema facial = facial erythema (HP:0001041)
• bruising = bruising susceptibility (HP:0000978)
• hematomas spontaneous = spontaneous hematomas (HP:0007420)
• hemorrhage subcutaneous = subcutaneous hemorrhage (HP:0001933)
• petechiae = petechiae (HP:0000967)
• purpura = purpura (HP:0000979)
• purpura anaphylactoid = anaphylactoid purpura (HP:0200144)
• telangiectasia = telangiectasia (HP:0001009)
• urticaria = urticaria (HP:0001025)
• urticaria dermatographic = dermatographic urticaria (HP:0011971)
• urticaria non-pruritic = non-pruritic urticaria (HP:0011137)
• vasculitis skin = vasculitis skin (HP:0200029)
• vasculitis punctate = punctate vasculitis skin lesions (HP:0200030)
• vessels superficial = prominent superficial blood vessels (HP:0007394)
• veins superficial = prominent superficial veins (HP:0001015)
• venous lateral = lateral venous anomaly (HP:0100885)
• veins scalp = prominent scalp veins (HP:0001043)
• veins trunk = prominent veins on trunk (HP:0007457)
• normal = vascular skin normal
• ? = unknown
• 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

Seizures: does individual have seizures (please specify)
All options:

• no = no seizures (-HP:0001250)
• seizures = seizures (HP:0001250, +)
• absence = absence seizures (HP:0002121)
• absence atypical = atypical absence seizures (HP:0007270)
• absence with eyelid myoclonia = absence seizures with eyelid myoclonia (HP:0011149)
• absence with special features = absence seizures with special features (HP:0011148)
• atonic (drop/astatic/hypotonic) = atonic seizures (drop, astatic, hypotonic) (HP:0010819)
• bilateral convulsive = bilateral convulsive seizures (HP:0007334)
• complex febrile = complex febrile seizures (HP:0011172)
• dacrystic = dacrystic seizures (HP:0010820)
• developmental stagnation = developmental stagnation at onset of seizures (HP:0006834)
• dialeptic = dialeptic seizures (HP:0011146)
• early onset absence = early onset absence seizures (HP:0011152)
• febrile = febrile seizures (HP:0002373)
• focal = focal seizures (HP:0007359)
• focal afebrile = seizures, focal (partial), afebrile (HP:0040168)
• focal autonomic = focal autonomic seizures (HP:0011154)
• focal autonomic altered responsiveness = focal autonomic seizures with altered responsiveness (HP:0011155)
• focal autonomic no altered responsiveness = focal autonomic seizures without altered responsiveness (HP:0011156)
• focal clonic = focal clonic seizures (HP:0002266)
• focal complex = complex focal seizures with impairment of consciousness or awareness (HP:0002384)
• focal motor = focal motor seizures (HP:0011153)
• focal myoclonic = focal myoclonic seizures (HP:0011166)
• focal simple = focal seizures without impairment of consciousness or awareness (HP:0002349)
• focal tonic = focal tonic seizures (HP:0011167)
• gelastic = gelastic seizures (HP:0010821)
• generalized clonic = generalized clonic seizures (HP:0011169)
• generalized myoclonic = generalized myoclonic seizures (HP:0002123)
• generalized recurrent = generalized seizures, recurrent (HP:0002197)
• generalized tonic = generalized tonic seizures (HP:0010818)
• generalized tonic-clonic = seizures, generalized, tonic-clonic (HP:0002069)
• generalized tonic-clonic photosensitive = seizures, tonic-clonic, photosensitive (HP:0007207)
• generalized tonic-clonic awakening = generalized tonic-clonic seizures on awakening (HP:0007193)
• hemiclonic (unilateral clonic) = hemiclonic seizures (unilateral clonic) (HP:0006813)
• hemifacial = hemifacial seizures (HP:0007332)
• hyperkinetic = hyperkinetic seizures (HP:0011174)
• hypocalcemic = hypocalcemic seizures (HP:0002199)
• hypoglycemic = hypoglycemic seizures (HP:0002173)
• hypokinetic = hypokinetic seizures (HP:0011173)
• maternal = maternal seizures (HP:0100622)
• myoclonic atonic = myoclonic atonic seizures (HP:0011170)
• petit mal = petit mal seizures (HP:0011147)
• photomyoclonic = photomyoclonic seizures (HP:0001327)
• salaam = salaam seizures (HP:0011097)
• simple febrile = simple febrile seizures (HP:0011171)
• simple partial occipital = simple partial occipital seizures (HP:0011165)
• symptomatic = symptomatic seizures (HP:0011145)
• versive = versive seizures (HP:0011175)
• ? = unknown
• n/a = not analysed

