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BRCA1, BRCA2 and their products

Tumor Genetic Testing BRCA1, BRCA2 and their productsBoth BRCA1 and BRCA2 are involved in maintenance of genome stability, as they are crucial for the process of DNA repair by homologous recombination (HRR), which is considered to be a conservative form of DNA repair, largely involved in repairing DNA lesions that stall DNA replication forks and/or cause DNA double-strand breaks. Although there are many ostensibly distinct

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Current methods for BRCA1/BRCA2 molecular analysis

Current Methods for BRCA1/BRCA2 molecular analysis BRCA testing is commonly performed by direct Sanger sequencing. This method is considered the ‘gold standard’ of DNA sequencing. It is technologically reliable, widely available, and has a relatively simple workflow. The drawbacks of Sanger sequencing are: • limited throughput • lower cost-effectiveness compared to next-generation sequencing (NGS) • inability to detect large genomic rearrangements (LGRs; e.g.: large deletions/duplications)

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BRCA1/BRCA2 related cancers

Tumor Genetic Testing Breast Cancer In women, breast cancer accounts for 15% of cancer-related deaths. 10% of women affected by breast cancer have a family history of the disease. Compared with women without a family history, women with one first-degree relative with premenopausal breast cancer are at 3.3-fold greater risk, and women with two first-degree relatives with breast cancer are at 3.6-fold greater risk.Hereditary forms

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BRCA1 and BRCA2: deep dive!

Tumor Genetic Testing Germline mutations in the BRCA1 and BRCA2 genes result in a high increased lifetime risk of developing breast and ovarian cancer and, to a lesser extent, other types of cancer such as prostate cancer, pancreatic cancer and melanoma. BRCA1 and BRCA2 related susceptibility to breast and ovarian cancer (also known as hereditary cancer and ovarian syndrome) are inherited in an autosomal dominant manner. Most individuals with a BRCA1 or

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10 FAQs on hereditary hearing loss

Based on our genetic testing and genetic counseling experience, we’d like to answer some of the most frequently asked questions on hereditary hearing loss. For the complete disease card on nonsyndromic deafness and hearing loss you can click here. Neither my partner nor me are affected by hearing loss. None of our relatives is affected either.  Are we still at risk of having babies affected by hearing loss? Yes. There

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SMOC1 – NM_001034852.2:c.211C>T

SMOC1 OMIM: *608488 14q24.2 – NM_001034852.2 c.211C>T (p.Arg71*) exon 2 rs number / neighbourhood rs532566349 TGAGTACCAG[C/T]GAGCCAAGTG Genomic Coordinates GRCh37/hg19: chr14:70418966 GRCh38/hg38: chr14:69952249 Frequency ExAC: T=8.238e-06 1000GP: T=0.0002 ESP: not reported Pathogenic for microphthalmia with limb anomalies Reference: PMID: 21750680, PMID: 18541965. #1 PMID: 21750680, PMID: 18541965. Clinical Sign HPO ID Unilateral anophthalmia HP:0000528 Lower limbs, postaxial oligodactyly HP:0006210 Pierre-Robin sequence HP:0000201     Affected individual –

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SMOC1 – NM_001034852.2:c.223C>T

SMOC1 OMIM: *608488 14q24.2 – NM_001034852.2 c.223C>T (p.Arg75*) exon 2 rs number / neighbourhood rs370866589 AGCCAAGTGC[C/T]GAGACCCGAC Genomic Coordinates GRCh37/hg19:  chr14:70418978 GRCh38/hg38:  chr14:69952261 Frequency ExAC: T=3.295e-05 1000GP: not reported ESP: T=0.000077 Pathogenic for microphthalmia with limb anomalies Reference: PMID: 21750680, PMID: 6544388. #1 PMID: 21750680, PMID: 6544388. Clinical Sign HPO ID Bilateral anophthalmia HP:0000528 Upper Limb, bilateral 4-5 metacarpal fusion HP:0005867 Lower Limb, postaxial oligodactyly HP:0006210 Severe mental retardation

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SMOC1 – NM_001034852.2:c.378+1G>T

SMOC1 OMIM: *608488 14q24.2 – NM_001034852.2 c.378+1G>T intron 3 rs number / neighbourhood no rs number CTTTACCCAG[g/t]tgaggcctcg Genomic Coordinates GRCh37/hg19: chr14:70420250 GRCh38/hg38: chr14:69953533 Frequency ExAC: not reported 1000GP: not reported ESP: not reported Pathogenic for microphthalmia with limb anomalies Reference: PMID: 21194680. #1 PMID: 21194680. Clinical Sign HPO ID True anophthalmia Bilateral HP:0011478 Mild mental retardation HP:0001256 Broad lateral eyebrows HP:0011229 Sparse eyelashes HP:0000653 Short

