Table 2 KCNQ4 variants detected in the Korean population with an unknown hearing loss phenotype.

From: Overlooked KCNQ4 variants augment the risk of hearing loss

Groupa (n)

Individual

Sex

Nucleotide changeb

Amino acid change

Exon

Zygosity

Amino acid sequence conservation

dbSNPc

ESPd

gnomADe

KRGDBf

PP2g

MTh

SIFTi

CADDj

DVDk

CODA WES (298)

N065

M

c.2071 A > G

p.Ser691Gly

14/14

Het

Xenopus tropicalis

rs200757822

ND

0.0000119

ND

Dam (0.97)

DC (0.9)

Del (0)

27.6

Unknown significance

N056

M

c.1565 C > T

p.Thr522Met

11/14

Het

Xenopus tropicalis

rs748693577

ND

0.0000359

ND

Dam (0.964)

DC (0.9)

Tol (0.13)

23

Unknown significance

CODA597, N163

M F

c.1339 C > T

p.Arg447Trp

10/14

Het

Gallus gallus

rs758333323

ND

0.0000335

ND

Dam (0.446)

Neu (0.98)

Del (0.02)

24.7

Unknown significance

N079

F

c.682 G > T

p.Gly228Cys

4/14

Het

Danio rerio

rs367890569

0.000116

0.00001282

ND

Dam (0.977)

DC (1)

Del (0)

33

Unknown significance

CODA WGS (252)

SP000113_hg38, SP000072_hg38

F F

c.1258 C > T

p.Arg420Trp

9/14

Het

Mus musculus

rs576041348

ND

0.0002

0.00136364

Dam (0.548)

DC (0.9)

Del (0.02)

25.5

Unknown significance

SP000217_hg38

F

c.1183 C > T

p.Arg395Trp

9/14

Het

Gallus gallus

rs373405864

0

0.0000487

0.000454545

Ben (0)

DC(1)

Del(0.03)

23.9

Unknown significance

KNIH (397)

NIH1609693850

NA

c.1165 G > A

p.Ala389Thr

9/14

Het

Gallus gallus

ND

ND

ND

ND

Ben (0.007)

DC (1)

Tol (0.23)

22.4

ND

SNU (445)

061293N-58N

NA

c.647 G > A

p.Arg216His

4/14

Het

Danio rerio

ND

ND

ND

ND

Dam (0.966)

DC (1)

Del (0)

33

ND

130720-I433-L6-61, 195 N

NA

c.1258 C > T

p.Arg420Trp

9/14

Het

Mus musculus

rs576041348

ND

0.0002

0.00136364

Dam (0.548)

DC (0.9)

Del (0.02)

25.5

Unknown significance

080223N-139N

NA

c.554 C > G

p.Ser185Trp

4/14

Het

Danio rerio

ND

ND

ND

ND

Dam (0.991)

DC (1)

Del (0)

32

ND

130703-I297-L5-70

NA

c.1807G > A

p.Gly603Arg

13/14

Het

Xenopus tropicalis

rs755220278

ND

0.000004044

ND

Ben (0.368)

DC (0.7)

Tol (0.3)

18.96

Unknown significance

092932N-250N

NA

c.460 G > T

p.Ala154Ser

3/14

Het

Danio rerio

ND

ND

ND

ND

Dam (0.999)

DC (1)

Tol (0.11)

25.8

ND

Pat05-11252

NA

c.1110 C > A

p.Asp370Glu

8/14

Het

Xenopus tropicalis

ND

ND

ND

ND

Dam (0.991)

DC (0.9996)

Tol (1)

19.33

ND

092840N-248N

NA

c.634 C > A

p.Leu212Met

4/14

Het

Danio rerio

ND

ND

ND

ND

Dam (0.969)

DC (1)

Del (0)

27.5

ND

092659N-238N

NA

c.262 T > C

p.Tyr88His

1/14

Het

Danio rerio

rs1429420446

ND

0.00003215

ND

Dam (0.502)

DC (0.9)

Del (0.01)

29.2

Unknown significance

  1. Ben benign, Dam probably damaging, Del deleterious, Neu neutral, DC disease-causing, Tol tolerated, Het heterozygous in the affected individual, F female, M male, ND no data or DNA not available, Neu neutral.
  2. aGroup indicates cohorts in which individuals with variants were found, comprising CODA, KNIH, and SNU.
  3. bVariants are numbered according to the human cDNA reference sequence NM_004700.4 (KCNQ4).
  4. cdbSNP database (http://www.ncbi.nlm.nih.gov/SNP).
  5. dExome Sequencing Project (https://evs.gs.washington.edu/EVS/).
  6. ePopulation frequency of KCNQ4 variants in gnomAD (https://gnomad.broadinstitute.org/).
  7. fThe Korean Reference Genome Database (http://coda.nih.go.kr/coda/KRGDB/index.jsp).
  8. gPolyPhen-2 HumVar prediction score (http://genetics.bwh.harvard.edu/pph2/).
  9. hMutationTaster (http://www.mutationtaster.org/).
  10. iSIFT Sorting Intolerant from Tolerant (http://sift.jcvi.org/).
  11. jphred-like scores (scaled C-scores) on the Combined Annotation-Dependent Depletion (http://cadd.gs.washington.edu/home/).
  12. kDeafness variation database (https://deafnessvariationdatabase.org/).
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