Title: Assessing variants of uncertain significance implicated in hearing loss using a comprehensive deafness proteome
Abstract
Hearing loss is the leading sensory deficit, affecting ~ 5% of the population. It exhibits remarkable heterogeneity across 223 genes with 6328 pathogenic missense variants, making deafness-specific expertise a prerequisite for ascribing phenotypic consequences to genetic variants. Deafness-implicated variants are curated in the Deafness Variation Database (DVD) after classification by a genetic hearing loss expert panel and thorough informatics pipeline. However, seventy percent of the 128,167 missense variants in the DVD are “variants of uncertain significance” (VUS) due to insufficient evidence for classification. Here, we use the deep learning protein prediction algorithm, AlphaFold2, to curate structures for all DVD genes. We refine these structures with global optimization and the AMOEBA force field and use DDGun3D to predict folding free energy differences (∆∆GFold) for all DVD missense variants. We find that 5772 VUSs have a large, destabilizing ∆∆GFoldthat is consistent with pathogenic variants. When also filtered for CADD scores (> 25.7), we determine 3456 VUSs are likely pathogenic at a probability of 99.0%. Of the 224 genes in the DVD, 166 genes (74%) exhibit one or more missense variants predicted to cause a pathogenic change in protein folding stability. The VUSs prioritized here affect 119 patients (~ 3% of cases) sequenced by the OtoSCOPE targeted panel. Approximately half of these patients previously received an inconclusive report, and reclassification of these VUSs as pathogenic provides a new genetic diagnosis for six patients.
Sayeb, Marwa; Riahi, Zied; Laroussi, Nadia; Bonnet, Crystel; Romdhane, Lilia; Mkaouar, Rahma; Zaouak, Anissa; Marrakchi, Jihene; Abdessalem, Ghaith; Messaoud, Olfa; et al(
, International Journal of Dermatology)
AbstractBackground
Co‐occurrence of two genetic diseases is challenging for accurate diagnosis and genetic counseling. The recent availability of whole exome sequencing (WES) has dramatically improved the molecular diagnosis of rare genetic diseases in particular in consanguineous populations.
Methods
We report here on a consanguineous family from Southern Tunisia including three members affected with congenital ichthyosis. The index case had a hearing loss (HL) and ichthyosis and was primarily suspected as suffering from keratitis‐ichthyosis‐deafness (KID) syndrome.WESwas performed for the index case, and all members of the nuclear family were sequenced (Sanger method).
Results
TheWESapproach allowed the identification of two strong candidate variants in two different genes; a missense mutation c.1334T>G (p.Leu445Trp) in exon 11 ofSLC26A4gene, associated with isolatedHLand a novel missense mutation c.728G>T (p.Arg243Leu) in exon 8 ofCYP4F22gene likely responsible for ichthyosis. These two mutations were predicted to be pathogenic by three pathogenicity prediction softwares (Scale‐Invariant Feature Transform [SIFT], Polymorphism Phenotyping [PolyPhen], Mutation Taster) to underlie theHLand ichthyosis, respectively.
Conclusions
The present study raises awareness about the importance of familial history for accurate diagnosis of syndromic genetic diseases and differential diagnosis with co‐occurrence of two distinct clinical entities. In addition, in countries with limited resources,WESsequencing for a single individual provides a cost effective tool for molecular diagnosis confirmation and genetic counseling.
To define a distinct, dominantly inherited, mild skeletal myopathy associated with prominent and consistent tremor in two unrelated, three‐generation families.
Methods
Clinical evaluations as well as exome and panel sequencing analyses were performed in affected and nonaffected members of two families to identify genetic variants segregating with the phenotype. Histological assessment of a muscle biopsy specimen was performed in 1 patient, and quantitative tremor analysis was carried out in 2 patients. Molecular modeling studies and biochemical assays were performed for both mutations.
Results
Two novel missense mutations inMYBPC1(p.E248K in family 1 and p.Y247H in family 2) were identified and shown to segregate perfectly with the myopathy/tremor phenotype in the respective families.MYBPC1encodes slow myosin binding protein‐C (sMyBP‐C), a modular sarcomeric protein playing structural and regulatory roles through its dynamic interaction with actin and myosin filaments. The Y247H and E248K mutations are located in the NH2‐terminal M‐motif of sMyBP‐C. Both mutations result in markedly increased binding of the NH2terminus to myosin, possibly interfering with normal cross‐bridge cycling as the first muscle‐based step in tremor genesis. The clinical tremor features observed in all mutation carriers, together with the tremor physiology studies performed in family 2, suggest amplification by an additional central loop modulating the clinical tremor phenomenology.