Seizures/Age/Onset: at what age did the seizures start (in y); 2y = at 2 years of age, 3y5m = at 3y and 5 monts of age

Seizure/Frequency: how often do the seizures occur; monthly, 1/2 month (twice a month), ? (unknown) n/a (not analysed)

Seizure/Type: what type of seizures does the individual have; febrile seizures (HPO_0002373), focal seizures (HPO_0007359), focal clonic seizures, (HPO_0002266), focal motor seizures (HPO_0011153), focal myoclonic seizures (HPO_0011166), etc.

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

Vision/Abnormality: does the individual have vision abnormalities (specify)
All options:

• normal = no abnormal vision (-HP:0000504)
• abnormal = abnormal vision (HP:0000504)
• acuity reduced = reduced visual acuity (HP:0007663)
• adjusting luminance changes = difficulty adjusting changes in luminance (HP:0030512)
• age = poor visual behavior for age (HP:0025152)
• amaurosis fugax = amaurosis fugax (HP:0100576)
• binocular vision = abnormal binocular vision (HP:0011514)
• blurred vision = blurred vision (HP:0000622)
• bradyopsia = bradyopsia (HP:0030511)
• color vision = abnormal color vision (HP:0000551)
• field defect = visual field defect (HP:0001123)
• hemeralopia = hemeralopia (HP:0012047)
• impairment = visual impairment (HP:0000505)
• loss = visual loss (HP:0000572)
• loss nonprogressive = nonprogressive visual loss (HP:0200068)
• loss progressive = progressive visual loss (HP:0000529)
• loss progressive slow = slow decrease in visual acuity (HP:0007924)
• metamorphopsia = metamorphopsia (HP:0012508)
• nyctalopia = nyctalopia (HP:0000662)
• photophobia = photophobia (HP:0000613)
• photopsia = photopsia (HP:0030786)
• vitreous floaters = vitreous floaters (HP:0100832)
• ? = unknown
• nr = not reported

Vision/Other: does the individual have other visual problems (specify)?

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

Other hearing problems: Are there any other problems related to the ears?

Speech: does the individual have normal speech and language development
All options:

• - = no speech delay
• speech delayed (HP:0000750)
• mild = mild speech delayed (HP:0000750)
• mild-moderate = mild-moderate speech delayed (HP:0000750)
• moderate = speech delayed (HP:0000750)
• moderate-severe = moderate-severe speech delayed (HP:0000750),
• severe =severe speech delayed (HP:0000750)
• no speech = no speech (HP:0001344)
• loss of speech = loss of speech (HP:0002371)
• poor speech = poor speech (HP:0002465)
• nasal = nasal speech (HP:0001611)
• nasal/dysarthic =nasal, dysarthic speech (HP:0008376)
• hyponasal = hyponasal speech (HP:0100271)
• articulation difficulties = articulation difficulties (HP:0009088)
• dysarthria = dysarthria (HP:0001260)
• grammar-specific = grammar-specific speech disorder (HP:0006977)
• incomprehensible = incomprehensible speech (HP:0002546)
• scanning = scanning speech (HP:0002168)
• slurred = slurred speech (HP:0001350)
• slowed slurred = slowed slurred speech (HP:0007164)
• apraxia = speech apraxia (HP:0011098)
• ? = unknown
• n/a = not analysed

Cognitive/Impairment: does the individual have cognitive impairment (HPO_0100543)
All options:

• normal (IQ >80)
• - = absent (normal)
• + = present
• undefined = IQ <80
• borderline = IQ 70-80
• normal-mild
• mild = IQ 50-70
• mild-moderate
• moderate
• moderate-severe = IQ <50
• severe
• ? = unknown
• n/a = not analysed

