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Table 2 Detailed information for candidate variants

From: Whole exome sequencing identified mutations causing hearing loss in five consanguineous Pakistani families

Pedigree

Variant

RS_number

Gene

Strand

DNA change

AA change

Type

SIFT (score)

PolyPhen2 (score)

MutationTaster (score)

CADD (score)

ACMG classify

HL1

19–3,590,186-T-C

rs1466835034

GIPC3

+

c.937 T > C

p.*313Gluext*98

homozygous

NA

NA

Polymorphism

Benign

Likely pathogenic

(NA)

(NA)

(not provided)

(11.43)

(PM2 + PM4 + PP1 + PP4)

HL2

18–44,063,569-C-T

rs774836161

LOXHD1

c.6136G > A

p.Glu2046Lys

homozygous

Damaging

Damaging

disease_causing

Damaging

Uncertain significance

(0.016)

(0.995)

(not provided)

(29.2)

(PM2 + PP1 + PP3 + PP4)

HL3

11–121,016,765-G-A

rs141024429

TECTA

+

c.4045G > A

p.Ala1349Thr

homozygous

Tolerated

Benign

disease_causing

Benign

Uncertain significance

(0.058)

(0.061)

(not provided)

(23.2)

(PM2 + PP1 + PP3 + PP4)

HL3

17–18,025,424-G-T

rs919809633

MYO15A

c.3310G > T

p.Gly1104Cys

compound heterozygous

Damaging

Benign

Polymorphism

Benign

Uncertain significance

(0)

(0.011)

(not provided)

(15.33)

(PM2 + PP1 + PP3 + PP4)

HL3

17–18,069,800-G-C

rs535441567

MYO15A

c.9913G > C

p.Glu3305Gln

compound heterozygous

Damaging

Damaging

disease_causing

Damaging

Uncertain significance

(0.007)

(0.83)

(not provided)

(27.9)

(PM2 + PP1 + PP3 + PP4)

HL4

2–179,320,814-G-A

NA

DFNB59

c.494G > A

p.Ser165Asn

homozygous

Damaging

Damaging

disease_causing

Damaging

Uncertain significance

(0.02)

(0.931)

(not provided)

(25.2)

(PM2 + PP3 + PP4)

HL4

22–38,120,515-C-T

rs760246167

TRIOBP

+

c.1952C > T

p.Ser651Phe

homozygous

Damaging

Benign

Polymorphism

Benign

Uncertain significance

(0.003)

(0.036)

(not provided)

(15.1)

(PM2 + PP3 + PP4)

HL5

21–43,795,850-A-G

NA

TMPRSS3

c.941 T > C

p.Leu314Pro

homozygous

Damaging

Damaging

disease_causing

Damaging

Uncertain significance

(0.001)

(1)

(not provided)

(28.9)

(PM2 + PP1 + PP3 + PP4)