Molecular Pathogenesis
The six genes known to be associated with the six subtypes of autosomal recessive spondylocostal dysostosis (AR SCDO) encode proteins that are key components of the Notch-signaling pathway, which (together with FGF and Wnt signaling) is one of the developmental pathways essential to normal somitogenesis [Dequéant et al 2006, Dequéant & Pourquié 2008]. The protein encoded by:
DLL3 is a ligand of Notch1 that inhibits signaling;
MESP2 is a member of the basic helix-loop-helix (bHLH) family of transcriptional regulatory proteins; MESP2 is a direct target of Notch1 receptor signaling;
LFNG is a glycosyltransferase that post-translationally modifies the Notch family of cell-surface receptors;
LFNG is a direct target of Notch1 receptor signaling;
LFNG is also a cycling
gene expressed in the presomitic mesoderm;
HES7 is a bHLH-Orange
domain transcriptional repressor protein;
HES7 is a direct target of Notch1 receptor signaling;
HES7 is also a cycling
gene expressed in the presomitic mesoderm;
TBX6 is a T-box
transcription factor; TBX6 activates
DLL1 gene expression, which is an activating ligand of the Notch1 receptor; it also activates
MESP2 gene expression;
RIPPLY2 is a negative regulator of TBX6; RIPPLY2 is a direct transcriptional target of MESP2 and of TBX6.
DLL3
Gene structure.
DLL3 consists of eight coding exons. Exon numbering for DLL3 follows that of the alternately spliced mouse Dll3 ortholog, so the human published transcript begins with exon 2. For a detailed summary of gene and protein information, see Table A, Gene.
Pathogenic variants. To date 30 pathogenic variants have been identified throughout DLL3, including frameshift, nonsense, missense, splicing site variants and partial- and whole-gene deletions; 24 have been published [Turnpenny et al 2007]. Approximately three fourths of the pathogenic variants predict protein-truncating variants, although it is possible that this class of pathogenic variants initiates nonsense-mediated decay of the transcript, and they are therefore null alleles (produce no protein).
Normal gene product. The human DLL3 transcript encodes a protein of 618 amino acids (NP_058637.1) and consists of a delta-serrate-lag2 region (DSL), six epidermal growth factor-like domains (EGF), and a transmembrane domain (TM). In animal models Dll3 shows spatially restricted patterns of expression during somite formation and is believed to have a key role in the cell-signaling processes giving rise to somite boundary formation [Dunwoodie et al 2002, Kusumi et al 2004], which proceeds in a rostrocaudal direction with a precise temporal periodicity driven by an internal oscillator, or molecular "segmentation clock," as reported by McGrew & Pourquié [1998] and Pourquié [1999].
Abnormal gene product. The pathogenic variants identified to date in DLL3 are predicted to result in truncated proteins (or no protein, as a result of nonsense-mediated decay), lack of functional domains, misfolding of the protein, or aberrant splicing [Bulman et al 2000, Bonafé et al 2003, Turnpenny et al 2003]. Individuals with milder features were homozygous for pathogenic missense variants located in the EGF domain of the DLL3 reading frame. There is some theoretic evidence [Authors, unpublished data] that these pathogenic missense variants would allow the EGF domains to adopt the correct fold in the DLL3 protein but perhaps be thermodynamically less stable than the wild type protein. However, some of the pathogenic missense variants identified in affected individuals cause a phenotype that is indistinguishable from that caused by protein-truncating variants. This is likely the result of the different effects conferred upon protein folding compared to those pathogenic missense variants associated with the slightly milder phenotype.
MESP2
Gene structure.
MESP2 has two exons spanning approximately 2 kb. For a detailed summary of gene and protein information, see Table A, Gene.
Benign variants. Sequence analysis identified a variable-length polymorphism beginning at c.535 containing a series of 12-bp repeat units coding glycine and glutamine [Whittock et al 2004b]. The smallest GlyGln region detected contains two type A units (GGG CAG GGG CAA, encoding the amino acids GlyGlnGlyGln), followed by two type B units (GGA CAG GGG CAA, encoding GlyGlnGlyGln) and one type C unit (GGG CAG GGG CGC, encoding GlyGlnGlyArg). The polymorphism comprises a variation in the number of type A units, with two, three, or four being present (see Table 3).
