Whole exome sequencing reveals homozygous mutations in RAI1, OTOF, and SLC26A4 genes associated with nonsyndromic hearing loss in Altaian families (South Siberia)

Alexander Y. Churbanov, Tatiana Karafet, Igor V. Morozov, Valeriia Yu Mikhalskaia, Marina V. Zytsar, Alexander A. Bondar, Olga L. Posukh

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Hearing loss (HL) is one of the most common sensorineural disorders and several dozen genes contribute to its pathogenesis. Establishing a genetic diagnosis of HL is of great importance for clinical evaluation of deaf patients and for estimating recurrence risks for their families. Efforts to identify genes responsible for HL have been challenged by high genetic heterogeneity and different ethnic-specific prevalence of inherited deafness. Here we present the utility of whole exome sequencing (WES) for identifying candidate causal variants for previously unexplained nonsyndromic HL of seven patients from four unrelated Altaian families (the Altai Republic, South Siberia). The WES analysis revealed homozygous missense mutations in three genes associated with HL. Mutation c.2168A>G (SLC26A4) was found in one family, a novel mutation c.1111G>C (OTOF) was revealed in another family, and mutation c.5254G>A (RAI1) was found in two families. Sanger sequencing was applied for screening of identified variants in an ethnically diverse cohort of other patients with HL (n = 116) and in Altaian controls (n = 120). Identified variants were found only in patients of Altaian ethnicity (n = 93). Several lines of evidences support the association of homozygosity for discovered variants c.5254G>A (RAI1), c.1111C>G (OTOF), and c.2168A>G (SLC26A4) with HL in Altaian patients. Local prevalence of identified variants implies possible founder effect in significant number of HL cases in indigenous population of the Altai region. Notably, this is the first reported instance of patients with RAI1 missense mutation whose HL is not accompanied by specific traits typical for Smith-Magenis syndrome. Presumed association of RAI1 gene variant c.5254G>A with isolated HL needs to be proved by further experimental studies.

Original languageEnglish (US)
Article numbere0153841
JournalPLoS One
Volume11
Issue number4
DOIs
StatePublished - Apr 1 2016

Fingerprint

Siberia
Exome
Audition
hearing
Hearing Loss
Genes
mutation
Mutation
genes
missense mutation
Missense Mutation
Smith-Magenis Syndrome
Founder Effect
Nonsyndromic Deafness
deafness
Genetic Heterogeneity
Deafness
Population Groups
founder effect
homozygosity

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Whole exome sequencing reveals homozygous mutations in RAI1, OTOF, and SLC26A4 genes associated with nonsyndromic hearing loss in Altaian families (South Siberia). / Churbanov, Alexander Y.; Karafet, Tatiana; Morozov, Igor V.; Mikhalskaia, Valeriia Yu; Zytsar, Marina V.; Bondar, Alexander A.; Posukh, Olga L.

In: PLoS One, Vol. 11, No. 4, e0153841, 01.04.2016.

Research output: Contribution to journalArticle

Churbanov, Alexander Y. ; Karafet, Tatiana ; Morozov, Igor V. ; Mikhalskaia, Valeriia Yu ; Zytsar, Marina V. ; Bondar, Alexander A. ; Posukh, Olga L. / Whole exome sequencing reveals homozygous mutations in RAI1, OTOF, and SLC26A4 genes associated with nonsyndromic hearing loss in Altaian families (South Siberia). In: PLoS One. 2016 ; Vol. 11, No. 4.
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abstract = "Hearing loss (HL) is one of the most common sensorineural disorders and several dozen genes contribute to its pathogenesis. Establishing a genetic diagnosis of HL is of great importance for clinical evaluation of deaf patients and for estimating recurrence risks for their families. Efforts to identify genes responsible for HL have been challenged by high genetic heterogeneity and different ethnic-specific prevalence of inherited deafness. Here we present the utility of whole exome sequencing (WES) for identifying candidate causal variants for previously unexplained nonsyndromic HL of seven patients from four unrelated Altaian families (the Altai Republic, South Siberia). The WES analysis revealed homozygous missense mutations in three genes associated with HL. Mutation c.2168A>G (SLC26A4) was found in one family, a novel mutation c.1111G>C (OTOF) was revealed in another family, and mutation c.5254G>A (RAI1) was found in two families. Sanger sequencing was applied for screening of identified variants in an ethnically diverse cohort of other patients with HL (n = 116) and in Altaian controls (n = 120). Identified variants were found only in patients of Altaian ethnicity (n = 93). Several lines of evidences support the association of homozygosity for discovered variants c.5254G>A (RAI1), c.1111C>G (OTOF), and c.2168A>G (SLC26A4) with HL in Altaian patients. Local prevalence of identified variants implies possible founder effect in significant number of HL cases in indigenous population of the Altai region. Notably, this is the first reported instance of patients with RAI1 missense mutation whose HL is not accompanied by specific traits typical for Smith-Magenis syndrome. Presumed association of RAI1 gene variant c.5254G>A with isolated HL needs to be proved by further experimental studies.",
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