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Table 3 TCF20 (NM_005650.3) variants identified in the present study

From: De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith–Magenis syndrome

Subject Type of mutation Coordinates hg19 Nucleotide change Effect Exon number Inheritance Additional variants
#1 Frameshift g.42610999_42611002dupGTGG c.310_313dupCCAC p.Gln106Profs*30 2 Maternal NR
#2 Frameshift g.42610718dupA c.594dupT p.Gly199Trpfs*56 2 De novo No
#3 Nonsense g.42610324G>A c.988C>T p.Gln330* 2 Mother negative No
#4 Frameshift g.4260792delG c.1520delC p.Pro507Leufs*5 2 De novo No
#5 Nonsense g.42609052G>A c.2260C>T p.Gln754* 2 Maternal No
#6 Frameshift g.42608984_42608985delCT c.2327_2328delAG p.Gln776Argfs*5 2 De novo NR
#7 Frameshift g.42608627delC c.2685delG p.Arg896Glyfs*9 2 Maternal de novo
c.1189C>T, p.Gln397* in SLC6A1
#8 Nonsense g.42608285A>T c.3027T>A p.Tyr1009* 2 De novo No
#9 Nonsense g.42608285A>T c.3027T>A p.Tyr1009* 2 Not known No
#10 Frameshift g.42607933delG c.3379delC p.Gln1127Serfs*10 2 De novo No
#11 Frameshift g.42607707dupC c.3605dupG p.Pro1203Serfs*15 2 Mother negative NR
#12 Frameshift g.42607678_42607679dupAC c.3633_3634dupGT p.Tyr1212Cysfs*13 2 De novo No
#13 Nonsense g.42607507G>A c.3805C>T p.Gln1269* 2 De novo NR
#14 Frameshift g.42607081dupC c.4231dupG p.Glu1411Glyfs*33 2 De novo No
#15 Frameshift g.42606763dupC c.4549dupG p.Asp1517Glyfs*30 2 De novo No
#16 Frameshift g.42606418delA c.4894delT p.Tyr1632Thrfs*6 2 De novo No
#17 Missense g.42606183 T>C c.5129A>G p.Lys1710Arg 2 De novo de novo
c.1307G>T (p.R436L) in ZBTB18
#18 Frameshift g.42605882dupT c.5430dupA p.Ala1811Serfs*4 2 De novo No
#19 Frameshift g.42605800_42605801dupGC c.5511_5512dupCG p.Leu1838Argfs*45 2 De novo No
#20 Frameshift g.42605782_42605783dupCA p.5529_5530dupTG p.Glu1844Valfs*39 2 De novo NR
#21 Frameshift g.42605775delG c.5537delC p.Pro1846Leufs*36 2 Not known No
#22 Frameshift g.42605742dupC c.5570dupG p.Cys1858Leufs*58 2 De novo No
#23 Frameshift g.42605659_42605660delTC c.5652_56553delGA p.Glu1884Aspfs*31 2 Not known No
#24 Canonical splicing g.42605656C>T c5655+1G>A N/A Intron 2 Not known No
#25 Nonsense g.42575645G>A c.5719C>T p.Arg1907* 3 De novo NR
#26 Nonsense g.42575645G>A c.5719C>T p.Arg1907* 3 De novo No
#27 Frameshift g.42575632delG c.5732delC p.Pro1911Argfs*17 3 Paternal No
#28 Frameshift g.42575632delG c.5732delC p.Pro1911Argfs*17 3 Paternal No
#29 Del
22q13.2q13.3
g.42394098-45037128del 2.64 Mb DEL Deletion of 37 genes Whole gene Not known (adopted) No
#30 Del
22q13.2
g.42607466-42770878del 163 kb DEL Deletion of Exon1 1 De novo No
#31 Del
22q13.2
g.42488512-42616581del 128 kb DEL Deletion of 3 genes Whole gene De novo No
#32 Del
22q13.2
g.42373034-42776457del 403 kb DEL Deletion of 11 genes Whole gene De novo No
Shafgen et al. [14] Nonsense (n = 1)
Frameshift (n = 1)
N/A N/A N/A 2 De novo No
Babbs et al. [6] Complex chromosomal rearrangement (n = 2)
Missense (n = 1)
Frameshift (n = 1)
N/A N/A N/A 2/partial gene deletion Possibly parental mosaicism/de novo No
Lelieveld et al. [15] Nonsense (n = 2)
Frameshift (n = 2)
N/A N/A N/A 2/3 De novo No
McRae et al. [16]* Inframe deletion (n = 1)
Missense variant (n = 1)
N/A N/A N/A 2 De novo No
  1. Abbreviations: N/A not applicable, NR not reported
  2. *The original study reported 7 patients, 5 of which (#2, #8, #10, #19, and #26) have been included in this study with more detailed phenotypic characterization