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SMOC1 – NM_001034852.2:c.378+1G>A

SMOC1 OMIM: *608488 14q24.2 – NM_001034852.2 c.378+1G>A intron 3 rs number / neighbourhood rs751356341 CTTTACCCAG[g/a]tgaggcctcg Genomic Coordinates GRCh37/hg19: chr14:70420250 GRCh38/hg38: chr14:69953533 Frequency ExAC: A=8.27e-06 (filtered out) 1000GP: not reported ESP: not reported Reported in ClinVar as pathogenic for anophthalmos with limb anomalies (Variation ID: 30728) Pathogenic for microphthalmia with limb anomalies Reference: PMID: 21194678, PMID: 10607960. #1 PMID: 21194678, PMID: 10607960. Clinical Sign HPO ID Bilateral anophthalmia HP:0000528 Small face HP:0000274

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SMOC1 – NM_001034852.2:c.274C>T

SMOC1 OMIM: *608488 14q24.2 – NM_001034852.2 c.274C>T (p.Gln92*) exon 3 rs number / neighbourhood rs781216969 AGATGCTGGC[C/T]AGAGCAAGTG Genomic Coordinates GRCh37/hg19: chr14:70420145 GRCh38/hg38: chr14:69953428 Frequency ExAC: T=8.24e-06 1000GP: not reported ESP: not reported Pathogenic for microphthalmia with limb anomalies Reference: PMID: 21750680. #1 PMID: 21750680. Clinical Sign HPO ID Bilateral anophthalmia HP:0000528 Upper limbs, contractures of fingers HP:0100490 Lower Limb, postaxial oligodactyly HP:0006210 Lower Limb, 2-3 toe cutaneous

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SMOC1 – NM_001034852.2:c.395dupA

SMOC1 OMIM: *608488 14q24.2 – NM_001034852.2 c.395dupA (p.Tyr132fs*1) exon 4 rs number / neighbourhood no rs number TGCCATACTTA[-/A]CACTGGGTAC Genomic Coordinates GRCh37/hg19: chr14:70442448 GRCh38/hg38: chr14:69975731 Frequency ExAC: not reported 1000GP: not reported ESP: not reported Pathogenic for microphthalmia with limb anomalies Reference: PMID: 21750680, PMID: 17375532. #1 PMID: 21750680, PMID: 17375532. Clinical Sign HPO ID Bilateral anophthalmia HP:0000528 Upper limbs, bilateral 4/5 metacarpal fusion HP:0005867 Lower Limb, postaxial oligodactyly

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SMOC1 – NM_001034852.2:c.664+1G>A

SMOC1 OMIM: *608488 14q24.2 – NM_001034852.2 c.664+1G>A intron 7 rs number / neighbourhood no rs number AGAAATTCAG[g/a]taaataacct Genomic Coordinates GRCh37/hg19: chr14:70461198 GRCh38/hg38: chr14:69994481 Frequency ExAC: not reported 1000GP: not reported ESP: not reported Reported in ClinVar as pathogenic for anophthalmos with limb anomalies (Variation ID: 30727) Pathogenic for microphthalmia with limb anomalies Reference: PMID: 21194678, PMID: 19208380. #1 PMID: 21194678, PMID: 19208380. Clinical Sign HPO ID Bilateral anophthalmia

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SMOC1 – NM_001034852.2:c.718C>T

SMOC1 OMIM: *608488 14q24.2 – NM_001034852.2 c.718C>T (Gln240*) exon 8 rs number / neighbourhood rs376672665 AGAGGCCCAG[C/T]AGAATCCCCG Genomic Coordinates GRCh37/hg19: chr14:70477524 GRCh38/hg38: chr14:70010807 Frequency ExAC: not reported 1000GP: not reported ESP: not reported The variant has been reported in ClinVar as pathogenic for anophthalmos with limb anomalies (Variation ID: 30726) The variant has been reported in the OMIM Allelic Variants List for the SMOC1 gene (.0001) Pathogenic for

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SMOC1 – NM_001034852.2:c.832C>T

SMOC1 OMIM: *608488 14q24.2 – NM_001034852.2 c.832C>T (p.Arg278Cys) exon 8 rs number / neighbourhood rs776638586 GGACACAGGG[C/T]GCCCGCTGCC Genomic Coordinates GRCh37/hg19: chr14:70477638 GRCh38/hg38: chr14:70010921 Frequency ExAC: T=1.658e-05 1000GP: not reported ESP: not reported Pathogenic for microphthalmia with limb anomalies Reference: PMID: 21750680, PMID: 6544388. #1 PMID: 21750680, PMID: 6544388. Clinical Sign HPO ID Bilateral anophthalmia HP:0000528 Upper limbs, clinodactyly of the 5th finger HP:0004209 Lower Limb, cutaneous syndactyly

