Table 1. Summary of recurrently mutated genes in our cases and a comparison with previously published studies.
Genes | Accession | Variant nomenclature | SIFT score | Polyphen-2 score | Case no6. |
Published | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
number | prediction | prediction | 1 | 2 | 3 | 4 | 5 | 6 | 7 | Study | ||||
Nucleotide change4 | Amino acid change | consequences | consequences | 7 | ||||||||||
ESTABLISHED: | NOTCH2 | NM_024408 | c.C7081T° | p.Q2361X | Damaging | Truncating | ✓ | [7,8] | ||||||
Genes | c.6836delA§ | p.H2279fs | Truncating | Truncating | ✓ | |||||||||
recurrently | MAP3K14 | NM_003954 | c.C200G* | p. A67G | Damaging | Probably damaging | ✓ | [8] | ||||||
mutated | TNFAIP3 | NM_006290 | c.T1343A* | p.M448K | Tolerated | Truncating | ✓ | [4,5,8] | ||||||
in SMZL1 | c.C1681T* | p. P561S | Tolerated | Truncating | ✓ | |||||||||
c.A328T* | p. T110S | Tolerated | Truncating | ✓ | ||||||||||
MLL2 | NM_003482 | c.2507_2508insC | p.Q836fs | Truncating | Truncating | ✓ | [8] | |||||||
SPEN | NM_015001 | c.C5179T° | p.Q1727X | Tolerated | Truncating | ✓ | [8] | |||||||
c.10286_10289del§ | p.3429_3430del | Truncating | Truncating | ✓ | ||||||||||
NOVEL: | AMOTL1 | NM_130847 | c.G1270A* | p.A424T | Tolerated | Benign | ✓ | [8] | ||||||
Recurrent | FAT4 | NM_024582 | c.G6628A* | p.A2210T | Tolerated | Benign | ✓ | [8] | ||||||
genes across | FBXO11 | NM_001190274 | c.G1587C* | p.W529C | Damaging | Truncating | ✓ | [8] | ||||||
studies2 | PLA2G4D | NM_178034 | c.23delG§ | p.G8fs | Truncating | Truncating | ✓ | [8] | ||||||
TRRAP | NM_003496 | c.367-10T>-^ | Splicing5 | Truncating | Truncating | ✓ | [8] | |||||||
USH2A | NM_206933 | c.G7553C* | p.S2518T | Tolerated | Benign | ✓ | [8] | |||||||
NOVEL: | CBFA2T3 | NM_175931 | c.C464T* | p.P155L | Damaging | Probably damaging | ✓ | Novel | ||||||
recurrent | c.G1445A | p. S482N | Damaging | Probably damaging | ✓ | |||||||||
genes in our study3 | CREBBP | NM_001079846 | c.A4349G* | p.Y1450C | Damaging | Truncating | ✓ | ✓ | Novel |
1 Identifies those genes that have previously been shown to be targeted by recurrent mutations in SMZL. 2 Shows those genes that were mutated in single SMZL cases in both our current study and in previously published work. 3 Shows the novel genes targeted by recurrent mutations in our study.
4 Identified non-synonymous (*), splice-site (^), frameshift (§) and stopgain (°) mutations
5 The TRRAP mutation in case 5 occurred within a splice-site and is predicted to resulted in aberrant splicing
6 Showed the presence (✓) and absence (white box) of each mutation in the patients in our series
7 Highlights the published studies that identified the mutations in each of the genes listed