Interpretation
Here, we link two novel missense mutations inMYBPC1with a dominant, mild skeletal myopathy invariably associated with a distinctive tremor. The molecular, genetic, and clinical studies are consistent with a unique sarcomeric origin of the tremor, which we classify as “myogenic tremor.” ANN NEUROL 2019
Bowles, Bradley; Ferrer, Alejandro; Nishimura, Carla J.; Pinto e Vairo, Filippo; Rey, Tristan; Leheup, Bruno; Sullivan, Jennifer; Schoch, Kelly; Stong, Nicholas; Agolini, Emanuele; et al(
, American Journal of Medical Genetics Part A)
Abstract
Biallelic loss‐of‐function variants in the thrombospondin‐type laminin G domain and epilepsy‐associated repeats (TSPEAR) gene have recently been associated with ectodermal dysplasia and hearing loss. The first reports describing aTSPEARdisease association identified this gene is a cause of nonsyndromic hearing loss, but subsequent reports involving additional affected families have questioned this evidence and suggested a stronger association with ectodermal dysplasia. To clarify genotype–phenotype associations forTSPEARvariants, we characterized 13 individuals with biallelicTSPEARvariants. Individuals underwent either exome sequencing or panel‐based genetic testing. Nearly all of these newly reported individuals (11/13) have phenotypes that include tooth agenesis or ectodermal dysplasia, while three newly reported individuals have hearing loss. Of the individuals displaying hearing loss, all have additional variants in other hearing‐loss‐associated genes, specificallyTMPRSS3,GJB2, andGJB6, that present competing candidates for their hearing loss phenotype. When presented alongside previous reports, the overall evidence supports the association ofTSPEARvariants with ectodermal dysplasia and tooth agenesis features but creates significant doubt as to whetherTSPEARvariants are a monogenic cause of hearing loss. Further functional evidence is needed to evaluate this phenotypic association.
McGuire Sams, Cierla; Shepp, Kasey; Pugh, Jada; Bishop, Madison R.; Merner, Nancy D.(
, BMC Medical Genomics)
AbstractBackground
Three genes clustered together on chromosome 12 comprise a group of hydroxycarboxylic acid receptors (HCARs):HCAR1,HCAR2, andHCAR3. These paralogous genes encode different G-protein coupled receptors responsible for detecting glycolytic metabolites and controlling fatty acid oxidation. Though better known for regulating lipid metabolism in adipocytes, more recently, HCARs have been functionally associated with breast cancer proliferation/survival;HCAR2has been described as a tumor suppressor andHCAR1andHCAR3as oncogenes. Thus, we sought to identify germline variants inHCAR1,HCAR2,andHCAR3that could potentially be associated with breast cancer risk.
Methods
Two different cohorts of breast cancer cases were investigated, the Alabama Hereditary Cancer Cohort and The Cancer Genome Atlas, which were analyzed through nested PCRs/Sanger sequencing and whole-exome sequencing, respectively. All datasets were screened for rare, non-synonymous coding variants.
Results
Variants were identified in both breast cancer cohorts, some of which appeared to be associated with breast cancer BC risk, includingHCAR1c.58C > G (p.P20A),HCAR2c.424C > T (p.R142W),HCAR2c.517_518delinsAC (p.G173T),HCAR2c.1036A > G (p.M346V),HCAR2c.1086_1090del (p.P363Nfs*26),HCAR3c.560G > A (p.R187Q), andHCAR3c.1117delC (p.Q373Kfs*82). Additionally,HCAR2c.515C > T (p.S172L), a previously identified loss-of-function variant, was identified.
Conclusions
Due to the important role of HCARs in breast cancer, it is vital to understand how these genetic variants play a role in breast cancer risk and proliferation and their consequences on treatment strategies. Additional studies will be needed to validate these findings. Nevertheless, the identification of these potentially pathogenic variants supports the need to investigate their functional consequences.
To foster trial‐readiness of coenzyme Q8A (COQ8A)‐ataxia, we map the clinicogenetic, molecular, and neuroimaging spectrum of COQ8A‐ataxia in a large worldwide cohort, and provide first progression data, including treatment response to coenzyme Q10 (CoQ10).
Methods
Cross‐modal analysis of a multicenter cohort of 59 COQ8A patients, including genotype–phenotype correlations, 3D‐protein modeling, in vitro mutation analyses, magnetic resonance imaging (MRI) markers, disease progression, and CoQ10 response data.
