MedGenome Labs Ltd.

3rd Floor, Narayana Nethralaya Building, Narayana Health City,

#258/A, Bommasandra, Hosur Road, Bangalore - 560 099, India.
Tel : +91 (0)80 67154989 / 990, Web: www.medgenome.com

DNA TEST REPORT - MEDGENOME LABORATORIES

LUVV AGGARWAL
Full Name / Ref No: Order ID/Sample ID: 80236/213216
[G18-4859]
Gender: Male Sample Type: Blood
Date of Birth / Age: 16 years Date of Sample Collection: NA
Referring Clinician: Dr. Ratna Puri, Date of Sample Receipt: 26th October 2018, 11:52 AM
Sir Ganga Ram Hospital, Date of Order Booking: 26th October 2018
New Delhi Date of Report: 7th December 2018, 6:30 PM
Test Requested: Clinical Exome

CLINICAL DIAGNOSIS / SYMPTOMS / HISTORY

Master Luvv Aggarwal, born of a non-consanguineous marriage, presented with clinical indications of progressive
proximal muscle weakness involving lower limb more than upper limb, claw hands, areflexia and hoarse voice with history
of delayed walking. His EMN/NCV showed demyelinating nerve involvement. He is suspected to be affected with Charcot-
Marie Tooth disease or muscular dystrophy and has been evaluated for pathogenic gene variations.

RESULTS
PATHOGENIC VARIANT CAUSATIVE OF THE REPORTED PHENOTYPE WAS IDENTIFIED

Gene (Transcript) # Location Variant Zygosity Disease (OMIM) Inheritance Classification

Charcot-Marie-
SH3TC2 (-) c.3325C>T Autosomal
Exon 14 Homozygous Tooth disease type- Pathogenic
(ENST00000515425.1) (p.Arg1109Ter) recessive
4C

ADDITIONAL FINDINGS: NO VARIANT(S) OF UNCERTAIN SIGNIFICANCE (VUS) IDENTIFIED

No other variant that warrants to be reported was detected. Variations with high minor allele frequencies which are likely
to be benign will be given upon request.
All the genes covered in the clinical exome assay have been screened for the given clinical indications. The coverage of
Charcot-Marie-Tooth disease and muscular dystrophy and congenital myopathy genes is given in appendix 1.
The coverage of the clinical exome assay genes will be provided upon request.

VARIANT INTERPRETATION AND CLINICAL CORRELATION

Variant description: A homozygous nonsense variation in exon 14 of the SH3TC2 gene (chr5:148389835G>A; Depth: 47x)
that results in a stop codon and premature truncation of the protein at codon 1109 (p.Arg1109Ter; ENST00000515425.1)
was detected (Table). The observed variation has previously been reported in patients affected with Charcot-Marie-Tooth
disease type 4C [23]. The observed variant is classified as pathogenic in ClinVar [24]. The p.Arg1109Ter variant has not been
reported in the 1000 genomes databases and has a minor allele frequency of 0.005%, 0.12% in the ExAC, our internal
databases respectively. The in silico prediction# of the variant is damaging by MutationTaster2. The reference codon is
conserved across species.

Page 1 of 6
Name/Sample ID: Luvv Aggarwal [G18-4859]/213216
MedGenome Labs Ltd.
3rd Floor, Narayana Nethralaya Building, Narayana Health City,
#258/A, Bommasandra, Hosur Road, Bangalore - 560 099, India.
Tel : +91 (0)80 67154989 / 990, Web: www.medgenome.com

OMIM phenotype: Charcot-Marie-Tooth disease type-4C (OMIM#601596) is caused by hpmozygous or compound

heterozygousmutations in the SH3TC2 gene (OMIM*608206). This disorder is characterized by delayed motor
development, distal lower limb muscle weakness due to peripheral neuropathy, difficulty in walking, decreased motor
nerve conduction velocity and loss of large myelinated fibers [10].
Based on the above evidence, this SH3TC2 variation is classified as a pathogenic variant and has to be carefully
correlated with the clinical symptoms.

RECOMMENDATIONS
Validation of the variant(s) by Sanger sequencing is recommended to rule out false positives.

