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. 2022 Jan 7;12:301. doi: 10.1038/s41598-021-04081-2

Table.2.

Relevant Variants identified by WES.

ID Gene
(Transcript ID)		 Genotype Change dbSNP Phenotype of patient Segregation (inheritance) Reference ClinVar report After curation Criteria applied
1

CDH23

(NM_022124.5)

 c.337del p.(Val113*) –

Usher syndrome

PL, PR, B, PF, CI

 Maternal This work – Pathogenic PM2, PVS1, PM3, PP4
c.3353del p.(Gly1118Alafs*7) – Paternal This work – Pathogenic PM2, PVS1, PM3 and PP4
2

MYO6

(NM_004999.4)

 c.1939T > C p.(Phe647Leu) rs752585373 PL, B, M Non available This work – VUS PM2, PP3
3

EYA4

NG_011596.2 (NM_004100.5)

 c.580+2T > C splicing – PL, B, M Maternal This work – Pathogenic PM2, PVS1, PP1_Sup
4

MYO7A

NG_009086.2 (NM_000260.4)

 c.733C > T p.(Gln245*) – C, PL, B, PF, CI Maternal This work – Pathogenic PVS1, PM2, PM3
c.1344-2A > G Splicing rs111033415 Paternal 65 Pathogenic Pathogenic PM2, PVS1, PM3_S, PP4
5

LARS2

(NM_015340.3)

 c.1481dup p.(Leu495Thrfs*31) rs762797278 C, B, PF, CI Paternal This work – Pathogenic PVS1, PM2, PM3, PP1_Sup
c.1886C > T p.Thr629Met rs398123036 Maternal 16 Pathogenic Likely Pathogenic PM2, PM3_S, PP1_Sup, PP4
6

ADGRV1

/GPR98

(NM_032119.3)

 c.12829C > T p.(Arg4277*) –

Usher syndrome

B, P, PR

 Non available father This work – Pathogenic PVS1, PM2, PM3, PP1_Sup, PP4
c.956dup p.(Asn319Lysfs*6) rs752179149 Maternal 66 Pathogenic Pathogenic PVS1, PM2, PM3, PP1_Sup, PP4
7

MITF

(NM_000248.3)

 c.877C > T p.(Arg293*) – C, B, PF, CI Segregation confirmed 15 – Pathogenic PM2, PVS1_S, PP1_S
8

TMPRSS3

(NM_024022.3)

 c.1276G > A p.Ala426Thr rs56264519 PL, B. sloping audiometry Maternal inheritance 67

Pathogenic/

Likely Path

 Pathogenic BS1_Sup, PM3_VS, PP1_S, PS3_Sup
c.242C > G p.(Ser81*) rs757110501 Paternal inheritance This work – Pathogenic PVS1, PM2, PM3, PP1_Sup
9

WFS1

(NM_006005.3)

 c.2590G > A p.(Glu864Lys) rs74315205 B, CI 68

Pathogenic/

Likely Path

 Likely Pathogenic PM2, PS4_M, PP1_Mod, PP3
10

USH2A

NG_009497.2 (NM_206933.4)

 c.1841-2A > G Splicing rs397518003 PR, B, M. No retinopathies Maternal inheritance 69 Pathogenic Pathogenic PM2, PM3_VS,PP4 PP1_M, PS3_S
c.10712C > T p.(Thr3571Met) rs202175091 Paternal inheritance 70

Pathogenic/

Likely Path

 Pathogenic PM2, PM3_VS, PP4, PP1_M
11

CDH23

NG_008835.1 (NM_022124.5)

 c.1096G > A p.(Ala366Thr) rs143282422

B, High-frequency affected

No retinopathies

 Maternal 71 Benign Benign BA1
c.1515-12G > A splicing rs369396703 Paternal – VUS (validated by HL–EP) Likely Pathogenic PM2_Sup, PM3, PP1_Sup, PP3, PP4
12

COL4A3

(NM_000091.5)

 c.3500G > A p.(Gly1167Glu) – Alport Syndrome. Hematuria De novo (maternal) This work – Pathogenic PM2, PS2, PM1, PM5, PP3
c.4649T > G p.(Val1550Gly) rs200655479 72 Conflicting Interpretation (VUS/LP) VUS PM2_Sup, PP3
13

DFNA5

(NM_004403.2)

 c.119dup p.(Lys41Glufs*113) rs758488919 No familial history De novo – Conflicting Interpretation (VUS/LB) Benign BA1, PS2
14

COL4A5

(NM_000495.3)

 c.1183C > T p.(Pro395Ser) – C, B, S This work – VUS PM2
15

COL4A5

(NM_000495.3)

 c.1759C > T p.(Pro587Ser) – PL, PR, B, M This work – VUS PM2, PP3
16

COL4A5

(NM_000495.3)

 c.3659G > A p.(Gly1220Asp) rs104886251 Alport Syndrome. Hematuria 73 Pathogenic Pathogenic PM2, PM1, PP3, PP4, PS4_Sup
17

WFS1

(NM_006005.3)

 c.2327A > T p.(Glu776Val) rs56002719 B, M, PR. High frequencies Maternal inheritance 74 Conflicting Interpretation (VUS/B/LB) Benign BA1, PP3, PP1_Sup, BS4
18

TECTA

(NM_005422.4)

 c.5668C > T p.(Arg1890Cys) rs121909063 PL, M-S Segregation confirmed. Paternal Inheritance 75 Likely pathogenic Pathogenic PM2, PP1_VS, PS4_Sup
19 LOXHD1 (NM_144612.6)

c.4480C > T

(homozygous)

 p.(Arg1494*) rs201587138 C, B, PF Segregation confirmed 76

Pathogenic/

Likely Path

 Pathogenic PVS1, BS1_Sup, PM3_S, PP1_M
20

ACTG1

(NM_001614.5)

 c.353A > T p.(Lys118Met) rs104894544 PL, B, M-S Segregation confirmed. Paternal Inheritance 77 Likely pathogenic Pathogenic PS4_Sup, PM2, PP5, PP1_S,PP3

All variants were curated following the Hearing Loss Expert Panel recommendations. The phenotype of the patients is indicated as follows: C congenital, PL postlingual, PR progressive, B bilateral, M moderate, PF profound, S severe, CI cochlear implanted.