Table 2.
Rare nonsynonymous coding variants identified in NEFH
| Group | Chr_Position | dbSNP | cDNA_change | AA _change | ExAC_EAS | gnomAD_exome_EAS | CADD | No. Carriers (n = 371) | No. Controls (n = 711) | P value | OR (95% CI) |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Case only | 22:29,876,600 | – | c.349C > T | p.Gln117Ter | – | 7.54E-05 | Damaging | 1 | 0 | 0.34 | Inf (Na-Inf) |
| 22:29,876,764 | – | c.513G > C | p.Gln171His | – | – | Tolerable | 1 | 0 | 0.34 | Inf (Na-Inf) | |
| 22:29,879,421 | rs539511579 | c.941C > T | p.Ala314Val | 2.32E-04 | 1.74E-04 | Damaging | 1 | 0 | 0.34 | Inf (Na-Inf) | |
| 22:29,885,163 | – | c.1534C > T | p.Pro512Ser | – | – | Damaging | 1 | 0 | 0.34 | Inf (Na-Inf) | |
| Control only | 22:29,876,270 | – | c.19G > A | p.Ala7Thr | – | – | Damaging | 0 | 1 | 1.00 | Na |
| 22:29,876,409 | rs772280985 | c.158C > T | p.Thr53Met | 0.00 | 0.00 | Damaging | 0 | 1 | 1.00 | Na | |
| 22:29,876,520 | rs61556467 | c.269C > T | p.Ala90Val | 0.00 | 0.00 | Damaging | 0 | 1 | 1.00 | Na | |
| 22:29,876,710 | rs763364083 | c.469_491del | p.Val157ArgfsTer115 | 0.00 | 1.29E-04 | – | 0 | 1 | 1.00 | Na | |
| 22:29,879,444 | rs778265423 | c.964C > T | p.Arg322Trp | 0.00 | 0.00 | Damaging | 0 | 1 | 1.00 | Na | |
| 22:29,884,842 | rs200464796 | c.1213C > A | p.Leu405Ile | 0.00 | 0.00 | Damaging | 0 | 1 | 1.00 | Na | |
| 22:29,885,182 | – | c.1553C > T | p.Ser518Leu | – | – | Damaging | 0 | 1 | 1.00 | Na | |
| 22:29,885,198 | rs138278265 | c.1569G > C | p.Glu523Asp | 0.00 | 0.00 | Tolerable | 0 | 1 | 1.00 | Na | |
| 22:29,885,215 | – | c.1586A > C | p.Glu529Ala) | – | – | Tolerable | 0 | 1 | 1.00 | Na | |
| 22:29,885,735 | – | c.2106_2110del | p.Lys703ProfsTer2 | – | – | – | 0 | 1 | 1.00 | Na | |
| 22:29,885,741 | – | c.2112_2232del | p.Pro705SerfsTer17 | – | – | – | 0 | 1 | 1.00 | Na | |
| 22:29,885,917 | – | c.2288C > T | p.Ser763Phe | – | – | Damaging | 0 | 1 | 1.00 | Na | |
| 22:29,886,118 | rs201757428 | c.2489C > T | p.Pro830Leu | 4.81E-04 | 2.91E-04 | Tolerable | 0 | 2 | 0.54 | Na | |
| 22:29,886,426 | rs777317391 | c.2797C > T | p.Pro933Ser | 9.53E-04 | 1.33E-03 | Tolerable | 0 | 1 | 1.00 | Na | |
| Both | 22:29,876,707 | rs774792100 | c.456G > C | p.Glu152Asp | 7.46E-03 | 4.57E-03 | Tolerable | 1 | 1 | 1.00 | 1.92 (0.12–30.70) |
| 22:29,881,766 | rs201416955 | c.1138G > A | p.Ala380Thr | 5.78E-03 | 5.33E-03 | Damaging | 3 | 8 | 0.76 | 0.72 (0.19–2.71) | |
| 22:29,885,581 | rs267607533 | c.1965_1988del | p.Glu658_Lys665del | 1.16E-04 | 8.37E-03 | – | 2 | 6 | 0.72 | 0.64 (0.13–3.17) | |
| 22:29,885,638 | rs190692435 | c.2009 T > A | p.Val670Glu | 1.17E-04 | 1.91E-03 | Tolerable | 2 | 5 | 1.00 | 0.77 (0.15–3.96) | |
| 22:29,885,644 | – | c.2015C > A | p.Ala672Glu | 1.17E-04 | 1.60E-03 | Tolerable | 1 | 5 | 0.67 | 0.38 (0.05–3.28) | |
| 22:29,885,990 | rs568759161 | c.2361C > G | p.Ser787Arg | 1.39E-03 | 2.38E-03 | Damaging | 5 | 1 | 0.02 | 9.64 (1.12–82.67) | |
| 22:29,886,382 | rs189881592 | c.2753A > G | p.Glu918Gly | 3.34E-03 | 3.53E-03 | Damaging | 2 | 2 | 0.61 | 1.92 (0.27–13.65) |
cDNA-level nomenclature was based on NM_021076.3. According to hg19/GRCh37, protein-level nomenclature was based on NP_066554.2; dbSNP, accession number of the variant in the Database of Single-Nucleotide Polymorphisms 147; MAF, minor allele frequency; ExAC_EAS and GnomAD_exome_EAS, MAFs of variants in the Exome Aggregation Consortium (ExAC) and GnomAD_exome databases for the East Asian population; In silico prediction by Combined Annotation Dependent Depletion (CADD); AA, amino acid; Ifn, infinity; 95% CI, 95% confidence interval; Na, not available,. A value of P < 0.05 was considered statistically significant (P < 0.0005 after Bonferroni correction)