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Table 1 Germline variants in the MNTI

From: A germline mutation of CDKN2A and a novel RPLP1-C19MC fusion detected in a rare melanotic neuroectodermal tumor of infancy: a case report

Gene Variant type Chr Position Ref/Seq Amino acid Transcript Read depth Existing annotation (Allelic frequency) Sift Polyphen Condel
CDKN2A SNV 9 21970916 C/T Ala/Thr ENST00000304494.9 322 CM004869 (0.027) deleterious benign neutral
CDKN2A SNV 9 21971137 T/G Asp/Ala ENST00000304494.9 105 COSM4163712 (NA) deleterious probably_damaging deleterious
CHD1 Indel 5 98192165 AGG/– Pro/Unknown ENST00000284049.7 NA NA NA NA NA
  1. No tumor-specific non-synonymous mutations were identified and these variants were also detected in germline DNA extracted from the patient’s blood. A heterozygous T/G mutation on chr 9:21971137 generates a mutant allele of CDKN2A which encodes a p16INK4A protein with substitution of aspartic acid for alanine at position 74. This change is predicted to be damaging or deleterious by the Sift, Polyphen and Condel algorithms and mutations of Asp74 in CDKN2A are documented in COSMIC as rare tumor variants. The other CDKNA mutation (Ala/Thr) is not predicted to be damaging to the function of p16INK4A. Common polymorphisms with a dbSNP annotation have been excluded
  2. SNV single nucleotide variant, NA = not available