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Table 2 HGMD-derived mutations identified as PCMs in the Denisovan, Neanderthal and/or chimpanzee genomes

From: Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations

  Mutation type and basis of disease aetiology
Mutation/
regulatory type
PCM state DM DP FP DFP Total
Coding sequence Human 5/5 38/43 11/11 17/18 71/77
  Neanderthal 0/0 1/1 0/0 0/0 1/1
  Denisovan 1/1 0/0 0/0 0/0 1/1
  Ancient 0/0 1/1 2/4 0/0 3/5
  Chimpanzee 4/4 7/8 2/4 0/0 13/16
  Denisovan and chimpanzee 3/3 4/5 0/0 0/0 7/8
  Neanderthal and chimpanzee 2/2 4/6 1/1 1/1 8/10
  Others 1/1 0/1 0/0 0/0 1/2
  Total 16/16 55/65 16/20 18/19 105/120
Regulatory Human 0 23 10 13 46
  Neanderthal 0 0 2 1 3
  Denisovan 0 0 0 3 3
  Ancient 0 2 0 1 3
  Chimpanzee 0 5 5 4 14
  Denisovan and chimpanzee 0 4 1 1 6
  Neanderthal and chimpanzee 0 1 1 0 2
  Others 0 0 0 1 1
  Total 0 35 19 24 78
  1. 'Human': The Denisovan nucleotide, Neanderthal nucleotide and chimpanzee nucleotide were identical to a human DM/disease-associated mutation; 'Neanderthal': The Neanderthal nucleotide was identical to the human DM/disease-associated mutation, whereas both the chimpanzee nucleotide and the Denisovan nucleotide were identical to the human wild-type nucleotide; 'Denisovan': The Denisovan nucleotide was identical to the human DM/disease-associated mutation, whereas both the chimpanzee nucleotide and the Neanderthal nucleotide were identical to the human wild-type nucleotide; 'Ancient': Both the Denisovan nucleotide and the Neanderthal nucleotide were identical to the human DM/disease-associated P mutation, whereas the chimpanzee nucleotide was identical to the human wild-type nucleotide. 'Chimpanzee': The chimpanzee nucleotide was identical to the human DM/disease-associated mutation, whereas both the Neanderthal nucleotide and the Denisovan nucleotide were identical to the modern human wild-type nucleotide. 'Denisovan and chimpanzee': Both the Denisovan nucleotide and the chimpanzee nucleotide were identical to the human DM/disease-associated mutation, whereas the Neanderthal nucleotide was identical to the human wild-type nucleotide; 'Neanderthal and chimpanzee': Both the Neanderthal nucleotide and the chimpanzee nucleotide were identical to the human DM/disease-associated mutation, whereas the Denisovan nucleotide was identical to the human wild-type nucleotide. Under coding sequence, 'a/b' means that there were a total number of 'b' mutations, of which 'a' were non-synonymous mutations (there were some synonymous mutations within the coding sequence; eg CM068190, CM077900).
  2. PCM, potentially compensated mutations; DM, disease-causing mutation; DP, disease-associated polymorphism with functional evidence; FP, polymorphism with functional evidence but lacking a reported disease association as yet; DFP, disease-associated polymorphism with functional evidence.