Results
Fifty‐nine patients (39 novel) with 44 pathogenicCOQ8Avariants (18 novel) were identified. Missense variants demonstrated a pleiotropic range of detrimental effects upon protein modeling and in vitro analysis of purified variants. COQ8A‐ataxia presented as variable multisystemic, early‐onset cerebellar ataxia, with complicating features ranging from epilepsy (32%) and cognitive impairment (49%) to exercise intolerance (25%) and hyperkinetic movement disorders (41%), including dystonia and myoclonus as presenting symptoms. Multisystemic involvement was more prevalent in missense than biallelic loss‐of‐function variants (82–93% vs 53%;p= 0.029). Cerebellar atrophy was universal on MRI (100%), with cerebral atrophy or dentate and pontine T2 hyperintensities observed in 28%. Cross‐sectional (n = 34) and longitudinal (n = 7) assessments consistently indicated mild‐to‐moderate progression of ataxia (SARA: 0.45/year). CoQ10 treatment led to improvement by clinical report in 14 of 30 patients, and by quantitative longitudinal assessments in 8 of 11 patients (SARA: −0.81/year). Explorative sample size calculations indicate that ≥48 patients per arm may suffice to demonstrate efficacy for interventions that reduce progression by 50%.
Interpretation
This study provides a deeper understanding of the disease, and paves the way toward large‐scale natural history studies and treatment trials in COQ8A‐ataxia.ANN NEUROL 2020;88:251–263
Tollefson, Mallory R., Gogal, Rose A., Weaver, A. Monique, Schaefer, Amanda M., Marini, Robert J., Azaiez, Hela, Kolbe, Diana L., Wang, Donghong, Weaver, Amy E., Casavant, Thomas L., Braun, Terry A., Smith, Richard J. H., and Schnieders, Michael J. Assessing variants of uncertain significance implicated in hearing loss using a comprehensive deafness proteome. Human Genetics 142.6 Web. doi:10.1007/s00439-023-02559-9.
Tollefson, Mallory R., Gogal, Rose A., Weaver, A. Monique, Schaefer, Amanda M., Marini, Robert J., Azaiez, Hela, Kolbe, Diana L., Wang, Donghong, Weaver, Amy E., Casavant, Thomas L., Braun, Terry A., Smith, Richard J. H., & Schnieders, Michael J. Assessing variants of uncertain significance implicated in hearing loss using a comprehensive deafness proteome. Human Genetics, 142 (6). https://doi.org/10.1007/s00439-023-02559-9
Tollefson, Mallory R., Gogal, Rose A., Weaver, A. Monique, Schaefer, Amanda M., Marini, Robert J., Azaiez, Hela, Kolbe, Diana L., Wang, Donghong, Weaver, Amy E., Casavant, Thomas L., Braun, Terry A., Smith, Richard J. H., and Schnieders, Michael J.
"Assessing variants of uncertain significance implicated in hearing loss using a comprehensive deafness proteome". Human Genetics 142 (6). Country unknown/Code not available: Springer Science + Business Media. https://doi.org/10.1007/s00439-023-02559-9.https://par.nsf.gov/biblio/10408468.
@article{osti_10408468,
place = {Country unknown/Code not available},
title = {Assessing variants of uncertain significance implicated in hearing loss using a comprehensive deafness proteome},
url = {https://par.nsf.gov/biblio/10408468},
DOI = {10.1007/s00439-023-02559-9},
abstractNote = {Abstract Hearing loss is the leading sensory deficit, affecting ~ 5% of the population. It exhibits remarkable heterogeneity across 223 genes with 6328 pathogenic missense variants, making deafness-specific expertise a prerequisite for ascribing phenotypic consequences to genetic variants. Deafness-implicated variants are curated in the Deafness Variation Database (DVD) after classification by a genetic hearing loss expert panel and thorough informatics pipeline. However, seventy percent of the 128,167 missense variants in the DVD are “variants of uncertain significance” (VUS) due to insufficient evidence for classification. Here, we use the deep learning protein prediction algorithm, AlphaFold2, to curate structures for all DVD genes. We refine these structures with global optimization and the AMOEBA force field and use DDGun3D to predict folding free energy differences (∆∆GFold) for all DVD missense variants. We find that 5772 VUSs have a large, destabilizing ∆∆GFoldthat is consistent with pathogenic variants. When also filtered for CADD scores (> 25.7), we determine 3456 VUSs are likely pathogenic at a probability of 99.0%. Of the 224 genes in the DVD, 166 genes (74%) exhibit one or more missense variants predicted to cause a pathogenic change in protein folding stability. The VUSs prioritized here affect 119 patients (~ 3% of cases) sequenced by the OtoSCOPE targeted panel. Approximately half of these patients previously received an inconclusive report, and reclassification of these VUSs as pathogenic provides a new genetic diagnosis for six patients.},
journal = {Human Genetics},
volume = {142},
number = {6},
publisher = {Springer Science + Business Media},
author = {Tollefson, Mallory R. and Gogal, Rose A. and Weaver, A. Monique and Schaefer, Amanda M. and Marini, Robert J. and Azaiez, Hela and Kolbe, Diana L. and Wang, Donghong and Weaver, Amy E. and Casavant, Thomas L. and Braun, Terry A. and Smith, Richard J. H. and Schnieders, Michael J.},
}
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