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Blueprint Genetics Microphthalmia, Anophthalmia and Anterior

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Blueprint Genetics Microphthalmia, Anophthalmia and Anterior Microphthalmia, Anophthalmia and Anterior Segment Dysgenesis Panel Test code: OP0601 Is a 61 gene panel that includes assessment of non-coding variants. Is ideal for patients with a clinical suspicion / diagnosis of microphthalmia, anophthalmia or an anterior segment dysgenesis disorder. About Microphthalmia, Anophthalmia and Anterior Segment Dysgenesis Anophthalmia and microphthalmia are rare developmental defects of the globe. Microphthalmia refers to an eye with reduced volume and may be associated with coloboma or with an orbital cyst. Anophthalmia is the absence of one or both eyes. Anophthalmia and microphthalmia may be unilateral or bilateral, and over 50% are associated with systemic abnormalities. Anophthalmia and microphthalmia may be inherited as an autosomal dominant, autosomal recessive, or X-linked manner. The major causative gene is SOX2 in which heterozygous loss-of-function variants account for 25% of cases. Examples of syndromes associated with anophthalmia/microphthalmia are CHARGE syndrome (CDH7) and COFS syndrome (ERCC2, ERCC5, ERCC6). Anterior segment dysgenesis (ASD) disorders encompass a wide variety of developmental conditions affecting the cornea, iris, and lens. It can be an isolated ocular anomaly or accompanied by systemic defects. Anterior segment anomalies are associated with an approximate 50% risk of glaucoma. The majority of genes associated with ASD show autosomal dominant inheritance. Axenfeld-Rieger syndrome is caused by variants in PITX2 and FOXC1 with an estimated prevalence of 1:200,000. Availability 4 weeks Gene Set Description Genes in the Microphthalmia, Anophthalmia and Anterior Segment Dysgenesis Panel and their clinical significance Gene Associated phenotypes Inheritance ClinVar HGMD ABCB6 Blood group, Langereis system, Pseudohyperkalemia, Dyschromatosis AD/BG 9 20 universalis hereditaria, Microphthalmia, isolated, with coloboma 7 ADAMTS18 Knobloch syndrome 2, Microcornea, myopic chorioretinal atrophy, and AR 4 14 telecanthus, Retinal dystrophy, early onset, autosomal recessive ALDH1A3 Microphthalmia, isolated 8 AR 8 23 BCOR Microphthalmia, syndromic, Oculofaciocardiodental syndrome XL 40 53 BMP4 Microphthalmia, syndromic, Orofacial cleft AD 8 39 BMP7 Anophthalmia, microphthalmia, and variable brain, ear, palate, and AD 2 6 skeletal anomalies CDK9 AR 1 CHD7 Isolated gonadotropin-releasing hormone deficiency, CHARGE syndrome AD 276 860 https://blueprintgenetics.com/ COL4A1 Schizencephaly, Anterior segment dysgenesis with cerebral involvement, AD 58 107 Retinal artery tortuosity, Porencephaly, Angiopathy, hereditary, with nephropathy, aneurysms, and muscle cramps, Brain small vessel disease COX7B Linear skin defects with multiple congenital anomalies 2 XL 5 5 CPAMD8 Anterior segement dysgenesis 8 4 6 CYP1B1 Glaucoma, primary open angle glaucoma, juvenile-onset, Glaucoma, AR 24 237 