Scenario 3: Genetic Analysis Case Study on FN1 gene

Scenario 3: Genetic Analysis Case Study on FN1 gene#

A Patient with Spondylometaphyseal Dysplasia and Corner Fractures#

A patient affected by spondylometaphyseal dysplasia with corner fractures, a rare form of AD osteocondrodysplasia of unknown genetic origin, underwent Whole Exome Sequencing (WES) analysis. This disclosed a de novo likely pathogenic mutation in the FN1 gene, a gene previously associated with glomerulopathy with fibronectin deposits, a rare kidney disease (KD) not present in the patient.

Research Questions#

Question 1: Mutation Prevalence#

Are there any other individuals with the same mutation or allelic variant?

PREFIX sio: <http://semanticscience.org/ontology/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX caresm: <http://example.com/caresm/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT ?individual ?individualLabel
WHERE {
  # Identify the mutation of interest
  ?mutation rdf:type sio:SIO_000115 ;
            rdfs:label "FN1 gene mutation"@en .

  # Find individuals with the same mutation
  ?individual rdf:type sio:SIO_000498 ;  # Individual
              sio:denotes ?mutation ;
              rdfs:label ?individualLabel .

  # Ensure the labels are in English
  FILTER(LANG(?individualLabel) = "en") .
}

Question 2: Phenotype#

What is their phenotype?

WORK IN PROGRESS#

Question 3: Genotype-Phenotype Correlation#

Is it possible to establish any genotype-phenotype correlation? WORK IN PROGRESS#

Question 4: Variant Frequency in Populations#

What is the variant frequency across different populations?

WORK IN PROGRESS#

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