Table 2.
Control-Specific Missense Variants Predicted to be Deleterious
| Gene | Nucleotide Change | Amino Acid Change | Frequencya(Race)b | General Score (Confidence Level)c | Structure or Function Hypotheses (Probability Scores) |
|---|---|---|---|---|---|
| CITED2 | c.792G>T | p.Gln264His | 1/141 (W) | 0.512 (NP) | NP |
| COL6A1d | c.3001A>C | p.Ser1001Arg | 1/141 (W) | 0.568 (NP) | NP |
|
COL6A2d |
c.3029T>G | p.Phe1010Cys | 1/141 (W) | 0.814 (NP) | NP |
| c.1129C>T | p.Arg377Cys | 1/141 (B) | 0.566 (A) | loss of MoRFe binding (p = 0.0068), loss of methylation at Arg377 (p = 0.0139) | |
| c.1336G>A | p.Asp446Asn | 1/141 (B) | 0.511 (NP) | NP | |
|
COL6A3 |
c.2180A>C | p.Tyr727Ser | 1/141 (W) | 0.769 (C) | gain of disorder (p = 0.0248) |
| c.1688A>G | p.Asp563Gly | 1/141 (W) | 0.760 (NP) | NP | |
| c.4090G>A | p.Val1364Met | 1/141 (B) | 0.686 (NP) | NP | |
| c.2666G>A | p.Arg889His | 1/141 (W) | 0.601 (NP) | NP | |
| c.4561G>A | p.Glu1521Lys | 1/141 (H) | 0.569 (A) | gain of MoRFe binding (p = 0.0014), gain of methylation at Glu1521 (p = 0.0144), loss of ubiquitination at Lys1518 (p = 0.0272) | |
| c.6263C>T | p.Pro2088Leu | 1/141 (B) | 0.516 (A) | gain of MoRFe binding (p = 0.043) | |
| c.2794G>T | p.Ala932Ser | 1/141 (W) | 0.515 (A) | gain of disorder (p = 0.0218) | |
|
COL18A1d |
c.373G>A | p.Val125Ile | 1/141 (B) | 0.714 (NP) | NP |
| c.1264C>T | p.Arg422Cys | 1/141 (H) | 0.554 (NP) | NP | |
| c.3637C>T | p.Arg1213Trp | 1/141 (W) | 0.610 (A) | loss of methylation at Arg1213 (p = 0.007) | |
| CTGF | c.172C>G | p.Arg58Gly | 1/141 (W) | 0.709 (NP) | NP |
|
FBLN2 |
c.2770A>C | p.Asn924His | 1/141 (W) | 0.909 (NP) | NP |
| c.2630C>T | p.Thr877Met | 1/141 (W) | 0.776 (NP) | NP | |
| c.2658C>A | p.Asn886Lys | 1/141 (B) | 0.615 (C) | gain of methylation at Asn886 (p = 0.0045), gain of catalytic residue at Asn886 (p = 0.007), gain of ubiquitination at Asn886 (p = 0.0452) | |
| c.3467C>T | p.Ala1156Val | 1/141 (W) | 0.610 (NP) | NP | |
| GATA5 | c.83C>T | p.Ala28Val | 1/141 (B) | 0.707 (NP) | NP |
| TBX20 | c.461C>G | p.Pro154Arg | 1/141 (B) | 0.718 (C) | gain of MoRFe binding (p = 3e-04), loss of ubiquitination at Lys158 (p = 0.0395) |
| VTN | c.728T>C | p.Ile243Thr | 1/141 (W) | 0.718 (NP) | NP |
| c.1267G>A | p.Asp423Asn | 1/141 (B) | 0.532 (C) | loss of sheet (p = 0.0126), loss of loop (p = 0.0374) | |
The cDNA positions for the nucleotide changes are based on the following reference sequences: CITED2, NM_006079.3; COL6A1, NM_001848.2; COL6A2, NM_001849.3; COL6A3, NM_004369.2; COL18A1, NM_130444.2; CTGF, NM_001901.2; FBLN2, NM_001004019.1; GATA5, NM_080473.4; TBX20, NM_001077653.1; and VTN, NM_000638.3.
Frequency is the number of individuals in which each variant was identified over the number of total cases resequenced for that gene.
Race codes are as follows: W, white; B, black; and H, Hispanic.
Confidence levels are as follows: A, actionable hypotheses; C, confident hypotheses; VC, very confident hypotheses; and NP, none predicted.
Gene is located on chromosome 21 (trisomic for this population).
Gain of MoRF binding represents gain of molecular recognition factor binding (interaction with other molecules is enhanced).