Pathogenic variants. A 4-bp duplication in exon 1, c.500_503dup, results in a premature stop codon in the second and final exon of the gene [Whittock et al 2004b]. The pathogenic variants identified in a compound heterozygous individual, c.271A>G and c.385A>T, are believed to be pathogenic. Other pathogenic variants, including a nonsense variant in exon 1, have been identified in individuals with spondylothoracic dysostosis (STD) [Cornier et al 2008]. See Table 3.
Table 3.
MESP2 Variants Discussed in This GeneReview
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Variant Classification | DNA Nucleotide Change | Predicted Protein Change | Reference Sequences |
---|
Benign
| c.535_46[2_4] 1 | p.Gly178_Gln181[2_4] 1 |
NM_001039958.1
NP_001035047.1
|
Pathogenic
| c.271A>G | p.Lys91Glu |
c.385A>T | p.Ile129Phe |
c.500_503dup | p.Gly169ProfsTer199 |
Variants listed in the table have been provided by the authors. GeneReviews staff have not independently verified the classification of variants.
GeneReviews follows the standard naming conventions of the Human Genome Variation Society (varnomen.hgvs.org). See Quick Reference for an explanation of nomenclature.
- 1.
Indicates that the sequence is polymorphic in the population and can vary from two to four repeats
Normal gene product.
MESP2 encodes a 397-amino acid bHLH transcription factor, which is a downstream target of the Notch-signaling pathway. The MESP2 amino terminus contains a bHLH region encompassing 51 amino acids divided into an 11-residue basic domain, a 13-residue helix I domain, an 11-residue loop domain, and a 16-residue helix II domain. In murine somitogenesis MesP2 has a key role in establishing rostrocaudal polarity, and defining the segment boundary, by participating in distinct Notch-signaling pathways [Takahashi et al 2003, Morimoto et al 2005].
Abnormal gene product. The 4-bp duplication, c.500_503dup, occurs after the bHLH domain and causes a frameshift resulting in a premature stop codon within the second (and final) MESP2 exon [Whittock et al 2004b] (see Genotype-Phenotype Correlations).
LFNG
Gene structure. This is an eight-exon gene. Alternatively spliced transcript variants encoding different isoforms have been described; however, they have not all been fully characterized. For a detailed summary of gene and protein information, see Table A, Gene.
Pathogenic variants. A homozygous pathogenic missense variant in a highly conserved phenylalanine close to the active site of the enzyme has been reported in exon 3 [Sparrow et al 2006]. See Table 4.
Table 4.
LFNG Variants Discussed in This GeneReview
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Variants listed in the table have been provided by the authors. GeneReviews staff have not independently verified the classification of variants.
GeneReviews follows the standard naming conventions of the Human Genome Variation Society (varnomen.hgvs.org). See Quick Reference for an explanation of nomenclature.
Normal gene product.
LFNG encodes a 379-amino acid transcript NP_001035257.1, a glycosyltransferase that modifies the Notch family of cell-surface receptors. LFNG is a fucose-specific beta-1,3-N-acetylglucosaminyltransferase that adds N-acetylglucosamine (GlcNAc) residues to O-fucose on the EGF-like repeats of Notch receptors [Brückner et al 2000, Moloney et al 2000]. LFNG localizes to the Golgi, where the modification of Notch receptors is believed to occur [Haines & Irvine 2003]. Studies have shown that Lfng gene expression is severely dysregulated in Dll3-null mice, suggesting that Lfng expression depends on Dll3 function [Dunwoodie et al 2002, Kusumi et al 2004].
Abnormal gene product. The phenylalanine residue affected by the pathogenic variant identified in SCDO3 is conserved in all known fringe proteins, from Drosophila melanogaster to humans [Correia et al 2003]. The resultant mutated LFNG protein does not localize correctly within the cell, is unable to modulate Notch signaling, and is enzymatically inactive [Sparrow et al 2006].
HES7
Gene structure. This is a four-exon gene. For a detailed summary of gene and protein information, see Table A, Gene.
Pathogenic variants. Homozygosity for a pathogenic missense variant, c.73C>T in exon 2, was found in the proband and its pathogenicity was again supported by functional studies [Sparrow et al 2008]. See Table 5.
Table 5.
HES7 Variants Discussed in This GeneReview
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Variants listed in the table have been provided by the authors. GeneReviews staff have not independently verified the classification of variants.
