Table 2 Variants detected in nine patients with CLAPO

From: CLAPO syndrome: identification of somatic activating PIK3CA mutations and delineation of the natural history and phenotype

Patient ID

Change

Frequency by deep sequencing

Frequency by confirmation technique

COSMIC a

Developmental disorders b (refs. 14,17,18,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38)

P1 (CM: skin biopsy in right hemithorax)

PIK3CA:NM_006218.2:c.344G>C; p.Arg115Pro

12% (1,290, 171)

7.5% (pyrosequencing), 10.2% (ddPCR)

1

6

P2 (CM: skin biopsy in left inguinal region)

PIK3CA:NM_006218:c.248T>C; p.Phe83Ser

11% (328, 41)

9.5% (pyrosequencing)

3

0c

P6 (LM: oral mucosa)

PIK3CA:NM_006218.2:c.1258T>C; p.Cys420Arg

12% (287, 39)

7.5% (pyrosequencing), 10.3% (ddPCR)

78

15

P9 (CM: skin biopsy on right leg)

PIK3CA:NM_006218.2:c.344G>C;p.Arg115Pro

16% (1,019, 195)

13.3% (pyrosequencing), 15.7% (ddPCR)

1

6

P9 (blood)

PIK3CA:NM_006218.2:c.344G>C;p.Arg115Pro

0% (217, 0)

1.26% (ddPCR)

1

6

P10 (CM: lower lip)

PIK3CA:NM_006218.2:c.1624G>A; p.Glu542Lys

10% (85, 9)

3.04% (ddPCR)

999

44

P13 (LM: tongue)

PIK3CA:NM_006218.2:c.3140A>T; p.His1047Leu

16% (87, 16)

10% (pyrosequencing), Sanger sequencing

315

30

  1. The tissue in which the variant was detected is specified in each case. Variant frequency by deep sequencing shows the percentage of mosaicism and the number of reads for each allele (wt, alternate). Frequency by confirmation technique includes which other technique(s) were used to validate the candidate variant and its percentage.
  2. CLAPO, capillary malformation of the lower lip, lymphatic malformation predominant on the face and neck, asymmetry, and partial/generalized overgrowth; CM, capillary malformation; ddPCR, droplet digital polymerase chain reaction; LM, lymphatic malformation.
  3. aCancer samples with identified PIK3CA mutations in COSMIC database (http://cancer.sanger.ac.uk/; accessed June 2017).
  4. bNumber of patients with vascular/overgrowth disorders previously reported with the specific PIK3CA variant.
  5. cIn silico prediction for Phe83Ser: CADD 15.97 (damaging ≥14), gerp2 5.44 (conserved >2.45), VEST.Pred 0.678 (damaging ≥0.65), Fathmm −0.54 (possibly damaging (−1,0.8)), mutation taster 0.9999 (disease-causing), LRT 0.00000099999 (deleterious).
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