1,620 Matching Annotations
  1. Oct 2026
    1. FSIP2_4

      CaseFSIP2_4 male, 43yo report, Tunisian

      CasePresentingHPOs HP:0003251, HP:0012207, HP:0012868

      (male infertility, asthenospermia, sperm tail anomaly)

      HPOsFreeText Sperm volume: 1.7mL, sperm concentration: 49.5 million/mL, total motility: 5h, vitality: 52%, normal spermatozoa: 0%, absent flagella: 6%, short flagella: 70%, coiled flagella: 14%, flagella of irregular caliber: 80%

      CaseNotHPOs n/a

      CasePreviousTesting Previous genetic analysis of DNAH1, CFAP43, and CFAP44 did not end in diagnosis. "Normal somatic karyotypes 46,XY and were negative for Y chromosome microdeletions."

      Variant NM_173651.3(FSIP2):c.16393_16396del (p.Asn5465Glufs)

      ClinVar 586971

      gnomAD not in gnomAD

      CaseAddInfo Consanguineous parents

      CasePMIDs 29449551

    1. Table 4Variants associated with a clinical phenotype in ≥5 homozygous subjects

      Variant 1. NM_000512.5:c.901G>T 2. NM_000512.5:c.1156C>T 3. NM_000512.5:c.120+1G>A 4. NM_000512.5:c.346G>A 5. NM_000512.5:c.1171A>G 6. NM_000512.5:c.860C>T 7. NM_000512.5:c.139G>A 8. NM_000512.5:c.280C>T 9. NM_000512.5:c.1019G>A 10. NM_000512.5:c.1168del

      Italics highlight common variants with table 2

    1. Family III

      Family#: Family III

      PresentingHPOs: HP:0003563 (decreased LDL cholesterol)

      PresentingHPOsFreeText: FHBL diagnosis was based on low levels of fasting calculated plasma LDL-C < 50 mg/dL without lipid lowering therapy. Affected relatives were diagnosed by LDL-C < 80 mg/dL and/or ApoB <50 mg/dL.

      FamilyMethod1: Next generation sequencing

      FamilyGenotypingMethod: Next generation sequencing panel for high-throughput sequencing of the coding regions of genes previously linked to FHBL (APOB, PCSK9, ANGPTL3) and ABL (MTTP, SAR1B). Sanger sequencing was performed for validation and co-segregation analysis among family members.

      ProbandLabel: Family III-II:2

      Variant: NM_000384.2:c.8799C>A (p.Cys2933*), heterozygous

      CAID: CA345993342

      gnomAD: Absent

    1. In this study we report the first development of a denaturating high performance liquid chromatography (dHPLC) protocol for the rapid and accurate detection of recently described mutations in the IDUA gene. Optimal PCR running and dHPLC partial denaturing conditions for mutation detection were established for each PCR amplicon corresponding to 14 IDUA exons and their adjacent intronic/flanking sequences. Results: A total of 12 different mutations, 5 nonsense, 4 missense, 1 deletion, and 2 splice site (intron), in 10 MPS I patients were screened. All mutations revealed a distinct dHPLC pattern thus enabling their accurate detection.

      This proband was "described and recently published by Vazna et al." (PMID: 19396826). Patient is compound heterozygous for c.1882C>T (p.Arg628Ter) and c.208C>T (p.Gln70Ter) (P based on classification by the ClinGen Lysosomal Diseases VCEP); phase confirmed in trans. PM3=0 points

    1. OA-16c.1635C>Gp.S545R333.71.0-5.020/117020/200 - HM

      Case#: Pedigree OA-16, North of England

      DiseaseAssertion: optic atrophy

      FamilyInfo: 2 additional affected individuals

      CasePresentingHPOs: HP:0000648

      CaseHPOFreeText: Snellen BCVA 20/200 - hand movement, mean age of onset= 3.7yrs

      CaseNotHPOs:

      CaseNotHPOFreeText:

      PreviouslyPublished: Cautious that they may overlap with the individuals from Hudson et al since both are from England, but the author notes that they "checked against the eOPA1 database (http://lbbma.univ-angers.fr/eOPA1/, Accessed 10-12-09) to determine whether they had been described in previous mutational reports."

