LPL - LPL-ROHINI (NATIONAL REFERENCE LAB)
SECTOR - 18, BLOCK -E ROHINI
DELHI 110085
Name : XXXXXXXXX Collected : 18/02/2019
Lab No. : XXXXXXXXX Age: XX Years Gender: XXXX Received : 19/02/2019
A/c Status: P Ref By : Dr. XXXXXXXXXXXX Reported : 18/03/2019
Clinical Summary
Suspicion of Megalencephalic Leukodystrophy
Key Results and Interpretatoins:
Variant of Unknown significance (VUS)
Gene Chromosome Observed Zygosity Inheritance Seq. Mutation Exon Associated /Position nucleotide/ Depth type No Disorder AA change
MLC1 chr22: XXX XXX Homozygous Autosomal 74x Stop gain X Megalencephalic recessive Ref=0, leukoencephalop Alt=74 athy with subcortical cysts
Note:
1. *Benign variants, and silent and intronic variants with no evidence towards pathogenicity, are not included in this report. 2. These results should be interpreted within the context of additional laboratory results, family history and clinical findings. 3. Genetic counselling is recommended to discuss the implications of this result. ations
Page 1 of 5 LPL - LPL-ROHINI (NATIONAL REFERENCE LAB)
SECTOR - 18, BLOCK -E ROHINI
DELHI 110085
Name : XXXXXXXXX Collected : 18/02/2019
Lab No. : XXXXXXXXX Age: XX Years Gender: XXXX Received : 19/02/2019
A/c Status: P Ref By : Dr. XXXXXXXXXXXX Reported : 18/03/2019
Disease - Gene Overview The patient showed Recessive (homozygous) stop gain mutation XXX in Exon X (NM_015166) of MLC1 gene. This variant was not observed in 1000 Genome Database and ExAC database (Healthy populations Database frequency <0.05). The variant predicted to be deleterious by Bioinformatics algorithms such as SIFT, Mutation Taster, fathmm-MKL_coding_pred and Phenolyzer.
Variant Overview Mutation in the MLC1 gene found to be associated with Megalencephalic leukoencephalopathy with subcortical cysts (MLC) (MLC1, OMIM #604004) is a form of leukodystrophy, characterized by infantile-onset macrocephaly and delayed-onset neurologic deterioration, (such as mild motor delay), which worsen with time, leading to poor ambulation, falls, increasing seizures, gradual onset of cerebellar ataxia, spasticity, extrapyramidal findings and late onset of mild mental deterioration. Individuals with this condition typically have an enlarged brain (megalencephaly) which is evident at birth or within the first year of life and abnormality of the white matter in the brain (leukoencephalopathy). Brain MRI can reveal diffusely abnormal and mildly swollen white matter as well as subcortical cysts in the anterior temporal and frontoparietal regions. Initial mental and motor development is normal in most individuals followed by late and mild mental deterioration with time. Disease severity ranges from independent walking for a few years to independent walking in the fifth decade. Individuals can survive from their teens or twenties to fifties. Other features include dystonia, athetosis, dysphagia, behavioral problems and dysarthria. 1-7 MLC1 gene encodes protein involved in transporting molecules across the blood-brain barrier and the brain- cerebrospinal fluid barrier. Mutations in this gene have been associated with megalencephalic leukoencephalopathy with subcortical cysts.8,9 Variant found in MLC1 gene reported as variant of uncertain significance (VUS) due to lack of sufficient literature evidences. This VUS variant cannot be categorized into Pathogenic or Benign and needs to be carefully correlated with clinical symptoms or parental studies (inherited or de novo). However, this information may change based on the progress in the understanding of the function of the variant in the future. A periodic review of the literature is recommended to determine relevance of these findings.
Recommendations: Based on the clinical features and the observed genetic findings the following have been recommended 1. Phenotype correlation and genetic counselling is recommended 2. Sanger validation of the NGS findings in the individual. 3. Sanger evaluation of the above-mentioned variant in the Parents and close relatives.
Test Methodology DNA extracted from blood was used to perform targeted gene capture using a custom capture kit. The libraries were sequenced to mean >100X coverage on Illumina sequencing platform. The sequences obtained are
Page 2 of 5 LPL - LPL-ROHINI (NATIONAL REFERENCE LAB)
SECTOR - 18, BLOCK -E ROHINI
DELHI 110085
Name : XXXXXXXXX Collected : 18/02/2019
Lab No. : XXXXXXXXX Age: XX Years Gender: XXXX Received : 19/02/2019
A/c Status: P Ref By : Dr. XXXXXXXXXXXX Reported : 18/03/2019
aligned to human reference genome (GRCh37/hg19) and variant analysis was performed using set of Bioinformatics Pipeline. Clinically relevant mutations were annotated using published variants in literature and a set of diseases databases – ClinVar, OMIM, GWAS, HGMD and SwissVar. Common variants are filtered based on allele frequency in 1000 Genome Phase 3, ExAC, EVS, dbSNP147, 1000 Japanese Genome etc. Non- synonymous variants effect is calculated using multiple algorithms such as PolyPhen-2, SIFT, MutationTaster2, Mutation Assessor and LRT. Only non-synonymous and splice site variants found in the clinical exome panel consisting of specific set of genes were used for clinical interpretation. Silent variations that do not result in any change in amino acid in the coding region are not reported.
rsID unique identifier referring to a single genomic position, and used to associate population frequency information with sequence changes at that position. Reported population frequencies are derived from a number of public sites that aggregate data from large-scale population sequencing projects, including ExAC (http://exac.broadinstitute.org) and dbSNP (http://ncbi.nlm.nih.gov/SNP). MedGen ID & a unique identifier referring to an article in MedGen, NCBI’s centralized database of OMIM information about genetic disorders and phenotypes. Search by MedGen ID at http://www.ncbi.nlm.nih.gov/medgen. An OMIM number is a unique identifier referring to a comprehensive entry in Online Mendelian Inheritance of Man (OMIM). Search by OMIM number at http://omim.org.