Behaviour/Abnormality: does the individual show abnormal behaviour (please specify)
All options:

• abnormal = abnormal behaviour (HP:0000708, +)
• attention span short = short attention span (HP:0000736)
• delusions = delusions (HP:0000746)
• drooling = drooling (HP:0002307)
• eating = abnormal eating behavior (HP:0100738)
• emotion/affect = emotion/affect behavior (HP:0100851)
• agorophobia = agorophobia (HP:0000756)
• anxiety = anxiety (HP:0000739)
• emotional liability = emotional liability (HP:0000712)
• mood changes = mood changes (HP:0001575)
• mood swings = mood swings (HP:0000720)
• autism spectrum disorder = autism spectrum disorder (HP:0000729)
• autism = autism (HP:0000717)
• autism high cognitive = autism with high cognitive abilities (HP:0000753)
• fatigue = fatigue (HP:0012378)
• hallucinations = hallucinations (HP:0000738)
• hyperactivity = hyperactivity (HP:0000752)
• hyperorality = hyperorality (HP:0000710)
• mania = mania (HP:0100754)
• obsessive-compulsive disorder = obsessive-compulsive disorder (HP:0000722)
• personality changes = personality changes (HP:0000751)
• personality disorder = personality disorder (HP:0012075)
• phonophobia = phonophobia (HP:0002183)
• photophobia = photophobia (HP:0000613)
• polydipsia = polydipsia (HP:0001959)
• psychosis = psychosis (HP:0000709)
• schizophrenia = schizophrenia (HP:0100753)
• sleep disturbance = sleep disturbance (HP:0002360)
• social interactions impaired = impaired social interactions (HP:0000735)
• normal = normal behaviour
• ? = unknown
• n/a = not analysed

Hair/Scalp: individual has abnormal scalp hair (specify)
All options:

• abnormal = abnormal scalp hair (HP:0100037)
• normal = normal scalp hair
• brittle = brittle scalp hair (HP:0004779)
• cheek = scalp hair on to lateral cheek (HP:0009554)
• hypotrichosis = hypotrichosis of scalp (HP:0004782)
• loss = loss scalp hair (HP:0200115)
• slow-growing = slow-growing scalp hair (HP:0100038)
• sparse = sparse scalp hair (HP:0002209)
• sparse anterior = sparse anterior scalp hair (HP:0004768)
• wooly = wooly scalp hair (HP:0040149)
• ? = unknown
• nr = not reported

Eyebrows: eyebrows (please specify)
All options:

• abnormal = abnormal eyebrow (HP:0000534)
• absent = absent eyebrow (HP:0002223)
• aplasia/hyploplasia = aplasia/hyploplasiaeyebrow (HP:0100840)
• arched = highly arched eyebrow (HP:0002553)
• broad = broad eyebrow (HP:0011229)
• broad lateral = broad lateral eyebrow (HP:0007933)
• curved = laterally curved eyebrow (HP:0007733)
• double = double eyebrow (HP:0010730)
• duplication = partial duplication eyebrow (HP:0045018)
• extended = laterally extended eyebrow (HP:0011230)
• extension = extension eyebrow towards upper eyelid (HP:0010731)
• flaring = mdial flaring eyeborw (HP:0010747)
• horizontal = horizontal eyebrow (HP:0011228)
• long = long eyebrow (HP:0004523)
• normal = normal eyebrow
• sparse = sparse eyebrow (HP:0000535)
• sparse lateral = sparse lateral eyebrow (HP:0005338)
• thick = thick eyebrow (+, HP:0000574)
• white = white eyebrow (HP:0002226)
• - = no thick eyebrow
• ? = unknown
• n/a = not analysed

Eyelashes: individual has abnormality of the eyelashes (please specify)
All options:

