1. NGS panel - Genetic testing for cataract


April 06, 2018

Disease summary:

Cataract refers to the clouding of the lens in the eye, defined as opacification of the normally transparent crystalline lens. Cataracts are common in older people and usually related to aging. They can be classified by the age at onset as congenital or infantile (<1yr); juvenile cataract (1-10yrs); presenile cataract (<45yrs) and senile or age-related cataract (>45yrs)1.

It is important to determine if the individual has non-syndromic (only the lens are affected) or syndromic (other organs in addition to the lens are affected) congenital cataracts. The most common causes of non-syndromic congenital cataracts are pathogenic variants in lens crystallin - associated genes (CRYAA, CRYAB, CRYBB1, CRYBB2, CRYBB3, CRYGC, CRYGD) which account for ~50% of all cases1, 2, 4

Autosomal dominant, autosomal recessive

1-6/10,000 for congenital cataract1; 1-15/10,000 in children 1, 3.

Major signs and symptoms of cataracts include 1, 3, 4:

  • Clouded, blurred or dim vision
  • Increasing difficulty with vision at night
  • Sensitivity to light and glare
  • Need for brighter light for reading and other activities
  • Seeing "halos" around lights
  • Frequent changes in eyeglass or contact lens prescription
  • Fading or yellowing of colors
  • Double vision in a single eye
  • Visual acuity test.
  • Slit-lamp examination.
  • Retinal exam.
  • Diagnosis is confirmed by the finding of pathogenic variant in one of the following genes: AGK, BCOR, BFSP1, BFSP2, CHMP4B, CRYAA, CRYAB, CRYBA1, CRYBA2, CRYBA4, CRYBB1, CRYBB2, CRYBB3, CRYGB, CRYGC, CRYGD, CRYGS, CTDP1, EPHA2, EYA1, FOXC1, FOXE3, FTL, FYCO1, GALK1, GCNT2, GJA3, GJA8, HSF4, LEMD2, LIM2, LSS, MAF, MIP, NHS, P3H2, PAX6, PITX3, SIPA1L3, SLC16A12, TDRD7, UNC45B, VIM, VSX2, WFS1.

The only effective treatment for cataracts is surgery 1, 2.

  • Corneal disease
  • Glaucoma
  • Optic nerve disease
  • Eye injury, eye tumors
  • Macular disease
  • Medications affecting central nervous system

To confirm/establish the diagnosis, CENTOGENE offers the following testing strategy for cataract using NGS Panel Genomic:

Step 1: Whole genome sequencing from a single filter card (drop of blood), covering the entire genic region (coding region, exon/intron boundaries, intronic and promoter) for all the genes included in the cataract panel. Copy Number Variants analysis derived from NGS data is also included.

Step 2: If no pathogenic variant is identified in Step1, continue with bioinformatics analysis covering genes that are either implicated or associated with overlapping phenotype or similar pathways.   

  • Individuals with early onset of cataracts.
  • Individuals with a positive family history of cataract.
  • Individuals with most common symptoms suggestive of cataracts (regardless of family history).

Confirmation of a clinical diagnosis through genetic testing of cataract can allow for genetic counseling and may direct medical management.

Overview of genes underlying hereditary forms of cataract, included in CENTOGENE´s cataract NGS panel

