ClinVar Genomic variation as it relates to human health

Published functional studies in zebra fish suggest a damaging effect with partial rescue of axis curvature or cilia motility phenotypes. In addition, reduced cilia beat amplitude or loss of beat coordination and cilia paralysis was observed in respiratory cells from patients homozygous for this variant (Panizzi et al,. 2012); This variant is associated with the following publications: (PMID: 30238669, 24357714, 22581229, 31469207, 23891469, 27637300, 26123568, 31273583, 28790179, 29363216, 31879361, 31980526, 32447765)

This variant is interpreted as a Likely Pathogenic, for Ciliary dyskinesia, primary, 17, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: PM2-Supporting => Present in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium with allele frequency compatible with recessive disease and high disease prevalence (1:2265 individuals in South Asia populations) (PMID:28790179). PS3 => Well-established functional studies show a deleterious effect (PMID:28790179) (PMID:22581229). PP1-Moderate => PP1 upgraded in strength to Moderate (PMID:26123568,24357714,22581229).

The p.His154Pro variant in CCDC103 has been reported in 25 homozygous and 1 comp ound heterozygous individuals with Primary ciliary dyskinesia and segregated in 7 affected family members (Panizzi 2012, D'Andrea 2013, Casey 2015, Boaretto 201 6, Shoemark 2017). All of these individuals were homozygous or compound heterozy gous. This variant has also been reported in ClinVar (Variation ID: 31698). This variant has been identified in 0.32% (97/30782) of South Asian chromosomes by t he Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs145457535). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. Co mputational prediction tools and conservation analyses do not provide strong sup port for or against an impact to the protein. Functional studies provide some ev idence that the p.His154Pro variant may reduce protein function (Panizzi 2012). However, these types of assays may not accurately represent biological function. In summary, the p.His154Pro variant in CCDC103 meets criteria to be classified as pathogenic for Primary ciliary dyskinesia in an autosomal recessive manner ba sed upon segregation studies, presence in affecteds, and functional evidence. AC MG/AMP Criteria applied: PS4, PP1_Strong; PS3_Moderate.

This mutation has been previously reported as disease-causing and was found once in our laboratory in a homozygous state in an 8-month-old male with CHD (TAPVR, DORV, malposed great vessels), heterotaxy. Heterozygotes are expected to be asymptomatic carriers.

The CCDC103 c.461A>C (p.His154Pro) variant has been identified in four studies in a total of ten probands with primary ciliary dyskinesia, including nine in a homozygous state and one in a compound heterozygous state (Panizzi et al. 2012; D'Andrea et al 2013; Casey et al 2015; Boaretto et al. 2016). The p.His154Pro variant was also found in a heterozygous state in 13 unaffected family members. The p.His154Pro variant was absent from 180 controls and is reported at a frequency of 0.00333 in the South Asian population of the Exome Aggregation Consortium. In vivo functional studies in zebrafish demonstrated that the p.His154Pro variant mRNA could not rescue a mutant phenotype, while the wild type CCDC103 mRNA was able to rescue the mutant phenotype, demonstrating a lack of function of the p.His154Pro variant protein (Panizzi et al. 2012). Based on the evidence, the p.His154Pro variant is classified as pathogenic for primary ciliary dyskinesia. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PS3,PP4,PP5. This variant was detected in homozygous state.

ACMG classification criteria: PS3 supporting, PS4 strong, PM3 strong, PP1 moderated, BP4 supporting

The missense c.461A>C(p.His154Pro) variant in CCDC103 gene has been reported in homozygous state in individuals affected with ciliary dyskinesia (Casey, J.P., et al.,2015). Functional studies have demonstrated a lack of function of the p.His154Pro variant protein (Panizzi JR, et. al.,2012;Shoemark A, et. al.,2018). The p.His154Pro variant is reported with an allele frequency of 0.1% in the gnomAD exomes database and is novel (not in any individuals) in 1000 Genomes database. This variant has been reported to the ClinVar database as Uncertain Significance/ Likely Pathogenic/ Pathogenic (multiple submission). The amino acid His at position 154 is changed to a Pro changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.His154Pro in CCDC103 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic.

The variant has multiple records in ClinVar with pathogenic interpretation (Variation ID: 31698)

This sequence change replaces histidine, which is basic and polar, with proline, which is neutral and non-polar, at codon 154 of the CCDC103 protein (p.His154Pro). This variant is present in population databases (rs145457535, gnomAD 0.3%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with primary ciliary dyskinesia (PMID: 22581229, 23891469, 24357714, 26123568). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 31698). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects CCDC103 function (PMID: 22581229). For these reasons, this variant has been classified as Pathogenic.

The p.H154P variant (also known as c.461A>C), located in coding exon 3 of the CCDC103 gene, results from an A to C substitution at nucleotide position 461. The histidine at codon 154 is replaced by proline, an amino acid with similar properties. This variant has been reported in multiple homozygous individuals of various ethnic backgrounds with primary ciliary dyskinesia (PCD); several affected individuals had laterality defects and ciliary analyses showing dynein arm defects (Panizzi JR et al. Nat. Genet., 2012 May;44:714-9; Zariwala MA et al. Am. J. Hum. Genet., 2013 Aug;93:336-45; D'Andrea G et al. Blood, 2013 Dec;122:4289-91; Casey JP et al. BMC Med. Genet., 2015 Jun;16:45). It has also been confirmed in trans with a second varoamt in an affected individual (Boaretto F et al. J Mol Diagn, 2016 11;18:912-922). In a study of 86 South Asian individuals with a clinical history consistent with PCD, 16 were found to be homozygous for this variant. In this study, this variant was often associated with normal nasal nitric oxide, areas of normal ciliary beat frequency, and normal ultrastructure on electron microscopy; however, respiratory capacity was reduced similarly to a comparator group, comprised of South Asian individuals with PCD who were negative for this alteration (Shoemark A et al. Thorax, 2018 02;73:157-166). Injection of the mutant mRNA in smh zebrafish partially rescued the phenotype, suggesting that this may be a hypomorphic variant (Panizzi JR et al. Nat. Genet., 2012 May;44:714-9). In addition, biochemical analysis has shown that the H154P alteration is highly disruptive of oligomerization ability, although mutant protein retains the ability to dimerize (Shoemark A et al. Thorax, 2018 02;73:157-166). This amino acid position is not well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

The CCDC103 c.461A>C variant is predicted to result in the amino acid substitution p.His154Pro. This variant was found in the homozygous and compound heterozygous state in multiple individuals with primary ciliary dyskinesia (PCD) and laterality defects (Panizzi et al. 2012. PubMed ID: 22581229; Zariwala et al. 2013. PubMed ID: 24094744; D'Andrea et al. 2013. PubMed ID: 24357714; Casey et al. 2015. PubMed ID: 26123568; Boaretto et al. 2016. PubMed ID: 27637300; Fassad et al. 2020. PubMed ID: 31879361; Burwick et al. 2021. PubMed ID: 32447765). Affected individuals had variable defects of the inner and outer dynein arms as well as defects in ciliary beating ranging from loss of beat coordination to complete ciliary paralysis (Panizzi et al. 2012. PubMed ID: 22581229; Zariwala et al. 2013. PubMed ID: 24094744). Heterozygous carriers were not affected (Panizzi et al. 2012. PubMed ID: 22581229; D'Andrea et al. 2013. PubMed ID: 24357714; Casey et al. 2015. PubMed ID: 26123568). This variant is reported in 0.32% of alleles in individuals of South Asian descent in gnomAD. Based on above information, this variant is classified as pathogenic.