Table 1.
Pathogenic or likely pathogenic variants in TCF4 identified in patients with intellectual disability (ID) by large-scale sequencing approaches
| Reference | Variant nomenclature | Inheritance | dbSNP | Previously reported in Clinvar | Previously described in PTHS screening | TCF4-LOVD Individual ID | SIFT | PP2 | Individual | Gender | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| This report | c.873C>A | p.(Tyr291*) | de novo | NA | NA | no | 000100 | NA | NA | MMPN166 | F |
| This report Tan et al. [15] |
c.990G>A | p.? | de novo, de novo | rs587784469 | RCV000147730.1 (Likely. pathogenic) | no | 000098 | NA | NA | - APN149 -Patient 6 |
M F |
| This report | c.1662del | p.(Asp554Glufs*4) | de novo | NA | NA | no | 000101 | NA | NA | B00H4MR | F |
| This report | c.1705C>T | p.(Arg569Trp) | de novo | NA | NA | yes [6] | 000026 | Deleterious | Prob. Damaging | MMPN68 | M |
| This report | c.1726C>T | p.(Arg576*) | de novo | NA | NA | no | 000102 | NA | NA | APN214 | M |
| This report | c.1733G>A | p.(Arg578His) | de novo | rs121909123 | RCV000079458.4|RCV000189738.1 (Pathogenic) | yes [22] | 000029 | Deleterious | Poss. Damaging | APN210 | F |
| This report | c.1841C>T | p.(Ala614Val) | de novo | NA | NA | yes [32] | 000021 | Deleterious | Prob. Damaging | B00H4R8 | F |
| This report | c.1927G>T | p.(Glu643*) | de novo | NA | NA | no | 000103 | NA | NA | B00H4U1 | F |
| Redin et al. [1] | c.514_517del | p.(Lys172Phefs*61) | de novo | rs398123561 | RCV000079461.4 (Pathogenic) | yes [6] | 000047 | NA | NA | APN41 | M |
| Redin et al. [1] | c.520C>T | p.(Arg174*) | de novo | NA | RCV000224478.1 (Pathogenic) | yes [6] | 000023 | NA | NA | APN117 | F |
| Grozeva et al. [12] | c.505C>T | p.(Gln169*) | NA | NA | NA | no | 000104 | NA | NA | 5410771 | M |
| Grozeva et al. [12] | c.550–1G>A g.52946888 C>T |
p.? | NA | NA | NA | no | 000105 | NA | NA | 5411380 | M |
| Tan et al. [15] | c.991–2A>G g.52927260 T>C |
p.? | NA | rs587784470 | RCV000147731.1 (Pathogenic) | no | 000106 | NA | NA | Patient 5 | F |
| Hamdan et al. [13] | c.1153C>T | p.(Arg385*) | de novo | rs121909122 | RCV000007797.4 (Pathogenic) | yes [4, 33] | 000003 | NA | NA | Case 045.400 | M |
| De Ligt et al. [11] | c.1727G>A | p.(Arg576Gln) | de novo | NA | RCV000431775.1 (Pathogenic) | yes [33] | 000027 | Deleterious | Poss. Damaging | Trio 15 | F |
All the c. positions were given according to NM_001083962.1 isoform (and NG_011716.2 isoform for intronic variants). PP2 Polyphen2 SIFT scores. Variants are classified following recommendations from the American College of Medical Genetics and Genomics