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Table 3 Description of compound heterozygous variants detected in the DSRCT patient. Each one of the variants was exclusively inherited by one of the parents. The genotype and variant frequency were obtained by leukocyte DNA sequencing. All variants were validated by Sanger sequencing

From: A genomic case study of desmoplastic small round cell tumor: comprehensive analysis reveals insights into potential therapeutic targets and development of a monitoring tool for a rare and aggressive disease

Gene cDNA change Protein change dbSNP (MAF) Mother Father Patient Polyphen Sift Mutation Taster
Genotype Variant Frequency Genotype Variant Frequency Genotype Variant Frequency
C2CD3 c.5653 T > C p.S1885P rs142277857 (0.001) T/C 43.1 T/T - T/C 53.57 PrD D P
c.3223A > C p.S1075R - A/A - A/C 50.91 A/C 41.67 PrD D DC
FAM13C c.1361G > A p.R454H rs369226393 G/A 56.4 G/G - G/A 50 B T P
c.439C > T p.P147S rs73299227 (0.0092) C/C - C/T 51,43 C/T 36.36 PD D* DC
GOLGA3 c.209G > A p.G70E rs2291256 (0.0581) G/A 52.3 G/G - G/A 47.06 B D* P
c.3728G > A p.R1243Q rs140646528 (0.0134) G/G - G/A 60 G/A 25 B T P
LAMB2 c.1424G > A p.R475Q rs370565848 G/A 36.4 G/G - G/A 60 PrD T P
c.5293G > A p.A1765T rs74951356 (0.0130) G/G - G/A 55.81 G/A 41.18 B T DC
MTMR6 c.685C > G p.P229A rs149526134 (0.0002) C/G 60.9 C/C - C/G 26.32 B T P
c.1795G > A p.A599T rs62619824 (0.0571 G/G - G/A 35.09 G/A 51.85 B T DC
RSPH1 c.742G > A p.G248R rs117385282 (0.0839) G/A 50 G/G - G/A 31.25 B T P
c.733G > A p.G245R rs151158140 (0.0026) G/G - G/A 50.77 G/A 58.33 PD T P
SLC9A9 c.1765A > G p.I589V rs2289491 (0.0290) A/G 31.1 A/A - A/G 28 B T P
c.1618A > G p.I540V rs16853300 (0.0066) A/A - A/G 48.62 A/G 36.36 B T P
SPICE1 c.2470A > C p.T824P rs57006145 (0.0313) A/C 40.4 A/A - A/C 62.16 PrD T DC
c.850G > A p.V284M rs73239152 (0.0078) G/G - G/A 47.54 G/A 29.27 B D DC
SYNE1 c.16277C > T p.T5426M rs2306914 (0.0463) C/T 39.1 C/C - C/T 41.07 B T P
c. 12442G > C p.D4148H rs117501809 (0.0124) G/G - G/C 49.15 G/C 28.57 PrD D P
TAF5L c.721G > A p.V241I rs55655740 (0.0042) G/A 36.0 G/G - G/A 48 B - DC
c.1123A > G p.T375A rs41304137 (0.0008) A/A - A/G 20 A/G 40 PrD T P
TTN c.106619 T > C p.I35540T rs55880440 (0.0046) T/C 40.0 T/T - T/C 57.69 - - P
c.65147C > T p.S21716L rs13021201 (0.0108) C/C - C/T 42.86 C/T 58.14 - - P
  1. MAF Minor allele frequency, PrD Probably damaging, B Benign, PD Possibly damaging, D Damaging, T Tolerated, DC Disease causing, P Polymorphism. (*) low confidence prediction