      GenotypingMethod: The entire coding region of the OPA1 and OPA3 genes was amplified by PCR and sequenced. Variants were confirmed by reverse sequencing.

      Variant: c.1635C>G; p.S545R

      ClinVar: 30461

      CAID: CA10575554

      SupplementalData:

    1. siblings

      FamilyLabel R07-429

      Family#PresentingHPOs HP:0001263, HP:0003072, HP:0003015, HP:0003300, HP:0000978, HP:0002099, HP:0003193, HP:0002721, HP:0002007, HP:0000316, HP:0000218, HP:0000767, HP:0008905, HP:0003027, HP:0002987, HP:0003049, HP:0001156, HP:0004209, HP:0006380, HP:0006460, HP:0002694, HP:0005930, HP:0011844, HP:0008788, HP:0003155, HP:0002850

      (GDD, Hypercalcemia, Flared metaphyses, Ovoid vertebral bodies, Easy bruising, Asthma, Allergic rhinitis, Immunodeficiency, Frontal bossing, Hypertelorism, High arched palate, Pectus excavatum, Rhizomelia, Mesomelia, Contractures of elbows, Ulnar deviation of the wrist, Brachydactyly, Fifth finger clinodactyly, Knee contractures, Increased laxity of ankles, Sclerosis of skull base, Epiphyseal abnormality, Abnormal appendicular skeleton morphology, Delayed pubic bone ossification, elevated alkaline phosphatase, decreased IgM)

      HPOsFreeText Born at term, significant developmental delay/special education, abnormal brain MRI, severe unclassified immunodeficiency, normal PTH concentration, mild hypercalcemia. Radiographic findings: widened/flared metaphyses with irregular ossification, moth-eaten long bones, fragmentation of the proximal metacarpals, and a distinctive transverse gap seen in the tibias. From table: eczema or atrophoderma, wheel chair bound-unable to bear weight on lower extremities, flattened supraorbital ridges, normal formed and positioned ears, mild pectus excavatum, Mesomelia with significant anterior bowing in the upper and lower extremities, Ulnar deviation at the wrists with laxity, telescoping fingers, Mild knee contractures, Significant laxity at the ankles with positional equinovarus, 2-3 syndactyly, Delayed ossification of the fontanel, Delayed ossification of the basal occipital bone, Delayed ossification of the posterior elements of the spine, Significant metaphyseal irregularities, Epiphyseal delay with irregular epiphyses, Subjectively large distance from the epiphyses to the metaphyseal edge, Ossification defect or gaps in the appendicular skeleton, Brachydactyly with metaphyseal irregularities and epiphyseal delay, IgE <1 (normal <20 IU/ml), CD3 T-lymphocytes 82% (normal 60-76%), Parathyroid hormone intact 19 (normal 11-51 pg/ml). Radiograph additionally showed widened/flared metaphyses with irregular ossifications and irregular ossification front, brachydactyly with irregular metacarpal and phalangeal metaphyses and delayed epiphyseal ossification, absence of pubic bone ossification, and delayed ossification of the basal occipital bone and subjectively increased density of the skull.

      FamilyNotHPOs n/a

      NotHPOsFreeText fixed equinovarus, walked with or without assistance

      CountryOrigin n/a

      Ethnicity n/a

      Race n/a

      Family#PreviousTesting PTH1R coding exons sequenced due to phenotype overlap with JMC. No variants identified.

      ProbandLabel R07-429A

      Variant NM_025164.4(SIK3):c.559C>T (p.Arg187Cys)

      ClinVar 587366

      gnomAD not in gnomAD

      FamilyAddInfo consanguineous

      FamilyPMIDs n/a

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