Table 3 of
Bosley, Mol Vis 2007;
13:1516-1528.
Table 3. Pathogenicity analysis for non-synonymous sequence changes
Previous reports of sequence variants were found in the Mitomap database, the Human Mitochondrial Genome Database, GenBank, and Medline listed publications. Interspecies conservation was assessed using the Polymorphism phenotyping (PolyPhen) database, which determines interspecies conservation for an altered amino acid by performing alignments with all available amino acid sequences for other species, and when necessary, using the Mamit-tRNA website. PolyPhen pathogenicity prediction was assessed utilizing the PolyPhen database. "Probably damaging" constitutes a high confidence of affecting protein function or structure. "Possibly damaging" reflects a likelihood of affecting protein function or structure, while "Benign" changes most likely lack phenotypic effect. "Unknown" means that PolyPhen could make no prediction due to lack of data. Sorting Intolerant From Tolerant (SIFT) returns predictions for which amino acid substitutions will affect protein function given a particular protein sequence. Protean (Protein Structure Prediction and Annotation) is part of the Lasergene V.6 software (DNASTAR, Inc. Madison, WI). It displays patterns, secondary structural characteristics, and physiochemical properties (hydropathy index, flexibility index and antigenic index). The Hydropathy Index was measured by Protean according to the Kyte-Doolittle method [11], which predicts the regional hydropathy of proteins from their amino acid sequence. Hydropathy values were assigned for all amino acids and were then averaged over a window size equal 7. Results below 0 are hydrophobic and above 0 are hydrophilic. Abbreviations include, amino acid (AA), transcription RNA (tRNA), cytochrome oxidase subunit 1 (COI), cytochrome B (CYTB), cytochrome c oxidase subunit III (COIII).
Nucleotide substitution Analysis ------------ ---------------------------------------------------------------------------------------------------- 3580 C->A This sequence change is located at codon 92 in the functional domain of the ND1 gene and changes a highly conserved Proline, a hydrophobic AA, to Threonine, a neutral AA, altering the hydropathy index from - 0.42 to - 0.52. Protean predicted a change of protein structure, and SIFT predicted that it should affect protein function. This mutation was not found in controls, and PolyPhen predicted that it should be probably damaging. It was considered potentially pathologic. 4136 A->G This sequence change is located at codon 277, outside the functional domain of the ND1 gene, and changes a highly conserved Tyrosine, a hydrophilic AA, to Cysteine, a neutral AA, altering the hydropathy index from -1.3 to 2.5. Protean predicted change of the protein structure, and SIFT predicted that it should affect protein function. This mutation was previously reported in Leber hereditary optic neuropathy [4]. It was not found in controls, and PolyPhen predicted that it should be possibly damaging. It was considered potentially pathologic. 4370 T->C This sequence change is located in the anticodon loop of tRNA glutamine and was predicted to change the shape of this conserved region. It was not found in local controls but was present in a heteroplasmic state in one patient with a level of 65%. It was previously reported in association with mitochondrial myopathy [5]. It was considered potentially pathologic. 5089 T->G This sequence change is located at codon 207 in the transmembrane domain of the ND2 gene. It changes a highly conserved Isoleucine, a hydrophobic AA, to Serine, a neutral AA, and alters the hydropathy index from -2.16 to -1.57. Protean predicted changes to the protein structure, and SIFT predicted that it should affect protein function. This sequence change was not found in controls, and PolyPhen predicted it to be probably damaging. It was considered potentially pathologic. 5516 A->C This sequence change is located in a highly conserved region of the acceptor stem of tRNA tryptophan. It was not detected in controls and was not previously reported as a polymorphism. It was considered potentially pathologic. 6261 G->A This sequence variant is located at codon 120 in transmembrane domain of the COI, which forms part of the catalytic subunit of the enzyme. It changes a moderately conserved Alanine, a hydrophobic AA, to Threonine, a neutral AA, altering the hydropathy index from -0.72 to -0.44. Protean predicted the introduction of a flexible region, and SIFT predicted that it should affect protein function. This sequence change was not found in controls, and PolyPhen predicted it to be possibly damaging. It was reported in lymphocytes of six patients with prostate cancer, where elevated levels of reactive oxygen species implied possible pathogenicity [6]. It was considered potentially pathologic. 6880 C->A This sequence variant is located at codon 326 in COI. It changes a highly conserved Threonine, a neutral AA, to Lysine, a hydrophilic AA, and alters the hydropathy index from -0.29 to -0.07. Protean predicted a change to the protein structure, and SIFT predicted that it should affect protein function. This mutation was not present in controls, but it was heteroplasmic in one patient with a heteroplasmy level of 65%. PolyPhen predicted it to be probably damaging. It was considered potentially pathologic. 8813 C->A This sequence variant is located at codon 96, outside the transmembrane domain of ATPase 6 gene. It changes a highly conserved Threonine, a neutral AA, to Asparagine, another neutral AA, and alters the hydropathy index from -0.06 to 0.26. Protean predicted a change to the structure of the protein, and SIFT predicted that it should affect protein function. Its heteroplasmy level was 50%, which is close to the accepted threshold of 60% [7]. This sequence change was absent in controls, and PolyPhen predicted it to be probably damaging. Given these factors, it was considered potentially pathologic. 9104 T->C This sequence variant is located at codon 193, outside the transmembrane domain of ATPase 6 gene. It changes a highly conserved Phenylalanine, a hydrophobic AA, to Serine, a neutral AA, which alters the hydropathy index from -30 to -2.60. Protean predicted no change to the secondary structure of the protein, and SIFT predicted that it should not affect protein function. This sequence change was absent in controls, but PolyPhen predicted it to be benign. It was considered non-pathologic. 