primary open angle, adult-onset, Glaucoma, primary congenital, Peters anomaly ERCC2 Xeroderma pigmentosum, Trichothiodystrophy, photosensitive, AR 26 98 Cerebrooculofacioskeletal syndrome 2 ERCC5 Xeroderma pigmentosum, Xeroderma pigmentosum/Cockayne AR 21 54 syndrome ERCC6* Xeroderma Pigmentosum-Cockayne Syndrome, De Sanctis-Cacchione AD/AR 87 135 syndrome FOXC1 Axenfeld-Rieger syndrome, Iridogoniodysgenesis, Peters anomaly AD 46 135 FOXE3 Aphakia, congenital primary, Anterior segment mesenchymal AR/AD 9 29 dysgenesis, Cataract 34, Aortic aneurysm, familial thoracic FOXL2 Premature ovarian failure, Blepharophimosis, epicanthus inversus, and AD 74 215 ptosis FRAS1 Fraser syndrome AR 27 58 FREM1 Bifid nose, Manitoba oculotrichoanal syndrome, Trigonocephaly AD/AR 14 35 FREM2 Fraser syndrome 2 AR 11 23 GJA1* Oculodentodigital dysplasia mild type, Oculodentodigital dysplasia AD/AR 31 107 severe type, Syndactyly type 3 GRIP1 Fraser syndrome AR 5 17 HCCS Linear skin defects with multiple congenital anomalies 1 (MIDAS XL 7 13 syndrome) HESX1 Septooptic dysplasia, Pituitary hormone deficiency, combined AR/AD 15 26 HMX1 Oculoauricular syndrome AR 3 4 MAB21L2 Microphthalmia/coloboma and skeletal dysplasia syndrome AD/AR 6 9 MFRP Microphthalmia, isolated 5, Nanophthalmos 2, Retinitis pigmentosa, AR 27 30 autosomal recessive MITF Tietz albinism-deafness syndrome, Waardenburg syndrome, Coloboma, AD/AR 32 58 osteopetrosis, microphthalmia, macrocephaly, albinism, and deafness (COMMAD) NAA10 Microphthalmia, syndromic 1 (Lenz microphthalmia) XL 16 10 NDP Exudative vitreoretinopathy, Norrie disease XL 31 167 OCRL Lowe syndrome, Dent disease XL 47 264 https://blueprintgenetics.com/ OTX2 Microphthalmia, syndromic, Pituitary hormone deficiency, combined, AD 23 73 Retinal dystrophy, early-onset, and pituitary dysfunction PAX2 Isolated renal hypoplasia, Papillorenal syndrome, Focal segmental AD 30 96 glomerulosclerosis 7 PAX6 Aniridia, cerebellar ataxia, and mental retardation (Gillespie syndrome), AD 144 550 Keratitis, Coloboma, ocular, Cataract with late-onset corneal dystrophy, Morning glory disc anomaly, Foveal hypoplasia, Aniridia, Optic nerve hypoplasia, Peters anomaly PITX2 Axenfeld-Rieger syndrome, Ring dermoid of cornea, AD 23 101 Iridogoniodysgenesis, Peters anomaly PQBP1 Renpenning syndrome XL 14 18 PRSS56 Microphthalmia, isolated 6 AR 10 24 PXDN Anterior segment dysgenesis 7 AR 7 14 RAB18# Warburg micro syndrome 3 AR 5 5 RAB3GAP1 Warburg micro syndrome AR 29 66 RAB3GAP2# Warburg micro syndrome, Martsolf syndrome AR 11 15 RARB Microphthalmia, syndromic 12 AD/AR 9 6 RAX Microphthalmia, isolated 3 AR 5 14 RBP4 Retinal dystrophy, iris coloboma, and comedogenic acne syndrome, AD/AR 8 7 Microphthalmia, isolated, with coloboma 10 SHH Holoprosencephaly, Microphthalmia with coloboma AD 42 218 SIPA1L3 Cataract 45 AR 2 4 SIX3 Holoprosencephaly AD 17 87 SIX6 Microphthalmia, isolated, with cataract 2, Optic disc anomalies with AR 2 8 retinal and/or macular dystrophy SLC38A8 Foveal hypoplasia 2 AR 11 18 SMCHD1 Facioscapulohumeral muscular dystrophy, Facioscapulohumeral AD 51 