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SMOC1 – NM_001034852.2:c.848C>A

SMOC1 OMIM: *608488 14q24.2 – NM_001034852.2 c.848C>A (p.Thr283Asn) exon 8 rs number / neighbourhood no rs number CTGCCTGGGA[C/A]CTCCACACGG Genomic Coordinates GRCh37/hg19: chr14:70477654 GRCh38/hg38: chr14:70010937 Frequency ExAC: not reported 1000GP: not reported ESP: not reported Pathogenic for microphthalmia with limb anomalies Reference: PMID: 21750680, PMID: 7573150. #1 PMID: 21750680, PMID: 7573150. Clinical Sign HPO ID Bilateral anophthalmia HP:0000528 Upper limbs, short 5th metacarpal HP:0010047 Lower limbs, right fusion

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SMOC1 – NM_001034852.2:c.857G>A

SMOC1 OMIM: *608488 14q24.2 – NM_001034852.2 c.857G>A (p.Arg286His) exon 8 rs number / neighbourhood no rs number ACCTCCACAC[G/A]gtaagccccc Genomic Coordinates GRCh37/hg19: chr14:70477663 GRCh38/hg38: chr14:70010946 Frequency ExAC: not reported 1000GP: not reported ESP: not reported Pathogenic for microphthalmia with limb anomalies Reference: PMID: 23646827. #1 PMID: 23646827. Clinical Sign HPO ID Bilateral anophthalmia HP:0000528 Syndactyly HP:0001159   Affected individual – variant in a homozygous state Affected

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SMOC1 – NM_001034852.2:c.910delG

SMOC1 OMIM: *608488 14q24.2 – NM_001034852.2 c.910delG (p.Asp305Metfs*59) exon 9 rs number / neighbourhood no rs number TACAGAGGCG[G/-]ATGACCCCTT Genomic Coordinates GRCh37/hg19: chr14:70478254 GRCh38/hg38: chr14:70011537 Frequency ExAC: not reported 1000GP: not reported ESP: not reported Pathogenic for microphthalmia with limb anomalies Reference: PMID: 21750680. #1 PMID: 21750680. Clinical Sign HPO ID Upper limb, cutaneous syndactyly HP:0010554 Lower Limb, cutaneous syndactyly from 3 to 5 toes HP:0010716 Horseshoe kidney

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SMOC1 – NM_001034852.2:c.1108C>T

SMOC1 OMIM: *608488 14q24.2 – NM_001034852.2 c.1108C>T (p.Gln370*) exon 11 rs number / neighbourhood no rs number GTATTTCAGC[C/T]AGCTGGACAG Genomic Coordinates GRCh37/hg19: chr14:70489981 GRCh38/hg38: chr14:70023264 Frequency ExAC: not reported 1000GP: not reported ESP: not reported Pathogenic for microphthalmia with limb anomalies Reference: PMID: 21750680, PMID: 8723070. #1 PMID: 21750680, PMID: 8723070 Clinical Sign HPO ID Bilateral anophthalmia HP:0000528 Upper limbs, bilateral 4/5 metacarpal fusion HP:0005867 Upper limbs, camptodactily HP:0100490

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SMOC1 Clinical Sign List

94.44% 17/18 clinical anophthalmia (unilateral or bilateral) HP:0000528 72.22% 13/18 clinical anophthalmia (unilateral or bilateral) HP:0000528 22,22% 4/18 true anophthalmia HP:0011478 61.11% 11/18 toe syndactyly HP:0001770 22.22% 4/18 2-3 toe cutaneous syndactyly HP:0005709 16.67% 3/18 3-5 toes syndactyly HP:0010716 11.11% 2/18 4-5 toe syndactyly HP:0004692 11.11% 2/18 cutaneous syndactyly of toes HP:0010621 5.56% 1/18 2-5 toe syndactyly HP:0010715 5.56% 1/18 2-4 toe cutaneous syndactyly HP:0005768

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SMOC1 Database – Homepage

Please, take a look to the readnote before proceeding. SMOC1 OMIM: *608488 14q24.2 – NM_001034852.2 Pathological Phenotypes: 1 Microphthalmia with limb anomalies OMIM: #206920 Microphthalmia with limb anomalies is caused by homozygous mutations in the SMOC1 gene. Distinctive features are unilateral or bilateral anophthalmia with limb anomalies. Intellectual disabilities is also a common feature. The most common limb anomalies are toe syndactyly, oligodactyly, metacarpal synostosis, camptodactyly

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