chr. locus
Protein Inh. % of pathogenic variants Allelic disorders
AGK 610345
Acylglycerol kinase AR Rare Cataract 38
Cataract and cardiomyopathy
Sengers syndrome
BCOR 300485
Bcl6 corepressor XLD Rare for cataract
>1% for MAC 5
Microphthalmia syndromic 2
Microphtalmia and cataract
Oculofaciocardiodental syndrome
BFSP1 603307
Beaded filament protein 1 AR Rare 6,7 Cataract 33
Juvenile cataract
BFSP2 603212
Beaded filament protein 2 AD 12/384 Chinese population 6,7 Cataract 12 multiple types
CHMP4B 610897
Chromatin modifying protein 4B AD Rare8 Cataract 31 multiple types
CRYAA 123580
Crystallin alpha 1 AD Rare9 Cataract 9 multiple types
Open angle glaucoma
CRYAB 123590
Crystallin alpha 2 AD, AR Rare9 Cataract 16 multiple types
Myofibrillar myopathy 2
Dilated cardiomyopathy 1II
Hypertrophic cardiomyopathy
CRYBA1 123610
Crystallin beta 1 AD Rare9 Cataract 10 multiple types
CRYBA2 600836
Crystallin beta 2 AD, AR Rare9 Cataract 42
CRYBA4 123631
Crystallin beta 4 AD Rare9 Cataract 23 multiple types
Primary angle-closure glaucoma
CRYBB1 600929
Crystallin beta B1 AD, AR Rare9 Cataract 17 multiple types
CRYBB2 123620
Crystallin beta B2 AD Rare9 Cataract 3 multiple types
CRYBB3 123630
Crystallin beta B3 AD, AR Rare9 Cataract 22
CRYGB 123670
Crystallin gamma-B AD Rare9 Cataract 39 multiple types
CRYGC 123680
Crystallin gamma-C AD Rare9 Cataract 2 multiple types
CRYGD 123690
Crystallin gamma-D AD Rare9 Cataract 4 multiple types
CRYGS 123730
Crystallin gamma-S AD Rare9 Cataract 20 multiple types
CTDP1 604927
Transcription factor CTD of POLR2A AR 7% carrier rate for c.863+389C>T in Roma/Gypsy population 10, 11 Congenital cataracts, facial dysmorphism, and neuropathy
EPHA2 176946
Ephrin receptor A2 AD 4.7% in Australia 12 Cataract 6 multiple types
EYA1 601653
eyes absent protein 1 AD 40% for BOR13 Anterior segment anomalies with or without cataract
Branchiootorenal Spectrum Disorders (BOR)
Branchiootic syndrome 1
Branchiootorenal syndrome 1, with or without cataracts
Otofaciocervical syndrome
FOXC1 601090
Transcription factor Forkhead box E3 AD Rare Anterior segment dysgenesis 3
Axenfeld-Rieger syndrome 3
FOXE3 601094
Transcription factor Forkhead box C2 AR 2.5% for MAC14 Anterior segment dysgenesis 2
Cataract 34 multiple types
Microphtalmia/Anophtalmia/coloboma (MAC)
FTL 134790
Ferritin light chain AD, AR 80% for Neuroferritinopathy 15 Hyperferritinemia-cataract syndrome
L-ferritin deficiency, dominant and recessive
Neurodegeneration with brain iron accumulation 3
FYCO1 607182
Transcription factor FYCO1 AR Rare Cataract 18
GALK1 604313
Galactokinese 1 AR Rare Galactokinase deficiency with cataracts
GCNT2 600429
Glucosaminyl transferase 2 AD, AR Rare Cataract 13 with adult I phenotype
Adult I phenotype without cataract
GJA3 121015
GAP junction protein A3; Connexin 46 AD Rare Cataract 14 multiple type
GJA8 600897
GAP junction protein A8; Connexin 50 AD Rare Cataract 1 multiple type
HSF4 602438
Heat-shock transcription factor 4 AD 2/69 in Chinese population16 Cataract 5 multiple type
LEMD2 616312
Nuclear transmembrane protein 25 AR Rare Cataract 46 juvenile-onset
LIM2 154045
Lens intristic membrane protein 2 AR Rare Cataract 19 multiple types
LSS 600909
Lanosterol synthase AR Rare Cataract 44
MAF 177075
Transcription factor MAF AD Rare Cataract 21 multiple types
Ayme-Gripp syndrome
MIP 154050
Major lens intrinsic protein AD Rare Cataract 15 multiple type
NHS 300457
NHS actin remodeling regulator XLD Rare Cataract 40, X-linked
Nance-Horan syndrome
P3H2 610341
Prolyl 3-hydrolase AR Rare Myopia, high, with cataract and vitreoretinal degeneration
PAX6 607108
Transcriptional factor paired box 6 AD 94% (67/71) for Anyridia17
80% in Wilms tumor with aniridia 18
2% for MAC 5
Cataract with late-onset corneal dystrophy, Coloboma of optic nerve, Coloboma, ocular, Aniridia Morning glory disc anomaly, Anterior segment dysgenesis 5, multiple subtypes
Foveal hypoplasia 1
Optic nerve hypoplasia
PITX3 602669
PAX6-regulated transcription factor 3 AD Rare Cataract 11 multiple types
Anterior segment dysgenesis 1, multiple subtypes
SIPA1L3 616655
SIPA1-proliferation protein 3 AR Rare Cataract 45
SLC16A12 611910
Monocarboxylate transporter 12 AD Rare Cataract 47 with microcornea
TDRD7 611258
Tudor domain regulating protein 7 AR Rare Cataract 36
UNC45B 611220
Myosin-specific shaperone UNC45 AD Rare Cataract 43
VIM 193060
Vimentin AD Rare Cataract 30 pulverulent
VSX2 142993
Homeobox protein 10 AR Rare Microphthalmia with coloboma 3
Isolated microphthalmia-2
WFS1 606201
Wolframin AD, AR Rare Cataract 41
Wolfram syndrome
Wolfram syndrome-like disease
Deafness, autosomal dominant 6/14/38