Sequencing the variant(s) in the parents and the other affected and unaffected members of the family is recommended
to confirm the significance.

Genetic counselling is advised for interpretation on the consequences of the variant(s).

TEST METHODOLOGY
Targeted gene sequencing: Selective capture and sequencing of the protein coding regions of the genome/genes is
performed. Mutations identified in the exonic regions are generally actionable compared to variations that occur in non-
coding regions. Targeted sequencing represents a cost-effective approach to detect variants present in multiple/large
genes in an individual.
DNA extracted from blood was used to perform targeted gene capture using a custom capture kit. The libraries were
sequenced to mean >80-100X coverage on Illumina sequencing platform. The sequences obtained are aligned to human
reference genome (GRCh37/hg19) using BWA program [2, 3] and analyzed using Picard and GATK version 3.6[4, 5] to
identify variants relevant to the clinical indication. We follow the GATK best practices framework for identification of
variants in the sample. Gene annotation of the variants is performed using VEP program [6] against the Ensembl release
87 human gene model [7]. Clinically relevant mutations were annotated using published variants in literature and a set
of diseases databases - ClinVar, OMIM, GWAS, HGMD and SwissVar [8-15]. Common variants are filtered based on allele
frequency in 1000Genome Phase 3, ExAC, EVS, dbSNP147, 1000 Japanese Genome and our internal Indian population
database [16-20]. Non-synonymous variants effect is calculated using multiple algorithms such as PolyPhen-2, SIFT,
Mutation Taster2, Mutation Assessor, and LRT. Only non-synonymous and splice site variants found in the clinical exome
panel consisting of 8332 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.
Total data generated (Gb) 5.4
Total reads aligned (%) 99.99
Reads that passed alignment (%) 94.45
Data Q30 (%) 93.55

*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).
A disease causing variation in a gene which can explain the patients' symptoms has been detected. This
Pathogenic
usually means that a suspected disorder for which testing had been requested has been confirmed.
A variant which is very likely to contribute to the development of disease however, the scientific evidence is
Likely
currently insufficient to prove this conclusively. Additional evidence is expected to confirm this assertion of
Pathogenic
pathogenicity.

Page 2 of 6
Name/Sample ID: Luvv Aggarwal [G18-4859]/213216
MedGenome Labs Ltd.
3rd Floor, Narayana Nethralaya Building, Narayana Health City,
#258/A, Bommasandra, Hosur Road, Bangalore - 560 099, India.
Tel : +91 (0)80 67154989 / 990, Web: www.medgenome.com

A variant has been detected, but it is difficult to classify it as either pathogenic (disease causing) or benign
Variant of
(non-disease causing) based on current available scientific evidence. Further testing of the patient or family
Uncertain
members as recommended by your clinician may be needed. It is probable that their significance can be
Significance
assessed only with time, subject to availability of scientific evidence.

#The transcript used for clinical reporting generally represents the canonical transcript (according to Ensembl release 87 gene model),
which is usually the longest coding transcript with strong/multiple supporting evidence. However, clinically relevant variants annotated
in alternate complete coding transcripts could also be reported.
Variants annotated on incomplete and nonsense mediated decay transcripts will not be reported.
#The in silico predictions are based on Variant Effect Predictor, Ensembl release 87 (SIFT version - 5.2.2; PolyPhen - 2.2.2); LRT version
- November, 2009 release from dbNSFPv3.1 and Mutation Taster2 based on build NCBI 37 / Ensembl 69 [21].

For any further technical queries please contact techsupport@medgenome.com.

DISCLAIMER
• The classification of variants of unknown significance can change over time and MedGenome cannot be held
responsible for this. Please contact MedGenome at a later date to inquire about any changes.
• Intronic variants are not assessed using this method.
• Large deletions of more than 10 bp or copy number variations /chromosomal rearrangements cannot be assessed
using this method.
• Certain genes may not be covered completely and few mutations could be missed. Variants not detected by the assay
that was performed may impact the phenotype.
• The mutations have not been validated by Sanger sequencing.
• Incidental or secondary findings (if any) that meet the ACMG guidelines [22] can also be given upon request.
• This is a laboratory developed test and the development and the performance characteristics of this test was
determined by MedGenome.

