PMC9998998_01
Trio-based WES identified compound heterozygous variants (p.Leu1283_Ser1285del; p.Thr1233Thrfs*20) in TENM3 in a patient with bilateral microphthalmia, global developmental delay, and microcephaly. (A) Pedigree and genotype information for members of family 1. Squares indicate males, circles indicate females, filled symbols indicate affected individuals, and open symbols indicate healthy individuals. Patient 1 is denoted by a black arrow. The proband carried compound heterozygous variants: c.3847_3855del; p.Leu1283_Ser1285del and c.3698_3699insA; p.Thr1233Thrfs*20. The mother (II-2) with heterozygosity of the p.Thr1233Thrfs*20 variant had left exophthalmia and graduated from middle school with poor grades. (B) Facial picture of the proband at the age of 5 months with microphthalmia, prominent and low-set ears, and microcephaly. (C) Fundus examination of patient 1 revealed the posterior pole of the retina colobomas involving the optic discs and the fovea. (D) A TA clone sequencing from the genomic DNA of patient 1 including the fragment of exon 19 showed the two variants: c.3847_3855del; p.Leu1283_Ser1285del and c.3698_3699insA; p.Thr1233Thrfs*20. WT, wild type; MUT, mutant type.
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F1
Initial genetic testing for patient 1 was carried out via WES, revealing two heterozygous variants in the TENM3 gene (Genbank association number: NM_001080477): c.3847_3855del; p.Leu1283_Ser1285del and c.3698_3699insA; p.Thr1233Thrfs*20 (Figure 1A). TA clone sequencing including the fragment of exon 19 demonstrated that the two variants occurred biallelically (Figure 1D). The two variants were absent from the control database gnomAD.
PMC9998998_02
Trio-based WES identified compound heterozygous variants (p.Leu1283_Ser1285del; p.Thr1233Thrfs*20) in TENM3 in a patient with bilateral microphthalmia, global developmental delay, and microcephaly. (A) Pedigree and genotype information for members of family 1. Squares indicate males, circles indicate females, filled symbols indicate affected individuals, and open symbols indicate healthy individuals. Patient 1 is denoted by a black arrow. The proband carried compound heterozygous variants: c.3847_3855del; p.Leu1283_Ser1285del and c.3698_3699insA; p.Thr1233Thrfs*20. The mother (II-2) with heterozygosity of the p.Thr1233Thrfs*20 variant had left exophthalmia and graduated from middle school with poor grades. (B) Facial picture of the proband at the age of 5 months with microphthalmia, prominent and low-set ears, and microcephaly. (C) Fundus examination of patient 1 revealed the posterior pole of the retina colobomas involving the optic discs and the fovea. (D) A TA clone sequencing from the genomic DNA of patient 1 including the fragment of exon 19 showed the two variants: c.3847_3855del; p.Leu1283_Ser1285del and c.3698_3699insA; p.Thr1233Thrfs*20. WT, wild type; MUT, mutant type.
fped-11-1111771-g001.jpg
PMC9998998_02_fped-11-1111771-g001.jpg
F1
Initial genetic testing for patient 1 was carried out via WES, revealing two heterozygous variants in the TENM3 gene (Genbank association number: NM_001080477): c.3847_3855del; p.Leu1283_Ser1285del and c.3698_3699insA; p.Thr1233Thrfs*20 (Figure 1A). TA clone sequencing including the fragment of exon 19 demonstrated that the two variants occurred biallelically (Figure 1D). The two variants were absent from the control database gnomAD.
Trio-based WES identified compound heterozygous variants (p.Ala314Val; p.Leu2155Pro) in TENM3 in a patient with speech delay and motor developmental delay. (A) Pedigree and genotype information on members of family 2. Squares indicate males, circles indicate females, filled symbols indicate affected individuals, and open symbols indicate healthy individuals. Patient 2 is denoted by a black arrow. The proband carried compound heterozygous variants: c.941C > T; p.Ala314Val and c.6464T > C; p.Leu2155Pro. (B) Facial picture of the proband at the age of 3 years old with resolved esotropia. His prominent and big ears were noted. (C) Fundus examination of patient 2 showed no structural anomalies. (D) Sequencing chromatograms of the compound heterozygous TENM3 variants (c.941C > T; p.Ala314Val and c.6464T > C; p.Leu2155Pro) in patient 2 and the parents. WT, wild type; Het, heterozygous.
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F2
At the age of 3 years old, his bilateral esotropia was resolved (Figure 2B). What's more, his anterior segment and fundus examination showed no structural anomalies (Figure 2C). Similarly, patient 2 had a WES that revealed compound heterozygous variants of the TENM3 gene, c.941C > T; p.Ala314Val and c.6464T > C; p.Leu2155Pro (Figure 2A). T (p.Ala314Val) mutation and his father carried the c.6464T > C (p.Leu2155Pro) mutation (Figure 2D).
Schematic diagram of TENM3 functional domains and TENM3 variants identified in this study. (A) Depicts the protein domain structure of human TENM3 showing the domain position of the index heterozygous TENM3 variants. aa, amino acids. (B) Evolutionary conservation of amino acid position Ala1283-Ser1285 and Leu2155 in TENM3 protein across evolution.
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F3
The Ala314 change was located in the transmembrane domain and was evolutionarily well-conserved from Homo sapiens to zebrafish (Figures 3A,B). The Leu2155 residue was located in the YD-repeats domain and was well-conserved to zebrafish as well (Figures 3A,B).
Molecular modeling of the wild type (WT) and mutant TENM3 protein (Mut). Three-dimensional structural modeling of the TENM3 protein showed that the mutations did not change the hydrogen bonding in protein (blue), but repulsive force (purple) was generated between the R group of amino acid side chain and other nearby groups.
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F4
In evaluating the deleteriousness of the two missense variants in patient 2, three-dimensional structural modeling of the TENM3 protein showed that the mutations did not change the hydrogen bonding in the protein (blue), but repulsive force (purple) was generated between the R group of amino acid side chain and other nearby groups, which is unfavorable to the folding of the active protein and results in protein conformational instability (Figure 4).