Exome sequencing reveals novel variants and unique allelic spectrum for hearing impairment in Filipino cochlear implantees

Graphical Abstract

To the Editor:

Genetic hearing impairment is mostly nonsyndromic (80%), and >6,000 causal variants in >100 genes have been identified. Generally in hearing-impaired patients of Asian descent, GJB2 variants are most common (36%), followed by variants in SLC26A4 (MIM 605646), MYO15A (MIM 602666) and CDH23 (MIM 605516).¹ Here we report seven novel variants in Filipino cochlear implantees, suggesting that the allelic spectrum for non-/syndromic hearing impairment in Filipinos is unique.

The UP Manila Research Ethics Board approved the study. Adult subjects and parents of pediatric patients provided informed consent. DNA samples and clinical data were obtained from 30 cochlear implantees with bilateral, severe-to-profound, congenital, non-progressive hearing loss as previously described.^2–3 After excluding one patient with GJB2 c.[35delG];[235delC],² twenty-nine DNA samples were submitted for exome sequencing, of which four are homozygous for SLC26A4 c.706C>G (p.(Leu236Val)).³ For the twenty-five GJB2-/SLC26A4-negative patients, homozygous/heterozygous coding variants within 132 non-/syndromic hearing impairment genes were selected if with MAF<0.005 in any gnomAD population. Rare variants were selected further if considered damaging by MutationTaster and/or >2 dbNSFP tools. Eleven Filipino-descent US families with no history of hearing impairment were ascertained for MAF estimation for speech delay (SDFIL) and were Sanger-sequenced for selected exome variants. Variants with zero MAF in the SDFIL cohort were then screened using samples from >88 unrelated Filipinos from the Cebu Longitudinal Health and Nutrition Survey, a cohort examined for various health outcomes. Screened exome variants were excluded due to increased MAF, lack of a second rare variant in an autosomal recessive gene and/or poor clinical correlation.

Of 30 Filipino cochlear implantees, we identified a genetic cause in sixteen (53%). Seven novel hearing loss variants were discovered (Table 1): CHD7 (MIM 608892) c.7312C>G (p.(Gln2438Glu)); COL4A3 (MIM 120070) c.764C>T (p.(Thr255Met)); DFNA5 (MIM 600994) c.1277_1279delATG (p.(Asp426del)); EYA4 (MIM 603550) c.1109G>A (p.(Arg370His)); MYH14 (MIM 608568) c.2971G>A (p.(Glu991Lys)); MYO15A c.263C>T (p.(Thr88Met)); and OTOA (MIM 607038) c.2301+1G>T. Patient #28 with the CHD7 variant has microcephaly and seizures, both known features of CHARGE syndrome (MIM 214800). Additionally he has left superior semicircular canal dehiscence (SSCD)³ but no vertigo or dizziness. Both DFNA5 c.1277_1279delATG and EYA4 c.1109G>A were previously identified through systematic clinical genetic screening and are annotated in ClinVar as variants of unknown significance. Patient #4 with the EYA4 variant complains of dizziness and balance problems; temporal bone findings include right enlarged vestibular aqueduct and a left jugular bulb diverticulum that impinges onto the ipsilateral vestibular aqueduct.³ COL4A3 c.764C>T was previously reported for familial kidney disease⁴ but not hearing impairment. MYH14 c.2971G>A is cited in LOVD as likely benign but was not clarified for nonsyndromic DFNA4A (MIM 600652) or peripheral neuropathy, myopathy, hoarseness and hearing loss (PNMHH; MIM 614369). This MYH14 variant is the only rare, damaging variant identified in patient #26, who has developmental delay and left foot inversion.

Table 1.

Pathogenic/likely pathogenic variants in Filipino cochlear implantees identified in this study^†