Sakthivel Murugan, PhD Vivek Gopalan, PhD V L Ramprasad, PhD Dr. Udhaya H. Kotecha, MD
Associate Director - Senior Bioinformatics COO/Lab Director (Paediatrics), Fellowship in
Diagnostics Scientist II Medical Genetics.
Consultant - Clinical Geneticist

END OF REPORT

REFERENCES
1. Richards S, Aziz N, Bale S, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus
recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology,
Genetics in Medicine, 2015 May;17(5):405-24

Page 3 of 6
Name/Sample ID: Luvv Aggarwal [G18-4859]/213216
MedGenome Labs Ltd.
3rd Floor, Narayana Nethralaya Building, Narayana Health City,
#258/A, Bommasandra, Hosur Road, Bangalore - 560 099, India.
Tel : +91 (0)80 67154989 / 990, Web: www.medgenome.com

2. Li, H. and R. Durbin. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 2010. 26(5): p. 589-
95.
3. Meyer, L.R., et al., The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res, 2013. 41(D1): p. D64-
9.
4. McKenna, A., et al., The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Genome Res, 2010. 20(9): p. 1297-303.
5. Li, H., et al., The Sequence Alignment/Map format and SAMtools. Bioinformatics, 2009. 25(16): p. 2078-9.
6. McLaren, W., et al., Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics,
2010. 26(16): p. 2069-70.
7. ENSEMBL: http://www.ensembl.org
8. Landrum, M J., et al., ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res., 2015.
9. Hamosh A., et al., Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders,
2005.33:D514-7.
10. OMIM: http://www.omim.org
11. GWAS: http://www.ebi.ac.uk/gwas/
12. Welter D., et al., The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res., 2014.
13. Stenson, P. D., et al., Human Gene Mutation Database (HGMDR): 2003 update. Hum. Mutat. 21, 577-581.
14. HGMD: http://www.biobase-international.com/product/hgmd
15. Mottaz, A., et al., Easy retrieval of single amino-acid polymorphisms and phenotype information using SwissVar. Bioinformatics,
2010.26(6): p. 851-2.
16. A global reference for human genetic variation. Nature, 2015. 526(7571): p. 68-74.
17. Analysis of protein-coding genetic variation in 60,706 humans. 2015, http://dx.doi.org/10.1101/030338
18. NHLBI: https://esp.gs.washington.edu/drupal
19. Nagasaki, M., Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals. Nat. Commun. 2015.
20. dbSNP: http://www.ncbi.nlm.nih.gov/SNP/
21. Mutation Taster2: http://www.mutationtaster.org/
22. Green R. C., et al., American College of Medical Genetics and Genomics. ACMG recommendations for reporting of incidental
findings in clinical exome and genome sequencing. Genet Med. 2013 Jul;15(7):565-74.
23. Gooding, R., et al., "A novel Gypsy founder mutation, p. Arg1109X in the CMT4C gene, causes variable peripheral neuropathy
phenotypes." Journal of medical genetics 42.12 (2005): e69.
24. https://www.ncbi.nlm.nih.gov/clinvar/RCV000002588/

APPENDIX 1: COVERAGE OF CHARCOT-MARIE TOOTH DISEASE, MUSCULAR DYSTROPHY

AND CONGENITAL MYOPATHY GENES
Percentage of coding Percentage of coding Percentage of coding
Gene Gene Gene
region covered region covered region covered
AARS 100.00 ACTA1 100.00 AIFM1 100.00
ANO5 100.00 ATL1 100.00 ATL3 100.00
B3GALNT2 92.51 B4GAT1 100.00 BAG3 100.00
BIN1 100.00 BVES 100.00 CAPN3 100.00
CAV3 100.00 CCDC78 100.00 CCT5 100.00
CFL2 100.00 CHKB 100.00 CNTN1 100.00
COL12A1 100.00 COL6A1 100.00 COL6A2 100.00
COL6A3 100.00 COX6A1 100.00 CRYAB 100.00
CTDP1 100.00 DAG1 100.00 DES 100.00

