Factor V of Leiden and thrombophilia: how many questions! What is Factor V Leiden? If I have the Factor V Leiden, have I a higher risk for deep veins thrombosis? Am I at risk of miscarriage with factor V Leiden? The factor V Leiden has been extensively studied in recent years. In the face of
How many genetic variants do we have? When sequencing the entire human genome (whole genome sequencing), the average number of variants detected in one person is about 4 million. From whole-exome sequencing, the number of genetic variants detected is very high too. So, how do we guess the clinical significance of all those variants? The
Breda Genetics panel recommended for this condition: Pan73 – Male infertility (AK7, AR, ARMC2, AURKC, AZF, BRDT, C14ORF39, CATSPER1, CATSPER2, CEP112, CFAP43, CFAP44, CFAP58, CFAP58, CFAP65, CFAP69, CFAP70, CFAP91, CFTR, DEFB126, DEFB128, DNAH1, DNAH17, DNAH2, DNAH8, DPY19L2, DZIP1, FANCM, FSHR, FSIP2, HSF2, KLHL10, LHCGR, M1AP, MAATS1, MEIOB, MSH4, MSH5, NANOS1, NR5A1, PICK1, PLCZ1, PLK4, PMFBP1,
Point mutations: an overview Mutations are inheritable changes in the DNA sequence. Mutations can be of different size and may affect a single gene (genic mutations), one or more chromosomes in their structure (chromosomal aberrations), or one or more chromosomes in number (genomic aneuploidies). Genic mutations involve one or few single nucleotides. So they can
Coding and non-coding exons in the genes structure Genes are the coding part of the genome and represent only 2% of the entire DNA chain. Despite this, the vast majority of pathogenic mutations causing rare disorders (up to 85%) falls right in the genes. Genes have a well-defined structure: they are made up of exons,
Summary Fragile X syndrome is an inherited disorder caused by a CGG repeat expansion in the FMR1 gene. The syndrome is characterized by mild-to-severe mental retardation, which may be associated with behavioural disturbances and typical physical signs. As being X-linked, the syndrome shows its typical manifestations in males, although some females may be mildly symptomatic. The syndrome is
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
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
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
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.
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
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
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
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
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,
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
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
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,
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
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
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