Submission Details

TTC21B was FIRST reported in relation to the autosomal recessive inherited diseases isolated nephronophthisis, NPHP12 (OMIM: 613820), and syndromic short-rib thoracic dysplasia (SRTD4), also termed Jeune asphyxiating thoracic dystrophy (JATD) (OMIM: 613819). Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found no difference in molecular mechanism or inheritance pattern. Therefore, NPHP12 and SRTD4 have been lumped into one disease entity. NPHP12 is characterized by reduced concentrating ability of the kidney, chronic tubulointerstitial nephritis, cystic kidney disease, and progression to end-stage kidney disease before age 30 years. In addition to cystic kidney disease, SRTD4 is characterized by constricted thoracic cage, short ribs, shortened tubular bones, and a 'trident' appearance of the acetabular roof. In the first report, Davis et al identified a TTC21B variant (p.Pro209Leu) in homozygosity in affected members with NPHP12 from 2 unrelated consanguineous families of Portuguese and Egyptian descents (Davis et al 2011, PMID: 21258341). In the same report, 3 additional families with early-onset NPHP with extrarenal manifestations and another proband with SRTD were presented. Two of these NPHP12 families were found to have the p.Pro209Leu allele in compound heterozygosity with another pathogenic TTC21B allele: p.Cys552Ter or a splice site mutation, respectively. The proband with SRTD and the 3rd proband with NPHP were found to have compound heterozygous TTC21B variants p.Arg411Ter, p.Leu795Pro and p.Trp150Arg, c.3264-3>G, respectively. The variants p.Cys552Ter and p.Trp150Arg were shown to be functionally null alleles in zebrafish expression studies whereas p.Pro209Leu, p.Arg411Ter and p.Leu795Pro were shown to be functionally hypomorphic (Davis et al 2011, PMID: 21258341). In addition, heterozygous functionally pathogenic alleles were found in about 5% of the total cohort, including 3 unrelated patients with Joubert syndrome 11 (JBTS11) suggesting that TTC21B might be a common contributor to the total mutational load in ciliopathies. Hallbritter et al reported 6 patients in 5 families from United States (n=2), Germany (n=2) and United Kingdom (n=1). Three of these NPHP12 families with extrarenal features were found to have the p.Pro209Leu allele in compound heterozygosity with another pathogenic TTC21B allele: c.2868+1G>T, p.Glu414Ter or p.Asp1308Gly. One proband from an American family was found to have a homozygous c.2264-2267dupTAGA loss of function variant and another proband was found to have compound heterozygous p.Arg411Ter and p.Thr483Aspfs*25 variants (Halbritter J et al 2013, PMID: 23559409). No functional data of these variants were provided. TTC21B pathogenic variants were also identified in 3 families with biopsy confirmed focal segmental glomerulosclerosis (FSGS) and tubulointerstitial lesions in which some family members presented with hypertension and myopia. Two families carried the homozygous p.Pro209Leu variant and the third was compound heterozygous for p.Pro209Leu and a novel p.His426Asp variant (Bullich et al 2017, PMID: 26940125). Cong et al identified the homozygous p.Pro209Leu variant in seven families with FSGS by whole exome sequencing combined with homozygosity mapping (Cong et al 2014, PMID: 24876116). Their in vitro studies in mammalian cells showed that function of the TTC21B encoded tetratricopeptide repeat protein 21B (also known as the intraflagellar transport 139 homolog, IFT139B), is not restricted to the cilium but extends to the regulation of podocyte cytoskeleton architecture as reported for most proteins implicated in FSGS. However, whether these FSGS lesions are secondary to chronic tubulointerstitial lesions associated with NPHP12 needs to be clarified. Additionally, whether p.Pro209Leu is the unique TTC21B pathogenic variant responsible for FSGS and tubule interstitial lesions also remains to be determined. Evidence supporting the NPHP-TTC21B relationship includes case-level data and experimental data. Genetic evidence on case-level data reached the maximum 12 points. Variants in TTC21B have been reported in at least 15 probands in 6 publications (Davis et al 2011, PMID: 21258341; Halbritter et al 2013, PMID 23559409; Abo El Fotoh WMM et al 2019, PMID: 32714622; Hibino et al 2020, PMID: 32238723; Hammarsjo et al 2021, PMID: 33875766; Strong et al 2021, PMID: 33547761). One publication described variants in this gene that segregated with disease in 3 additional family members (Davies et al 2011, PMID: 21258341). This gene-disease association is supported by experimental evidence including expression data, protein interactions, rescue assays and model systems. Murine TTC21B is reminiscent of other intraflagellar transport proteins, such as IFT88, IFT57 and IFT20, that are similarly localized in a punctate manner in the axoneme from the ciliary base to the tip (Tran et al 2008, PMID: 18327258). Ttc21b was shown to be widely expressed, with more intense expression in the maxillary prominence, branchial arches, limb buds, somites, and spinal cord in normal embryonic mice at day 10.5, and knockout resulted in a ciliopathy phenotype of preaxial polydactyly, split and fused ribs, cortical layering abnormalities, delayed eye and forebrain development and neural tube defects (Tran et al 2008, PMID: 18327258). Murine TTC21B localizes specifically to the transition zone of the mouse photoreceptor sensory cilia, as evidenced by localization just proximal to endogenous murine retinitis pigmentosa 1 (RP1), which is located in the outer segment portion of the photoreceptor sensory cilia axoneme (Davis et al 2011, PMID: 21258341). In a zebrafish model, a single ortholog of TTC21B in the zebrafish genome was shown with having 68% identity and 84% similarity, with expression at the early embryonic shield stage. A translation-blocking morpholino (tb-MO) targeting tc21b injected into two-cell–stage embryos resulted in shortening of the embryonic axis, widening and kinking of the notochord, and broadening and thinning of the somites. These morphant phenotypes were partially rescued with co-injection of wildtype human TTC21B mRNA. In ciliated murine inner medullary collecting duct (mIMCD3) cells, endogenous TTC21B was localized to the basal body and the ciliary axoneme, and cells stably transfected with Ttc21b short hairpin RNA (shRNA) displayed shortened cilia. Davis et al subsequently used these cell lines to test allele pathogenicity based on the ability of transiently transfected mutant constructs to rescue. In a mouse model, Davies et al generated a rodent-specific shRNA vector targeting the Ttc21b transcript. In vivo electroporation of shRNA-*Ttc21b *in neonatal rat retinas resulted in significantly shortened, abnormally shaped, photoreceptor sensory cilia. Rodent specific shRNA-resistant Ttc21b partially rescued cilia length and structure (Davis et al 2011, PMID: 21258341). Thus, the score for experimental evidence for this gene-disease association was 5 points. In summary, there is definitive evidence to support the NPHP12-TTC21B relationship. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Kidney Cystic and Ciliopathy Disorders GCEP on 11/10/2021 (SOP Version 8).