Page 4 of 6
Name/Sample ID: Luvv Aggarwal [G18-4859]/213216
MedGenome Labs Ltd.
3rd Floor, Narayana Nethralaya Building, Narayana Health City,
#258/A, Bommasandra, Hosur Road, Bangalore - 560 099, India.
Tel : +91 (0)80 67154989 / 990, Web: www.medgenome.com

Percentage of coding Percentage of coding Percentage of coding

Gene Gene Gene
region covered region covered region covered
DHTKD1 100.00 DMD 100.00 DNAJB2 100.00
DNAJB6 100.00 DNM2 100.00 DNMT1 100.00
DST 100.00 DYNC1H1 100.00 DYSF 100.00
EGR2 100.00 EMD 100.00 FAM134B 100.00
FGD4 100.00 FHL1 100.00 FIG4 100.00
FKRP 100.00 FKTN 100.00 FLNC 100.00
GAN 100.00 GARS 100.00 GDAP1 100.00
GJB1 100.00 GMPPB 100.00 GNB4 100.00
GNE 100.00 HARS 100.00 HINT1 100.00
HK1 97.01 HNRNPA2B1 100.00 HNRNPDL 100.00
HOXD10 100.00 HSPB1 100.00 HSPB8 100.00
IGHMBP2 100.00 INF2 100.00 ISCU 100.00
ISPD 100.00 ITGA7 100.00 JPH1 100.00
KARS 100.00 KBTBD13 100.00 KIF1A 100.00
KIF1B 100.00 KIF5A 100.00 KLHL40 100.00
KLHL41 100.00 LAMA2 100.00 LAMP2 100.00
LARGE 100.00 LDB3 100.00 LIMS2 100.00
LITAF 90.52 LMNA 100.00 LMOD3 100.00
LRSAM1 100.00 MARS 100.00 MED25 100.00
MEGF10 100.00 MFN2 100.00 MME 98.13
MORC2 100.00 MPZ 100.00 MTM1 100.00
MTMR2 100.00 MYF6 100.00 MYH2 100.00
MYH7 100.00 MYOT 100.00 NAGLU 100.00
NDRG1 100.00 NEB 89.87 NEFH 98.53
NEFL 100.00 NGF 100.00 NTRK1 100.00
PABPN1 100.00 PDK3 100.00 PLEC 100.00
PLEKHG5 100.00 PMP22 100.00 POGLUT1 100.00
POMGNT1 100.00 POMGNT2 100.00 POMK 100.00
POMT1 100.00 POMT2 100.00 PRDM12 96.47
PRPS1 100.00 PRX 100.00 RAB7A 100.00
REEP1 100.00 RYR1 100.00 SBF1 100.00
SBF2 100.00 SCN11A 100.00 SCN9A 100.00
SEPN1 90.92 SGCA 100.00 SGCB 100.00
SGCD 100.00 SGCG 100.00 SH3TC2 100.00
SLC12A6 100.00 SLC25A46 100.00 SMCHD1 100.00
SOX10 100.00 SPEG 100.00 SPG11 100.00
SPTLC1 100.00 SPTLC2 100.00 SURF1 100.00
SYNE1 99.78 SYNE2 100.00 TCAP 100.00
TFG 100.00 TMEM43 100.00 TMEM5 100.00
TNNT1 100.00 TNPO3 100.00 TOR1AIP1 100.00
TPM2 100.00 TPM3 100.00 TRAPPC11 100.00
TRIM2 100.00 TRIM32 100.00 TRPV4 100.00
TTN 99.44 TTR 100.00 VCP 100.00

Page 5 of 6
Name/Sample ID: Luvv Aggarwal [G18-4859]/213216
MedGenome Labs Ltd.
3rd Floor, Narayana Nethralaya Building, Narayana Health City,
#258/A, Bommasandra, Hosur Road, Bangalore - 560 099, India.
Tel : +91 (0)80 67154989 / 990, Web: www.medgenome.com

Percentage of coding Percentage of coding Percentage of coding

Gene Gene Gene
region covered region covered region covered
WNK1 100.00 YARS 100.00

Page 6 of 6
Name/Sample ID: Luvv Aggarwal [G18-4859]/213216