*Genetic test results are reported based on the recommendations of American College of Medical Genetics [1], as described below:
Variant A change in a gene. This could be disease causing (pathogenic) or not disease causing (benign).
Pathogenic A disease causing variation in a gene which can explain the patients’ symptoms has been detected. This usually means that a suspected disorder for which testing had been requested has been confirmed. Likely Pathogenic A variant which is very likely to contribute to the development of disease however, the scientific evidence is currently insufficient to prove this conclusively. Additional evidence is expected to confirm this assertion of pathogenicity.
Variant of A variant has been detected, but it is difficult to classify it as either pathogenic (disease Uncertain causing) or benign (non-disease causing) based on current available scientific evidence. Significance Further testing of the patient or family members as recommended by your clinician may be needed. It is probable that their significance can be assessed only with time, subject to availability of scientific evidence.
Page 3 of 5 LPL - LPL-ROHINI (NATIONAL REFERENCE LAB)
SECTOR - 18, BLOCK -E ROHINI
DELHI 110085
Name : XXXXXXXXX Collected : 18/02/2019
Lab No. : XXXXXXXXX Age: XX Years Gender: XXXX Received : 19/02/2019
A/c Status: P Ref By : Dr. XXXXXXXXXXXX Reported : 18/03/2019
Limitations: This exome sequence test is designed to evaluate single nucleotide variants within the huma n exome; however, this technology is only able to sequence 90 - 95% of the human reference to the requisite 10-fold coverage needed for reliable detection of heterozygous variants. Next generation sequencing technologies (NGS), including clinical exome analysis, have a false positive rate of 5-10%. Additionally, certain types of genetic abnormalities are difficult to identify in sequencing data and have not been validated for clinical use including insertions, deletions, copy number alterations, long repetitive sequences, triplet repeat expansions, chromosomal rearrangements, polyploidy, repetitive regions including mono-, di- and tri-nucleotide repeats, GX rich regions, intronic variants inside and outside the splice-site and epigenetic effects. Large insertions, deletions, duplications, inversions and complex rearrangements cannot be characterized accurately by NGS as it uses short - read sequencing data. Only variations in genes potentially related to the patient’s phenotype are reported. Misinterpretation of results may occur, if the information provided is inaccurate or incomplete. Rare polymorphisms may lead to false negative or positive results. This does not imply that reported variants can always explain all symptoms of the patient. More clinical details assist in more precise evaluation. If results obtained do not match with the clinical findings given, additional testing should be considered. Re-filtering based on additional clinical information can be done when required even after the final report has been issued. Few genes are not completely covered in our clinical exome panel and thus, there might be chances of missing few mutations.
Disclaimer: Variants believed to be benign based on medical literature, or with population frequencies greater than or equal to 5%, or resulting in synonymous amino acid changes, or occurring in 5’ or 3’ untranslated regions are generally not reported. Incidental findings (if any) that meet ACMG guideline can be given upon request. This test has developed, validated and performed at third party lab. It has not been cleared or approved by the U.S. Food and Drug Administration (FDA) for diagnostic purposes. Hence, test is recommended for research use only. This is a screening test and variants if found, need to be confirmed by Sanger sequencing, as it might be associated with having false positive/ false negative results. Sanger sequencing report to be followed.
Page 4 of 5 LPL - LPL-ROHINI (NATIONAL REFERENCE LAB)
SECTOR - 18, BLOCK -E ROHINI
DELHI 110085
Name : XXXXXXXXX Collected : 18/02/2019
Lab No. : XXXXXXXXX Age: XX Years Gender: XXXX Received : 19/02/2019
A/c Status: P Ref By : Dr. XXXXXXXXXXXX Reported : 18/03/2019
References:
1. https://www.omim.org/entry/604004 2. https://ghr.nlm.nih.gov/gene/MLC1#conditions 3. https://ghr.nlm.nih.gov/condition/megalencephalic-leukoencephalopathy-with-subcortical-cysts 4. https://www.nature.com/articles/hgv201419 5. https://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=EN&Expert=2478 6. https://www.ncbi.nlm.nih.gov/books/NBK1535/ 7. https://rarediseases.info.nih.gov/diseases/3445/megalencephalic-leukoencephalopathy-with- subcortical-cysts 8. https://www.ncbi.nlm.nih.gov/gene/23209 9. https://www.genecards.org/cgi-bin/carddisp.pl?gene=MLC1
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Dr. Anand C Annan Dr. Atul Thatai Dr. Gaurav Verma MD (Path), PhD (Molecular & Cellular Pathology), PhD, National Head PhD (Clinical Genetics) Head Oncopathology R&D Molecular Diagnostics, Sr. Manager – Scientific Affairs, NRL, Dr Lal PathLabs Ltd. NRL, Dr Lal PathLabs Ltd. NRL, Dr Lal PathLabs Ltd.
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