• abnormal = abnormal eylashes (HP:0000499)
• abnormal lower = abnormal lower eylashes (HP:0040052)
• abnormal upper = abnormal upper eylashes (HP:0040051)
• absent = absent eyelashes (HP:0000561)
• eyelashes, absent/sparse (HP:0200102)
• eyelashes, loss (HP:0011457)
• eyelashes, absent, inner (HP:0007708)
• eyelashes, absent, lower (HP:0007646)
• eyelashes, absent, upper (HP:0040056)
• eyelashes, curly (HP:0007665)
• eyelashes, curly, short (HP:0007691)
• eyelashes, double row (distichiasis, HP:0009743)
• eyelashes, three rows (HP:0008009)
• eyelashes, multiple rows (HP:0008496)
• eyelashes, long (trichomegaly, HP:0000527)
• eyelashes, long, irregular rows (HP:0007740)
• eyelashes, long, lower (HP:0040053)
• eyelashes, long, upper (HP:0007840)
• eyelashes, normal
• eyelashes, prominent (HP:0011231)
• eyelashes, short (HP:0010764)
• eyelashes, short, lower (HP:0040055)
• eyelashes, short, upper (HP:0040054)
• eyelashes, sparse (HP:0000653)
• eyelashes, sparse, lower (HP:0007766)
• eyelashes, sparse, upper (HP:0040050)
• eyelashes, trichiasis (inward groth, HP:0001128
• eyelashes, white (HP:0002227)
• ? = unknown
• n/a = not analysed

MotorSkills: development motor skills; age head control (in months), age sitting (without support, in months), age walking (without support, in months); head:7m, sit:10m, walk:24m, delayed gross motor development (HP:0002194), delayed fine motor development (HP:0010862)

Lacrimal_Duct: does the individual have a lacrimal duct abnormality (HPO_0011481, tear duct); present (+), absent (-), unknown (?), not analysed (n/a)
All options:

• + = present
• - = absent
• ? = unknown
• n/a = not analysed

Ptosis: does the individual have ptosis; ptosis (HPO_0000520), congenital ptosis (HPO_0007970), bilateral congenital ptosis (HPO_0007911), bilateral ptosis (HPO_0001488), unilateral ptosis (HPO_0007687), progressive ptosis (HPO_0007838), no ptosis (-), unknown (?), not analysed (n/a)
All options:

• + = ptosis (HPO_0000520)
• congenital = congenital ptosis (HPO_0007970)
• bilateral congenital = bilateral congenital ptosis (HPO_0007911)
• bilateral = bilateral ptosis (HPO_0001488)
• unilateral = unilateral ptosis (HPO_0007687)
• progressive = progressive ptosis (HPO_0007838)
• - = no ptosis
• ? = unknown
• n/a = not analysed

Choanal_Stenosis: does the individual have choanal stenosis (HPO_0000452); present (+), absent (-), unknown (?), not analysed (n/a)
All options:

• + = present
• - = absent
• ? = unknown
• n/a = not analysed

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

Philtrum/Width: width philtrum; normal, broad (HPO_0000289), narrow (HPO_0011829), unknown (?), not analysed (n/a)
All options:

• normal
• + = broad
• - = normal (not broad)
• broad
• narrow
• ? = unknown
• n/a = not analysed

Face/Philtrum: individual has abnormal philtrum (specify)
All options:

• abnormal = abnormal philtrum (HP:0000288)
• deep = deep (depressed/prominent) philtrum (HP:0002002)
• flat = flat (simple/smooth) philtrum (HP:0000319)
• hypoplastic = hypoplastic philtrum (HP:0005326)
• long = long philtrum (HP:0000343)
• narrow = narrow philtrum (HP:0011829)
• raphe = philtrum with midline raphe (HP:0011826)
• short = short philtrum (HP:0000322)
• sinus = midline sinus of philtrum (HP:0011828)
• tented = tented philtrum (HP:0011825)
• wide = wide (broad) philtrum (HP:0000289)
• normal = normal philtrum
• ? = unknown
• n/a = not analysed

Facial/Mouth/Wide: does the individual have a wide mouth (HPO_0000154); present (+), absent (-), unknown (?), not analysed (n/a)
All options:

• + = present
• - = absent
• ? = unknown
• n/a = not analysed

Cleft: does the individual have a facial cleft (please specify)
All options:

• - = no cleft
• chin = cleft chin (HP:0011323)
• face = cleft facial (HP:0002006)
• face midline = cleft facial midline (HP:0100629)
• face transverse = cleft facial transverse (HP:0100731)
• lip bilateral = cleft lip bilateral (HP:0100336)
• lip unilateral = cleft lip unilateral (HP:0100333)
• lip lower = cleft lip lower (HP:0010281)
• lip median = cleft lip median (HP:0000161)
• lip non-mdiline = cleft lip non-mdiline (HP:0100335)
• lip upper = cleft lip upper (HP:0000204)
• lip upper incomplete = cleft lip upper incomplete (HP:0011340)
• lip submucous = cleft lip submucous (HP:0009101)
• lip/palate bilateral = cleft lip/palate bilateral (HP:0002744)
• lip/palate median = cleft lip/palate median (HP:0008501)
• mandible = cleft mandible (HP:0010752)
• oral = cleft oral (HP:0000202)
• palate = cleft palate (HP:0000175)
• palate bilateral = cleft palate bilateral (HP:0100337)
• palate unilateral = cleft palate unilateral (HP:0100334)
• palate median = cleft palate median (HP:0009099)
• palate non-mdiline = cleft palate non-mdiline (HP:0100338)
• palate hard = cleft palate hard (HP:0410005)
• palate hard submucous = cleft palate hard submucous (HP:0000176)
• palate soft = cleft palate soft (HP:0000185)
• palate soft submucous = cleft palate soft submucous (HP:0011819)
• palate primary = cleft palate primary (HP:0410003)
• palate secondary = cleft palate secondary (HP:0410004)
• palate hard = cleft palate hard (HP:0410005)
• ? = unknown
• n/a = not analysed

Ears/Abnormal: individual has abnormal ears (please specify)
All options:

• abnormal = ear abnormality (HP:0000598)
• normal = normal ears (-HP:0000598)
• small = small ears (HP:0008551)
• ? = unknown
• nr = not reported

Ears/Tags: does the individual have ear tags (HPO_0000384, preauricular skin tags); present (+), absent (-), unknown (?), not analysed (n/a)
All options:

• + = present
• - = absent
• ? = unknown
• n/a = not analysed

Hypertrichosis: does the individual have hypertrichosis (HPO_0000998); present (+), absent (-), unknown (?), not analysed (n/a)
All options:

• + = present
• - = absent
• ? = unknown
• n/a = not analysed

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

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

Pectus_Excavatum: Does the patient have pectus excavatum (HPO_0000767); present (+), pectus carinatum (pc), absent (-), unknown (?), not analysed (n/a)
All options:

• + = present
• pc = pectus carinatum
• - = absent
• ? = unknown
• n/a = not analysed

Elbow/Dislocated: does the patient have dislocated elbows (HPO_0003042); present (+), absent (-), unknown (?), not analysed (n/a)
All options:

• + = present
• - = absent
• ? = unknown
• n/a = not analysed

Patella/Small: does the patient have a small patella (HPO_0003065, patellar hypoplasia); present (+), unilateral (uni), bilateral (bi), absent (-), unknown (?), not analysed (n/a)
All options:

• + = present
• uni = unilateral
• bi = bilateral
• - = absent
• ? = 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

Phalanges/Distal/Absent_5th: is the 5th distal phalanx absent; present (+), partial, hypoplastic, absent (-), unknown (?), not analysed (n/a)
All options:

• Partial
• -
• +
• ?
• hypoplastic
• NA

Nails/Small: small nails (HPO_0001792); present (+), fifth only (5th), multiple, incl. 5th (multiple), present, not incl. 5th (+ not 5th), absent (-), unknown (?), not analysed (n/a)
All options:

• + = present
• 5th = fifth only
• multiple = multiple, incl. 5th
• + not 5th = present, not incl. 5th
• - = absent
• ? = unknown
• n/a = not analysed

Joints/Interphalangeal/Proximal: does the patient have prominent interphalangeal joints (HPO_0006237); present (+), absent (-), unknown (?), not analysed (n/a)
All options:

• + = present
• - = absent
• ? = unknown
• n/a = not analysed

Phalanges/Distal/Prominent: does the patient have prominent distal phalanges; present (+), absent (-), unknown (?), not analysed (n/a)
All options:

• + = present
• - = absent
• ? = unknown
• n/a = not analysed

Joint/Laxity: does the patient have joint laxity (HPO_0001388); present (+), absent (-), unknown (?), not analysed (n/a)
All options:

• + = present
• - = absent
• ? = unknown
• n/a = not analysed

Intestine/Abnormality: does the patient have intestinal anomalies (HPO_0002242, intestine abnormality); when yes, please specify

Heart/Abnormality: heart, abnormality (HPO_0001627, caridac defect); present (+), absent (-), unknown (?), not analysed (n/a), please specify (e.g. ASD: atrial septal defect; IAA: interrupted aortic arch; VSD: ventricular septal defect; PDA: patent ducts arteriosus; PS: pulmonary artery stenosis)

Kidney/Abnormality: does the patient have a kidney abnormality (HP:0000077), renal abnormality); present (+), absent (-), unknown (?), not analysed (n/a)
All options:

• + = abnormal kidney (HP:0000077)
• kidney abnormal = abnormal kidney (HP:0000077)
• failure = renal failure (HP:0000083)
• no failure = no renal failure (-HP:0000083)
• glomerulus abnormal= abnormal glomerulus (HP:0000095)
• glomerulus normal= normal glomerulus (-HP:0000095)
• - = normal kidney
• ? = unknown
• n/a = not analysed

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

Infections: does the patient have (recurrent) infections; please specify (tissue, agent, etc.)
All options:

• yes = (recurrent) infections (HP:0002719, +)
• no = no (recurrent) infections (-)
• recurrent due to aspiration (HP:0004891)
• recurrent in infancy/early childhood (HP:0005437)
• bronchopulmonaryrecurrent (HP:0006538)
• CNS (HP:0011450)
• cutaneous fungal recurrent (HP:0011370)
• gastrointestinal tract recurrent (HP:0004798)
• nail monilial chronic (HP:0008396)
• pneunomia recurrent (HP:0006532)
• respiratory recurrent (HP:0002205)
• respiratory tract (HP:0011947)
• respiratory tract acute (HP:0011948)
• respiratory tract upper and lower recurrent (HP:0200117)
• respiratory tract lower recurrent (HP:0002783)
• respiratory tract upper recurrent (HP:0002788)
• sinopulmonary recurrent (HP:0005425)
• skin recurrent (HP:0001581)
• skin bacterial recurrent (HP:0005406)
• skin viral recurrent (HP:0011371)
• urinary tract recurrent (HP:0000010)
• vulvovaginal candidiasis recurrent (HP:0012204)
• recurrent Aspergillus (HP:0002724)
• recurrent bacterial (HP:0002718)
• recurrent bacterial gram-negative (HP:0005420)
• recurrent Burkholderia cepacia (HP:0002842)
• recurrent candida (HP:0005401)
• recurrent E. coli (HP:0002740)
• recurrent enteroviral (HP:0002743)
• recurrent fungal (HP:0002841)
• recurrent Haemophilus influenzae (HP:0005376)
• Heliobacter pylori (HP:0005202)
• recurrent Klebsiella (HP:0002742)
• recurrent meningococcal disease (HP:0005381)
• recurrent mycobacterial (HP:0011274)
• recurrent mycobacterium avium complex (HP:0011275)
• recurrent Neisserial (HP:0005430)
• recurrent opportunistic infections (HP:0005390)
• recurrent protozoan infections (HP:0005386)
• recurrent Serratia marcescens (HP:0002741)
• recurrent Staphylococcal (HP:0007499)
• recurrent Staphylococcus aureus (HP:0002726)
• recurrent Streptococcus pneumoniae (HP:0005366)
• recurrent systemic pyogenic (HP:0005429)
• recurrent viral (HP:0004429)
• recurrent viral severe (HP:0005364)
• ? = unknown
• n/a = not analysed

Epiphyses/Cone_shaped: does the patient have cone shaped epiphyses (HPO_0010579, fingers or toes); present (+), absent (-), unknown (?), not analysed (n/a)
All options:

• + = present
• - = absent
• ? = unknown
• n/a = not analysed

Brain/MRI: details brain MRI

Brain/Corpus_Callosum/Agenesis: does the patient have agenesis of the corpus callosum (HPO_0001274); present (+), partial, dysgenesis, absent (-), unknown (?), not analysed (n/a)

Missing hypoplastic phalanx of fingers or toes: Does the patient have hypoplastic phalanges of the fingers or toes?