ID	Geno- type	Gene	Expected MOI	RefSeq NM_	cDNA Variant	Amino Acid Variant	Damaging Prediction	CADD	gnomAD MAF Overall	gnomAD MAF NFE	gnomAD MAF EAS
2‡	Het	DFNA5	DFNA5	004403	c.1277_1279delATG	p.(Asp426del)	MT	--	0.0006	0	0.0005
4§	Het	EYA4	DFNA10	004100	c.1109G>A	p.(Arg370His)	Fa,LRT,mLR, mSVM,MA,MT, PP2_HD/HV, PR,SI	35	0.00004	0.00006	0
10‡	Het	KCNQ4	DFNA2A	004700	c.546C>G	p.(Phe182Leu)	MT	22	0.0003	0	0.004
14¶	Hom	OTOA	DFNB22	144672	c.2301+1G>T	NA	MT	27.1	0	0	0
15‡	Cpd het	CDH23	DFNB12; AR USH1D	022124	c.68–3C>T	NA	MT	--	0.0005	0.000008	0.008
15‡	Cpd het	CDH23	DFNB12; AR USH1D	022124	c.4762C>T	p.(Arg1588Trp)	LRT,MA,MT, PP2_HD/HV, PR,SI	23.3	0.0002	0.00007	0.001
16	Het	WFS1	DFNA6/14/38; AD/AR Wolfram	006005	c.708C>G	p.(Ser236Arg)	Fa,LRT,mLR,MT	12.9	0	0	0
17‡	Hom	MYO15A	DFNB3	016239	c.263C>T	p.(Thr88Met)	Fa, PP2_HD	18.6	0.00007	0	0
21	Het	COL4A3	AD/AR Alport	000091	c.764C >T	p.(Thr2 55Met)	Fa,mLR,mSVM, MT,PP2_HD/HV,SI	33	0.00009	0.000009	0.00006
26	Het	MYH14	DFNA4A; AD PNMHH	001145809	c.2971G >A	p.(Glu991Lys)	Fa,mLR,mSVM,MA,MT,PP2_HD/HV,PR,SI	28.9	0.00001	0	0.00007
28	Het	CHD7	AD CHARGE	017780	c.731 2C> G	p.(Gln24 38Glu)	LRT,MT, PP2_HD/HV	25.3	0	0	0

^†All variants listed were not found in Filipino controls from SDFIL and CLHNS. Novel variants are in bold font.

^‡Confirmed to have nonsyndromic hearing impairment (if including GJB2-/SLC26A4-positive patients, total 9 of 15 or 60% of those with genetic variants).

^§Prior to surgery, patient #4 had a steeply sloping audiogram with 45–50 dB hearing at 500–1000 kHz and profound loss at 4000 Hz. All other patients listed in Table 1 had flat audiograms with severe-to-profound hearing loss. Additional clinical information on these patients were previously provided in reference #3.

^¶Patient #14 has global developmental delay and a history of maternal rubella, low birth weight, exchange transfusion for jaundice, antibiotic treatment and mechanical ventilation for neonatal pneumonia, and intraventricular hemorrhage.

Abbreviations: AD, autosomal dominant; AR, autosomal recessive; CADD, Combined Annotation-Dependent Depletion; Cpd het, compound heterozygous; DFNA#, nonsyndromic autosomal dominant hearing loss; DFNB#, nonsyndromic autosomal recessive hearing loss; EAS, East Asian; Fa, FATHMM; gnomAD, Genome Aggregation Database; HD, HumDiv; Het, heterozygous; Hom, homozygous; HV, HumVar; LRT, Likelihood Ratio Test; MA, MutationAssessor; MAF, minor allele frequency; mLR, MetaLR; MT, MutationTaster; mSVM, MetaSVM; NFE, non-Finnish European; PNMHH, peripheral neuropathy, myopathy, hoarseness and hearing loss; PP2, PolyPhen2; PR, PROVEAN; RefSeq, Reference Sequence; SI, SIFT; USH1D, Usher syndrome Type I

Variants CDH23 c.68–3C>T and c.4762C>T (p.(Arg1588Trp)), KCNQ4 (MIM 603537) c.546C>G (p.(Phe182Leu)), and WFS1 (MIM 606201) c.708C>G (p.(Ser236Arg)) have been previously reported for hearing impairment. Patient #10 with the KCNQ4 variant has SSCD on the left³ but no vestibular symptoms. WFS1 c.708C>G was reported in a patient with compound heterozygous WFS1 variants and autosomal recessive Wolfram syndrome (MIM 222300).⁵ Patient #16 has no second WFS1 coding variant but has birth history of cord coil, white matter disease and mild motor delay.

Clinical data helped identify the correct gene when multiple potentially causal variants were present. Patients with pathogenic variants had higher pre-surgical audiometric thresholds at >1kHz (Wilcoxon p<0.05). However there was no significant difference in post-surgical thresholds, suggesting that carriage of the genetic variants reported here does not determine the outcome of cochlear implantation, with average implant-aided hearing at 38dB across frequencies. Therefore for carriers of these variants, cochlear implantation remains an excellent option for rehabilitation.