GeneReviews follows the standard naming conventions of the Human Genome Variation Society (varnomen.hgvs.org). See Quick Reference for an explanation of nomenclature.
Normal gene product.
HES7 encodes a 225-amino acid protein that belongs to the bHLH superfamily of DNA-binding transcription factors. HES proteins (and HEY, encoded by HEY1 and HEY2) belong to the bHLH superfamily of more than 125 DNA-binding transcription factors. HES superfamily proteins are characterized by the following:
HES (and HEY) genes are direct targets of Notch signaling and act on their own promoters to repress transcription. Because of their short half-life autorepression is relieved, allowing a new wave of transcription and translation every 90-120 minutes (in mouse).
Abnormal gene product. The c.73C>T pathogenic variant affects the DNA-binding domain of the HES7 protein. Functional studies showed that the abnormal product was not able to repress gene expression by DNA binding or protein heterodimerization.
TBX6
Gene structure.
TBX6 is an eight-exon gene. For a detailed summary of gene and protein information, see Table A, Gene.
Pathogenic variants. Heterozygosity for an extension variant, c.1311A>T (p.Ter437CysextTer81), was found in the proband and two other affected individuals in the family and its pathogenicity was supported by functional studies [Sparrow et al 2013b]. See Table 6.
Table 6.
TBX6 Variants Discussed in This GeneReview
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Variants listed in the table have been provided by the authors. GeneReviews staff have not independently verified the classification of variants.
GeneReviews follows the standard naming conventions of the Human Genome Variation Society (varnomen.hgvs.org). See Quick Reference for an explanation of nomenclature.
Normal gene product.
TBX6 encodes a 436-amino acid protein that belongs to the T-box superfamily of DNA-binding transcription factors [Ghosh et al 2017]. The T-box is necessary and sufficient for sequence-specific DNA binding and all members bind to the DNA consensus sequence TCACACCT. During somite formation, Tbx6 activates the Dll1 (ligand of the Notch1 receptor) and Mesp2 promoters (target of Notch1 signalling) [Hofmann et al 2004].
In mouse, Tbx6 is required for specification of paraxial mesoderm; this is absent and replaced by neural-tube-like structures in Tbx6 homozygous null embryos [Chapman & Papaioannou 1998]. Embryos heterozygous null for Tbx6 have vertebral defects with incomplete penetrance [Sparrow et al 2013b].
Abnormal gene product. The c.1311A>T extension variant, p.Ter437CysextTer81, results in loss of the translation stop codon and the addition of 81 amino acids. TBX6 p.Ter437CysextTer81 has reduced transcriptional activating activity compared with the wild type TBX6 [Sparrow et al 2013b]. The additional 81 amino acids added to the C-terminal may affect the ability of TBX6 to interact with other proteins that are critical in vertebral formation, such as MESP2 and RIPPLY2 [Hitachi et al 2008; Kawamura et al 2008].
RIPPLY2
Gene structure.
RIPPLY2 is a four-exon gene. For a detailed summary of gene and protein information, see Table A, Gene.
Pathogenic variants. Compound heterozygous variants were identified in the proband: a maternal nonsense variant, c.238A>T (p.Arg80Ter) and a paternal c.240-4T>G, which lies in the highly conserved splice site consensus sequence 5′ to the terminal exon [McInerney-Leo et al 2015]. Functional studies support pathogenicity of c.238A>T (p.Arg80Ter). The pathogenicity of c.240-4T>G has not been tested.
Table 7.
RIPPLY2 Variants Discussed in This GeneReview
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Variants listed in the table have been provided by the authors. GeneReviews staff have not independently verified the classification of variants.
GeneReviews follows the standard naming conventions of the Human Genome Variation Society (varnomen.hgvs.org). See Quick Reference for an explanation of nomenclature.
Normal gene product.
RIPPLY2 encodes a 128 amino acid protein. RIPPLY proteins contain:
RIPPLY proteins are negative regulators of T-box proteins (including TBX6), converting them from transcriptional activators to repressors [Kawamura et al 2008]. RIPPLY proteins simultaneously bind to the DNA binding domain of T-box proteins (via their Ripply homology domain), and to Groucho/TLE transcriptional corepressor proteins (via the highly conserved tetrapeptide WRPW motif in their amino terminal region) [Kawamura et al 2005].
Abnormal gene product. The p.Arg80Ter pathogenic variant results in loss of protein function [McInerney-Leo et al 2015].