ClinVar Genomic variation as it relates to human health

The splice donor variant c.12469+2T>C in TNXB (NM_001365276.2) has been reported previously in heterozygous state in individuals with clinical features of EhlersDanlos syndrome and a diagnosis of congenital adrenal hyperplasia ( Lao et al, 2021 ) . The c.12469+2T>C variant is observed in 64/2,496 (2.5641%) alleles from individuals of Ashkenazi Jewish background in gnomAD Exomes. This variant mutates a splice-donor sequence, potentially resulting in the retention of large segments of intronic DNA by the mRNA and nonfunctional proteins. The c.12469+2T>C variant is a loss of function variant in the gene TNXB, which is intolerant of Loss of Function variants. The nucleotide change in TNXB is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance.

BS1, BP4, BP7, PS3_supporting, PVS1_strong

Observed in the heterozygous state in individuals with clinical features of EhlersDanlos syndrome and a diagnosis of congenital adrenal hyperplasia (PMID: 33332743); Published functional studies suggest that the c.12463+2T>C variant reduces the splicing efficiency at TNXB intron 42 via an allele-specific decrease in mRNA (PMID: 33332743); In silico analysis indicates that this variant does not alter splicing; This variant is associated with the following publications: (PMID: 33332743)

This sequence variant is a single nucleotide substitution (T>C) at the +2 position downstream of exon 42 of 44 of the TNXB gene. As this variant alters a canonical splice donor site, it is expected to cause intron retention and transcription termition prior to exon 43. As such, the variant may generate a non-functiol allele through either the expression of a truncated protein or a loss of TNXB expression due to nonsense-mediated decay. This is a previously reported variant (ClinVar) which has been observed in the literature in two unrelated families with congenital adrel hyperplasia and Ehlers-Danlos syndrome (PMID: 33332743). The variant is present and somewhat frequent in the gnomAD control population dataset (861/78586 alleles, 1 homozygote, 1.096%); however, this site is noted as low quality in the gnomAD database, so the data may be iccurate. Functiol studies indicate suggest that the variant leads to a moderate decrease in intron 42 splicing efficiency, though the full clinical consequence of this decrease is unclear. At this time, there is insufficient evidence to determine if this variant is pathogenic or benign. Therefore, we consider it to be a variant of uncertain significance. ACMG Criteria: PP3, PS3

The TNXB c.12463+2T>C variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant has been reported to be associated with a moderate hypermobility Ehlers-Danlos syndrome (EDS) phenotype in the affected congenital adrenal hyperplasia (CAH) patients due to a reduced splicing efficiency at TNXB intron 42 (Lao et al. 2020. PubMed ID: 33332743). This variant was also reported in an individual with congenital anomalies of the kidney and urinary tract (Table S3, Rao. 2019. PubMed ID: 31328266). In the gnomAD variant database based on next-generation sequencing technology, the highest minor allele frequency of this variant has been found at ~2.7% in Ashkenazi Jewish and 2.5% in South Asian with one homozygous individual documented; however, this may not be an accurate indication of its allele frequency because it is located in a highly homologous region (exons 32 to 44) of the gene and there are limitations of current capture-based short-read next-generation sequencing technology to sequence this type of homologous sequence (Mandelker et al. 2016. PubMed ID: 27228465). Of note, at PreventionGenetics, we have previously found this variant in several unrelated patients, at least one of whom inherited this variant from an unaffected mother. In summary, the clinical significance of this variant is still uncertain due to insufficient evidence.