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Table 2 Summary statistics of whole exome sequencing in two unrelated patients with CAPOS syndrome

From: A novel recurrent mutation in ATP1A3 causes CAPOS syndrome

 

Family 1, subject III-1

Family 2, subject II-2

Total reads

108,841,666

104,389,738

Chastity-passed reads

103,868,186

102,337,954

Reads aligned with mapping quality ≥10

92,611,315

91,501,102

Average exome read deptha

69x

65x

Non-synonymous single nucleotide variants

10,911

11,254

Splice-site single nucleotide variants

517

524

Coding insertions/deletionsb

805/416

810/501

Non-silent variantsc not in dbSNP 129 or 130

2,259

2,209

Noveld heterozygous, autosomal variants

390

224

Genes with novel non-identical heterozygous variants in both probands

9e

Genes with novel identical heterozygous variants in both probands

3f

Variant segregating in all 10 affected family members tested in three CAPOS families

ATP1A3

chr19:47,166,267C > T (hg18)g

c.2452G > Ah

 

p.Glu818Lys

  1. aAverage read depth of exons annotated using Ensembl 54 (including potential PCR duplicates) calculated as (sum of the number of reads aligned per site for all exonic sites) / (total number of exonic sites).
  2. bSupported by ≥7 reads.
  3. cIncludes non-synonymous single nucleotide variants, splice-site single nucleotide variants (within 2 bases of exon boundaries), and small, coding insertions and deletions as annotated using Ensembl 54 gene models.
  4. dNot previously reported in dbSNP129 or 130, 1000 Genomes Project, or 1834 non-cancer genomes collected in Canada’s Michael Smith Genome Sciences Centre’s local database.
  5. eNon-identical variants of 6 of these genes were called with sufficient quality in both probands to warrant confirmation by Sanger sequencing. Variants of the following genes were tested but did not segregate with the disease in either family: WDR26, C12orf56, LMO7, and DNAH17. A variant of SIGLEC1 segregated as expected in Family 2, but the variant found in Family 1 did not segregate as expected. A variant of MUC16 segregated as expected in Family 1, but neither of two different variants of this gene found in Family 2 segregated as expected.
  6. fOnly one of these variants (c.2452G > A of ATP1A3) was called with sufficient quality in both probands to warrant confirmation by Sanger sequencing. This variant showed the expected segregation pattern with the disease in both families.
  7. gLocation in hg19 is chr19:42,474,427C > T.
  8. hAnnotation is on Ensembl transcript ENST00000302102, version 5.
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Orphanet Journal of Rare Diseases

ISSN: 1750-1172