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Content of the database This database contains information about the pathogenic variants which are reported in papers indexed in PubMed for the SMOC1 gene and the related mendelian disease microphthalmia with limb anomalies. In the SMOC1 homepage you can find: a link to a revised list of the most common features of the disorder. In this list percentage, number of patients who show the clinical sign, type

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Deafness and hereditary hearing loss, nonsyndromic

Summary Hereditary hearing loss and deafness may be conductive, sensorineural, or a combination of both; syndromic (associated with malformations of the external ear or other organs or with medical problems involving other organ systems), or nonsyndromic (no other visible abnormalities of the external ear or any related medical problem); and prelingual (before language develops) or postlingual (after language development). Molecular genetic testing plays a prominent

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Free Mutation: ATM gene, c.4388T>G (p.Phe1463Cys)

Submission date 3 Oct 2016 Gene ATM Mutation (gDNA level) chr11-108160480-T-G Mutation (cDNA level) c.4388T>G Reference sequence NM_000051.3 Prediction at protein level F1463C (p.Phe1463Cys) Mutation type missense Exon/intron location exon 29 of 63 Amino acid location aa 1463 of 3057 Gene associated phenotype(s) Ataxia-telangiectasia; Breast cancer, susceptibility to ClinVar ID 127388 dbSNP ID rs138327406 Clinical information (terms) breast cancer Clinical information (codes) HP:0003002 Sex female

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Free Mutation: ATM, c.6067G>A (p.Gly2023Arg)

Submission date 19 Sept 2016 Gene ATM Mutation (gDNA level) chr11-108186610-G-A Mutation (cDNA level) c.6067G>A Reference sequence NM_000051.3 Prediction at protein level G2023R (p.Gly2023Arg) Mutation type missense Exon/intron location exon 41 of 63 Amino acid location aa 2023 of 3057 Gene associated phenotype(s) Ataxia-telangiectasia ClinVar ID 127416 dbSNP ID rs11212587 Clinical information (terms) unaffected patient Clinical information (codes) – Sex female A priori interpretation uncertain

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Free Mutation: CUL4B, c.26G>A (p.Gly9Glu)

Gene CUL4B Mutation (gDNA level) chrX-119708447-C-T Mutation (cDNA level) c.26G>A Reference sequence NM_003588.3 Prediction at protein level G9E (p.Gly9Glu) Mutation type missense Exon/intron location exon 2 of 22 Amino acid location aa 9 of 914 Gene associated phenotype(s) Mental retardation, X-linked, syndromic 15 (Cabezas type) ClinVar ID na dbSNP ID rs149016283 Clinical information (terms) facial dysmorphism, growth delay, relative macrocephaly, moderate intellectual disability, ventricular septum

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Free Mutation: COL6A3, c.1688A>G (p.Asp563Gly)

Gene COL6A3 Mutation (gDNA level) chr2-238289767-T-C Mutation (cDNA level) c.1688A>G Reference sequence NM_004369.3 Prediction at protein level D563G (p.Asp563Gly) Mutation type missense Exon/intron location exon 5 of 44 Amino acid location aa 563 of 3178 Gene associated phenotype(s) Bethlem myopathy 1; Dystonia 27; Ullrich congenital muscular dystrophy 1 ClinVar ID 94910 dbSNP ID rs112913396 Clinical information n.a. A priori interpretation possibly not affecting function Notes Single

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Transposons

Mobile elements Transposons are mobile DNA elements which inserted themselves into the human genome during the evolution. So it is common to refer to them as transposon insertions. Transposons arise from RNA-based or DNA-based mechanisms and are therefore categorized in two classes: retrotransposons and DNA transposons. Retrotransposons Retrotransposons are fragments of cDNA which are transcribed from RNA and then inserted in a permissive sequence of the genome (splicesosomal

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Free Mutation: Results

Dear Colleague, the interpretation you requested is ready: Gene SLC6A1 Mutation (gDNA level) chr3-11059037-G-A Mutation (cDNA level) c.140G>A Reference sequence NM_003042.3 Mutation (protein level) W47* (p.Trp47*) Exon location exon 3 of 16 Amino acid location aa 47 of 600 Associated phenotype Myoclonic-atonic epilepsy Interepretation very likely pathogenic Notes Pathogenic mutations in this gene have been postulated to result in loss of function. This mutation is likely

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Retinitis pigmentosa

Panel testing recommended at Breda Genetics for this condition: Retinitis pigmentosa, classic (ABCA4, AIPL1, ARL6, BBS2, BEST1, C2ORF71, C8ORF37, CA4, CDHR1, CERKL, CLRN1, CNGA1, CNGB1, CRB1, CRX, CYP4V2, DHDDS, EYS, FAM161A, FSCN2, GUCA1B, HGSNAT, IDH3B, IMPDH1, IMPG2, IFT172, KIZ, KLHL7, LRAT, MAK, MERTK, NEK2, NR2E3, NRL, OFD1, PDE6A, PDE6B, PDE6G, PRCD, PROM1, PRPF3, PRPF31, PRPF4, PRPF8, PRPH2, RBP3, RDH12, RGR, RHO, RLBP1, ROM1, RP1, RP2,

