Next-Generation Sequencing Identifies Pathogenic Variants in HGF, POU3F4, TECTA, and MYO7A in Consanguineous Pakistani Deaf Families

Table 1

Characterization and classification of the pathogenic variants.

Gene	Variants	MutationTaster	PROVEAN^a	SIFT^b	PolyPhen-2	ClinVar	MAF^c	ACMG classification^d
TECTA (NM_005422.4)	c.536del (p. Leu180Serfs20)^e	Disease causing	—	—	—	—	0	Likely pathogenic
MYO7A (NM_001127180.2)	c.3719 G>A (p. Arg1240Gln)	Disease causing	Deleterious (-3.72)	Damaging (0.000)	Probably damaging	Pathogenic	0.0000745	Likely pathogenic
HGF (NM_000601.6)	482+1986-1988del	—	—	—	—	Pathogenic	0	Likely pathogenic
POU3F4 (NM_000307.5)	c.706G>A (p. Glu236Lys)^e	Disease causing	Deleterious (-4.0)	Damaging (0.000)	Probably damaging	—	0	Likely pathogenic

^aPROVEAN: negative score indicates deleterious, with the cut-off score set as −2.5. ^bSIFT: deleterious to neutral from scores 0 to 1, with the cut-off score set as 0.05. ^cThe MAF was shown from gnomAD database. ^dThe classification followed the ACMG guidelines for interpretation of sequence variants. ^eNovel variants identified in this study.