79 muscular dystrophy, type 2 SMOC1 Microphthalmia with limb anomalies AR 9 15 SOX2* Microphthalmia, syndromic AD 34 104 STRA6 Microphthalmia, syndromic, Microphthalmia, isolated, with coloboma AR 22 33 TBC1D20 Warburg micro syndrome 4 AR 6 6 TENM3 Microphthalmia, isolated, with coloboma 10 AR 9 2 TFAP2A Branchiooculofacial sydrome AD 23 42 VPS13B Cohen syndrome AR 351 203 https://blueprintgenetics.com/ VSX2 Microphthalmia, isolated 2, Microphthalmia, isolated, with coloboma 3 AR 9 13 YAP1 Ocular coloboma with or without hearing impairment, cleft lip/palate, AD 2 10 and/or mental retardation ZIC2 Holoprosencephaly AD 22 114 *Some regions of the gene are duplicated in the genome. Read more. # The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads), and/or the gene has exons listed under Test limitations section that are not included in the panel as they are not sufficiently covered with high quality sequence reads. The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#). Due to possible limitations these genes may not be available as single gene tests. Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), mitochondrial (mi), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Mitomap databases. Non-coding disease causing variants covered by the panel Gene Genomic HGVS RefSeq RS-number location HG19 CHD7 Chr8:61734568 c.2836-15C>G NM_017780.3 CHD7 Chr8:61757794 c.5051-15T>A NM_017780.3 CHD7 Chr8:61763034 c.5405-18C>A NM_017780.3 rs199981784 CHD7 Chr8:61763035 c.5405-17G>A NM_017780.3 rs794727423 CHD7 Chr8:61763039 c.5405-13G>A NM_017780.3 rs1131690787 COL4A1 Chr13:110802675 c.*35C>A NM_001845.4 COL4A1 Chr13:110802678 c.*32G>A/T NM_001845.4 COL4A1 Chr13:110802679 c.*31G>T NM_001845.4 CYP1B1 Chr2:38303243 c.-322A>C NM_000104.3 CYP1B1 Chr2:38303258 c.-337G>T NM_000104.3 rs552932800 ERCC5 Chr13:103514354 c.881-26T>G NM_000123.3 ERCC6 Chr10:50681659 c.2599-26A>G NM_000124.3 rs4253196 FOXC1 Chr6:1610252 c.-429C>G NM_001453.2 rs77888940 NAA10 ChrX:153195397 c.*43A>G NM_003491.3 NAA10 ChrX:153195400 c.*40A>G NM_003491.3 NAA10 ChrX:153195401 c.*39A>G NM_003491.3 NDP ChrX:43818099 c.-207-1G>A NM_000266.3 https://blueprintgenetics.com/ NDP ChrX:43832545 c.-208+5G>A NM_000266.3 NDP ChrX:43832548 c.-208+2T>G NM_000266.3 NDP ChrX:43832549 c.-208+1G>A NM_000266.3 NDP ChrX:43832685 c.-343A>G NM_000266.3 rs895911086 NDP ChrX:43832722 c.-391_-380delCTCTCTCTCCCTinsGTCTCTC NM_000266.3 NDP ChrX:43832724 c.-396_-383delTCCCTCTCTCTCTC NM_000266.3 rs770996360 OCRL ChrX:128674707 c.40-14A>G NM_000276.3 OCRL ChrX:128687279 c.239-4023A>G NM_000276.3 OCRL ChrX:128696350 c.940-11G>A NM_000276.3 PAX6 Chr11:31685945 c.*125537G>T NM_000280.4 rs606231388 PAX6 Chr11:31812434 c.1033-42_1033-26delATGTGTTCCTCAGTAACinsG NM_000280.4 PAX6 Chr11:31816377 c.524-41T>G NM_000280.4 PAX6 Chr11:31823338 c.142-14C>G NM_000280.4 rs1131692291 PAX6 Chr11:31828391 c.-52+5delG NM_000280.4 PAX6 Chr11:31828391 c.-52+3_-52+6delAAGTinsTG NM_000280.4 PAX6 Chr11:31828392 c.-52+3_-52+4delAA NM_000280.4 PAX6 Chr11:31828395 c.-52+1delG NM_000280.4 PAX6
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