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

Stenosis_Pyloric: does the patient have pyloric stenosis (HPO_0002021); present (+), absent (-), unknown (?), not analysed (n/a)
All options:

• + = present
• - = absent
• ? = unknown
• n/a = not analysed

Gastro-Esophoegal_Reflux: does the patient have gastro-esophoegal reflux (HPO_0002020); present (+), absent (-), unknown (?), not analysed (n/a)
All options:

• + = present
• - = absent
• ? = 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

Eye/Cornea: does the individual have an abnormal cornea (specify)
All options:

• anisometropia = anisometropia (HP:0012803)
• astigmatism = astigmatism (HP:0000483)
• astigmatism hyperopic = astigmatism hyperopic (HP:0000484)
• asymmetry = corneal asymmetry (HP:0009915)
• band-shaped = band-shaped corneal dystrophy (HP:0007709)
• congenital = congenital corneal dystrophy (HP:0008005)
• curvature = abnormal curvature (HP:0100691)
• curvature increased = increased corneal curvature (HP:0100692)
• degeneration = corneal degeneration (HP:0007705)
• dystrophy = corneal dystrophy (HP:0001131)
• dystrophy mosaic = mosaic corneal dystrophy (HP:0007836)
• dystrophy mosaic central = mosaic central corneal dystrophy (HP:0100690)
• dystrophy punctate = punctate corneal dystrophy (HP:0007809)
• embryotoxon = posterior embryotoxon (HP:0000627)
• endothelium = abnormal endothelium (HP:0011488)
• epibulbar dermoid = epibulbar dermpoid (HP:0001140)
• epithelium = abnormal epithelium (HP:0011495)
• flat = flat cornea (HP:0007720)
• granular = granular corneal dystrophy (HP:0007802)
• hypermetropia = hypermetropia (HP:000540)
• hypermetropia high = high-grade hypermetropia (HP:0008499)
• keratitis = keratitis (HP:0000491)
• keratoconjunctivitis = keratoconjunctivitis (HP:0001096)
• keratoconjunctivitis sicca = keratoconjunctivitis sicca (HP:0001097)
• keratoconus = keratoconus (HP:0000563)
• keratoglobus = keratoglobus (HP:0001119)
• lattice = lattice corneal dystrophy (HP:0001149)
• marginal = marginal corneal dystrophy (HP:0007880)
• megalocornea = megalocornea (HP:0000485)
• microcornea = microcornea (HP:0000482)
• myopia = myopia (HP:0000545)
• myopia congenital = myopia congenital (HP:0008012)
• myopia severe = myopia severe >-6D (HP:0011003)
• opacity = corneal opacity (HP:007957)
• perforation = corneal perforation (HP:0100583)
• presbyopia = presbyopia (HP:?)
• prominent = abnormally prominent line of Schwalbe (HP:0007873)
• punctate = punctate keratitis (HP:0011859)
• reflex decreased = corneal reflex decreased (HP:0008000)
• refraction = abnormality refraction (HP:0000539)
• ribbonlike = ribbonlike corneal degeneration (HP:0200066)
• Schwalbe line = abnormal line of Schwalbe (HP:0008048)
• sensation decreased = corneal sensation decreased (HP:0012155)
• size = abnormal size (HP:0001120)
• speckled = speckled corneal dystrophy (HP:0007962)
• stroma = abnormal stroma (HP:0011492)
• thickness = abnormal thickness (HP:0011486)
• normal = normal cornea
• ? = unknown
• nr = not reported

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

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
• strabismus = strabismus (HP:0000486)
• strabismus congenital = congenital strabismus (HP:0000487)
• strabismus comitant = comitant strabismus
• strabismus incomitant = incomitant strabismus
• 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:0000063)
• 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
• nr = not reported

Facial/Lips: abnormality lips (please specify)
All options:

• abnormal = abnormality lip (HP:0000159)
• abnormal lower = abnormality lower lip (HP:0000178)
• abnormal upper = abnormality upper lip (HP:0000177)
• freckle = lip freckle (HP:0010798
• fused = fused lips (HP:0100788)
• hyperpigmentation = hyperpigmentation lip (HP:0100816)
• long upper = long upper lip (HP:0011341)
• pit = lip pit (HP:0100267)
• pit commissural = commissural lip pit (HP:0002710)
• pit lower = lower lip pit (HP:0000196)
• pit paramedian = paramedian lip pit (HP:0100269)
• pit upper = upper lip pit (HP:0100268)
• pursed = pursed lips (puckered, HP:0000205)
• short upper = short upper lip (HP:0000188)
• telangiectasia = lip telangiectasia (HP:0000214)
• vermillion abnormal upper = abnormal upper lip vermillion (HP:011339)
• vermillion thick = thick vermillion (HP:0012471)
• vermillion thick lower= thick lower lip vermillion (HP:0000179)
• vermillion thick upper = thick upper lip vermillion (HP:0000215)
• vermillion thin = thin vermillion (HP:0000233)
• vermillion thin lower= thin lower lip vermillion (HP:0010282)
• vermillion thin upper = thin upper lip vermillion (HP:0000219)
• normal = normal lips
• ? = unknown
• n/a = not applicable

Legend

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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
• - = not applicable
• 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)
• ASMM RTQ-PCR = allele-specific methylated multiplex real-time quantitative PCR
• ASO = allele-specific oligo hybridisation
• BESS = Base Excision Sequence Scanning
• CAGE = Cap analysis gene expression
• 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 = microscope (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
• MSREs = Methylation sensitive restriction enzymes
• MS-SeQMA = Methylation-specific Sequence-based quantitative methylation analysis
• Ms-SNuPE = Methylation-sensitive single-nucleotide primer extension
• MyoD = myoD induced differentiation
• Northern = Northern blotting
• OM = optical mapping
• PAGE = Poly-Acrylamide Gel-Electrophoresis
• PCR = Polymerase Chain Reaction
• PCRdig = PCR + restriction enzyme digestion
• 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)
• PFGE = Pulsed-Field Gel-Electrophoresis (+Southern)
• PTT = Protein Truncation Test
• QMPSF = Quantitative Multiplex PCR of Short Fluorescent fragments
• 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
• 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

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 a protein's function, in the format 'R/C' where R is the value reported by the source and C is the value concluded by the curator; '+' indicating the variant affects function, '+?' probably affects function, '+*' affects function, not associated with individual's disease phenotype, '#' affects function, not associated with any known disease phenotype, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect not classified.

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)
• DNA modified (VariO:0337)

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)
• sequence retaining amino acid indel (VariO:0029)
• post translational modification (VariO:0028)

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)
• variation at five prime cis splice site (VariO:0367)
• variation at canonical five prime splice site (VariO:0368)
• variation at three prime cis splice site (VariO:0370)
• variation at canonical three prime splice site (VariO:0372)
• cryptic splice site activation (VariO:0373)
• cryptic splice donor activation (VariO:0374)
• cryptic splice acceptor activation (VariO:0375)
• exon loss (VariO:0381)

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

Haplotype: haplotype on which variant was found

ClassClinical: Classification of the variant based on the clinical consequences as published or submitted. NOTE: this classification may differ from the opinion of the curator as given in a variant SUMMARY-record or the 'Functional effect concluded'). Classification should preferably be performed using standardised criteria; e.g. ACMG: 5 (dominant) (= disease associated, dominant inheritance), ACMG: 5 (recessive) (= disease associated, recessive inheritance), pathogenic (dominant), pathogenic (recessive), likely pathogenic (recessive) , VUS (= variant of unknown significance), likely benign (= likely not disease-associated), benign (= not disease-associated), non-disease phenotype, drug response, risk factor, associated with, etc. NOTE: pathogenic/likely pathogenic should go together with "variant (probably) affects function" In ClassFunctional

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?
• deletion
• deletion, small
• deletion, large
• 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

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.