[Retracted] Identification of Hearing Loss-Associated Variants of PTPRQ, MYO15A, and SERPINB6 in Pakistani Families

Table 1

Genes, identified variants, and their American College of Medical Genetics and Genomics (ACMG) classification.

Family	Gene	cDNA change	Protein change	CADD	GnomAD	Mutation taster	Polyphen2	ACMG classification
GCFHL01	PTPRQ	c.55-2A>G	N/A	N/A	N/A	Disease causing	N/A	Pathogenic (PVS1, PM2, PP3, and PP5)
LUHL011	MYO15A	c.10208-10211insCCACCAGGCCCGTGCCTC	N/A	N/A	N/A	Disease causing	N/A	Pathogenic (PVS1, PM2, PP3, and PP5)
LUHL-01	SERPINB6	c.1079G>A	p.(Arg360Gln)	N/A	0.001	Disease causing	Benign	Likely pathogenic (PS3, PP2, PP3, and BP4)

CADD: Combined Annotation Dependent Depletion (https://cadd.gs.washington.edu/); GnomAD: https://gnomad.broadinstitute.org. PVS1: pathogenic very strong [null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single, or multiexon deletion) in a gene where LOF is a known mechanism of disease]; PM2: pathogenic moderate 2 [absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium]; PP3: pathogenic supporting 3 [multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.)]; PP5: pathogenic supporting 5 [reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation]; BP4: benign supporting 4 [benign computational verdict because of 1 benign prediction from GERP vs. no pathogenic predictions].