9300 G->A This sequence variant is located at AA position 32 in the transmembrane domain of COIII gene. It changes a moderately conserved Alanine, a hydrophobic AA, to Threonine, a neutral AA, which alters the hydropathy index from -0.48 to -0.20. Protean predicted no change in the protein structure, and SIFT predicted that it should not affect protein function. This sequence change was found in 1.2% of controls, and PolyPhen predicted it to be Benign. It was considered non-pathologic. 9904 T->G This sequence variant is located at AA position 233 in the outside transmembrane domain of COIII gene. It changes a highly conserved Phenylalanine, a hydrophobic AA, to Cysteine, a neutral AA, which changes the hydropathy index from 0.84 to 0.88. Protean predicted a change in protein structure, and SIFT predicted that it should affect protein function. This sequence alteration was absent in controls, and PolyPhen predicted it to be probably damaging. It was considered potentially pathologic. 9948 G->A This sequence variant is located at AA position 248 of the transmembrane domain of the COIII gene and changes a highly conserved Valine, a hydrophobic AA, to Isoleucine, a hydrophobic AA. Protean predicted a change in the protein structure, and SIFT predicted that it should affect protein function. This mutation was previously reported as a somatic mutation in tissues from a patient with papillary thyroid carcinoma [8]. It was not found in controls, and PolyPhen predicted it to be probably damaging. It was considered potentially pathologic. 10946 A->G This sequence variant is located at AA position 63 in the transmembrane domain of the ND4 gene and changes a moderately conserved Threonine, a neutral AA, to Alanine, a hydrophobic AA, altering the hydropathy index from -0.58 to -0.86. Protean predicted no change in the protein structure, and SIFT predicted that it should not affect protein function. This sequence variant was not found in controls, and PolyPhen predicted it to be benign. It was considered non-pathologic. 11865 T->G This sequence variant is located at AA position 369 in the transmembrane functional domain of ND4 gene. It changes a moderately conserved Leucine, a hydrophobic AA, to Tryptophan, another hydrophobic AA, altering the hydropathy index from 0.84 to 0.88. Protean predicted a change in protein structure, and SIFT predicted that it should affect protein function. This sequence alteration was absent in controls, and PolyPhen predicted it to be probably damaging. It was considered potentially pathologic. 13253 C->G This sequence variant is located at AA position 306 in transmembrane functional domain of ND5 gene. It changes a highly conserved Threonine, a neutral AA, to Serine, another neutral AA, altering the hydropathy index from - 0.7 to - 0.8. Protean predicted a change in protein structure, and SIFT predicted that it should affect protein function. This sequence alteration was absent in controls, and PolyPhen predicted it to be probably damaging. It was considered potentially pathologic. 13936 C->A This sequence variant is located at AA position 534 outside the transmembrane domain of the ND5 gene. It changes a highly conserved Histidine, a hydrophilic AA, to Asparagine, a neutral AA, altering the hydropathy index from 0.46 to 0.49. Protean predicted a change of protein structure, and SIFT predicted that it should affect protein function. This sequence change was absent in controls, and PolyPhen predicted it to be probably damaging. It was considered potentially pathologic. 14516 A->G This sequence variant is located at AA position 53 in the transmembrane domain of the ND6 gene. It changes a highly conserved Leucine, a hydrophobic AA, to Serine, a neutral AA, altering the hydropathy index from -1.81 to -1.36. Protean predicted a change of protein structure, and SIFT predicted that it should affect protein function. This sequence change was absent in controls, and PolyPhen predicted it to be Probably Damaging. It was considered potentially pathologic. 14525 T->G This sequence variant is located at AA position 50, outside the transmembrane domain of the ND6 gene. It changed a moderately conserved Tyrosine, a hydrophilic AA, with Serine, a neutral AA, altering hydropathy index from -0.83 to -0.38. Protean predicted significant changes to the protein structure, and SIFT predicted that it should affect protein function. This sequence alteration was absent in controls, and PolyPhen predicted it to be probably damaging. It was considered potentially pathologic. 14831 G->A This sequence variant is located at AA position 29, outside the transmembrane domain of the CYTB gene. It changed a moderately conserved Alanine, a hydrophobic AA, to Threonine, a neutral AA, altering the hydropathy index from 0.14 to 0.42. Protean predicted no change in protein structure, and SIFT predicted that it should not affect protein function. This sequence change was found in 1.9% of controls, and PolyPhen predicted it to be Benign. This sequence variant was reported in the setting of Leber hereditary optic neuropathy [9] but is listed on the Mitomap database as a polymorphism. It was considered non-pathologic. 15674 T->C This sequence variant is located at AA position 310 in the C-terminal domain of CYTB, where a pathologic mutation may affect ubiquinol/ubiquinone binding activity. It changes a highly conserved Serine, a neutral AA, to Proline, a hydrophobic AA, altering the hydropathy index from 0.61 to 0.70. Protean predicted no change to the protein structure, and SIFT predicted that it should affect protein function. This sequence alteration was absent in controls, and PolyPhen predicted it to be possibly damaging. It was considered potentially pathologic. 15924 A->G This sequence variant is located in the anticodon loop of tRNA threonine, a highly conserved nucleotide region. Although, this sequence change was not detected in controls, it is now thought to be a haplogroup specific polymorphism [10]. It was considered non-pathologic. 15968 T->C This sequence variant is located at the D-stem loop of tRNA proline, a highly conserved region. It was not detected in controls or reported previously as a polymorphism. It was considered potentially pathologic. |