Table 1.
Novel and Known Rare Variants in the Coding and Flanking Intronic Sequence of FZD6 Gene
| Nucleotide changea (rs ID) | Amino acid change | Resequencing 473 pt/639 ct | Amino acid conservation | Dompred Predictionb | PANTHER prediction (subPSECscore)c | PolyPhen prediction (PSIC score)d | mirSVR regression model (mirSVR score)e |
|---|---|---|---|---|---|---|---|
| c.374+7A>C | - | 1/0 | - | - | - | - | - |
| c.418C>T(rs80216383) | p. His140Tyr | 2/1f | No | Random coiled, alteration | Deleterious (−4.05) | Possibly damaging (2.11) | - |
| c.765C>T | p.Gly255Gly | 3/0 | Yes | Random coiled, - | - | - | - |
| c.1125G>A | p.Leu374Leu | 1/0 | Yes | Alpha-helix, - | - | - | - |
| c.1163C>A | p. Ala388Asp | 1/2 | Yes | Alpha-helix,alteration | Deleterious (−5.52) | Possibly damaging (1.92) | - |
| c.1214G>A | p.Arg405Gln | 2/0 | Yes | Random coiled,alteration | NA | Benign (0.38) | - |
| c.1392+67A>T | - | 1/0 | - | - | - | - | |
| c.1392+115C>T | - | 1/0 | - | - | - | - | |
| c.1393-109G>T | - | 1/0 | - | - | - | - | |
| c.1531C>T | p.Arg511Cys | 1/0 | Yes | Random coiled,alteration | Not deleterious (−2.47) | Possibly damaging (2.45) | - |
| c.1532G>A | p.Arg511His | 1/0 | Yes | Random coiled,alteration | Deleterious (−3.65) | Benign (0.15) | - |
| c.1809C>T | p.Asp603Asp | 1/0 | No | Random coiled, - | - | - | - |
| c.1810G>A(rs79408516) | p.Gly604Arg | 2/1f | No | Random coiled, no alteration | Not deleterious (−1.99) | Benign (0.004) | |
| c.1843_1844insA | p.Cys615X | 1/0 | Yes | - | - | - | - |
| c.1858T>A(rs116195528) | p.Ser620Thr | 2/1f | No | Random coiled, no alteration | Not deleterious (−1.02) | Benign (0.01) | - |
| c.1991C>A(rs12549394) | p.Ala664Glu | 2/2 | No | Random coiled, no alteration | NA | Benign (0.35) | - |
| c.*20C>T | - | 1/0 | - | - | - | - | Probably alterating miRNA binding site (−0.6) |
| Rare variants | 24/7 | ||||||
| Rare functional deleterious variants | 9/3 (P = 0.036) | ||||||
FZD6 GenBank RefSeq number NM_001164615.1 and NG_028909.1. Nucleotide numbering reflects cDNA numbering with +1 corresponding to the A of the ATG translation initiation codon 1 in the reference sequence.
Location in protein secondary structure/potential structure alteration.
subPSEC score: substitution position-specific evolutionary conservation score. Continuous values range from 0 (neutral) to about −10 (most likely to be deleterious). −3 is the cutoff point.
PSIC (position-specific independent counts) score: <1 benign, >1 possibly damaging, >2 probably damaging.
mirSVR is a regression model that computes a weighted sum of a number of sequence and context features of the predicted miRNA–mRNA duplex. mirSVR downregulation scores are calibrated to correlate linearly with the extent of downregulation and therefore enable accurate scoring of genes with multiple target sites by simple addition of the individual target scores (mirSVR cut off score ≤ −0.1). The mutation altered the binding site for MIR628.
These two patients and one control individual are carriers of three FZD6 in cis mutations: p. His140Tyr , p.Gly604Arg, p.Ser620Thr.
pt, patients; ct, controls; NA, not aligned; 3′UTR, 3′-untranslated region. Deleterious variants not found in controls are in bold.