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Cerebroretinal microangiopathy with calcifications and cysts (Coats plus syndrome)

Panel testing recommended at Breda Genetics for this condition: Cerebroretinal microangiopathy with calcifications and cysts – Coats plus syndrome – and its differential diagnosis (CTC1, POT1, SNORD118, SLC20A2, PDGFRB, PDGFB) If negative: Dyskeratosis congenita and its differential diagnosis (ADC, CTC1, DKC1, NHP2, NOP10, PARN, POT1, RETL1, SNORD118, TERC, TERT, TINF2, WRAP53) If negative again: Aicardi-Goutières syndrome (ADAR, IFIH1, RNASEH2A, RNASEH2B, RNASEH2C, SAMHD1, TREX1) Summary Cerebroretinal

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Sequencing the DNA of a single cell

Overview Whole genome sequencing on DNA of a single cell has been reported by several authors. Singe cell genome sequencing is of interest in a number of niche applications, such as the measuring of the genomic diversity in one individual’s gamete genomes, the mutation phase determination, and somatic DNA changes in tumors or after exposure to mutagenic agents. Sequencing library preparation Sequencing library preparation for single cell DNA

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17q21.31 microdeletion / KANSL1 mutations: Koolen-de Vries syndrome

Summary Koolen syndrome or Koolen-de Vries syndrome is characterized by moderate to severe intellectual disability, hypotonia, amiable behavior, and highly distinctive facial features. Koolen syndrome is most frequently a chromosomal disorder (when caused by microdeletion 17q21.31, also called monosomy 17q21.31), but can also arise as a monogenic disorder (when caused by a point mutation in the KANSL1 gene). Detailed clinical description Mild to severe global psychomotor developmental delay in

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Sequencing library: what is it?

Summary The sequencing library’s preparation is the first step in any Next Generation Sequencing analysis. There are different ways to prepare a sequencing library, depending on the sequencing platform (Life Technologies, Illumina, Roche, Pacific Biosciences) and the planned analysis (whole genome sequencing, whole exome sequencing, targeted DNA sequencing, whole-transcriptome sequencing, targeted RNA sequencing, ChIP-seq, RIP-seq, epigenetic studies and more). The NGS library can also be successfully

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Stargardt disease

Summary Recommended panel testing at Breda Genetics for this condition: Stargardt disease (ABCA4, BEST1, C1QTNF5, CDH3, CNGB3, ELOVL4, PROM1, PRPH2, RP1L1, RPGR, TIMP3, RIMS1) Stargardt disease is the most common form of inherited juvenile macular degeneration. Decreased central vision with decreased color perception is a hallmark of Stargardt disease, whereas side vision is usually preserved. The condition can be caused by mutations in one of

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Exploring “Omics”: a review of Genomics and Metabolomics

Overview: what is “Omics”? The term “Omics” is an English language Neologism which is utilized to informally refer to the totality of any biological field of study. Using the suffix “–ome”, new areas of study have been demarcated such as genome, proteome or metabolome, while new ones are constantly being added on a regular basis (transcriptome, interactome, proteome etc…). What this essentially does is that

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Congenital cataract, isolated

Summary Recommended panel testing at Breda Genetics for this condition: Cataract, isolated, classic (AGK, BFSP1, BFSP2, CHMP4B, CRYAA, CRYAB, CRYBA1 , CRYBA2, CRYBA4, CRYBB1, CRYBB2, CRYBB3, CRYGC, CRYGD, CRYGS, EPHA2, FYCO1, GCNT2, GJA3, GJA8 , HSF4, LEMD2, LIM2, LSS , MAF, MIP, NHS , PITX3 , SIPA1L3, TDRD7, UNC45B, VIM, WFS1) or Cataract, isolated, extended (AGK, BFSP1, BFSP2, CHMP4B, CRYAA, CRYAB, CRYBA1 , CRYBA2, CRYBA4, CRYBB1,

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Driver mutations

Mutations in cancer development: drivers and passengers Those genetic mutations that drive the development of cancer are defined as driver mutations. Driver mutations allow cancer to grow and invade the human body. Several genetic mutations are found in cancer cells, however just a few can be classified as drivers. All other mutations, which play just a secondary role in cancer development, are usually called passenger mutations. Somatic origin Driver

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Arthrogryposis, distal, type 9 (DA9)

Summary Distal arthrogryposis type 9 (DA9 – also known as congenital contractural arachnodactyly or Beals / Beals-Hecht syndrome) is caused by heterozygous mutation in the fibrillin-2 gene (FBN2), which is crucial for microfibril structure. The transmission is autosomal dominant. Due to its genetic etiology, it show some clinical overlap with Marfan syndrome, which is caused by mutation in the fibrillin-1 gene (FBN1). Beals syndrome patients

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Arthrogryposis, distal, type 8 (DA8)

Summary Distal arthrogryposis type 8 (DA8 – also known as multiple pterygium syndrome) is caused by heterozygous mutation in the MYH3 gene. The transmissions is autosomal dominant. Mutations in the same gene can also cause DA2A and DA2B. Detailed clinical features Wide variability in severity can be observed among affected subjects. Ptosis and severe scoliosis due to hemivertebrae are present in some. Limb findings can

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