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Table 1 TMC1 novel dominant variants and their pathogenicity prediction analysis

From: Novel autosomal dominant TMC1 variants linked to hearing loss: insight into protein-lipid interactions

Proband

Genomic Position:

Change

(GRCh37/hg19)

HGVS

Location (Exon/Domain)

Zygosity

/Inheritance

In silico Predictions

Alternative Allele Frequency

ACMG/AMP 2018 Guideline

Clinvar

Nucleotide change

Amino Acid change

CADD Phred

REVEL

KRGDB

(1722 individuals)

GMAF

(gnomAD)

Criteria

Classification

Classification

SH 386–847

Chr9:75406833T-C

c.1256T > C

p.Phe419Ser

Exon 16/TM4

Het/AD

25.8

0.832

Absent

Exome (0.00001194)

Genome (Absent)

PM2, PP3

VUS

ND

SH 676–1332

Chr9:75407146T-C

c.1444T > C

p.Trp482Arg

Exon 17/Linker between TM5/6

Het/AD

28

0.701

0.000293945

Exome (0.000003977)

Genome (Absent)

PM2, PP1, PP3

VUS

ND

  1. * Het, heterozygote; AD, Autosomal dominant; TM, Transmembrane domain; MAF, minor allele frequency; VUS, variant uncertain significance; ND, not determined
  2. Refseq transcript accession number NM_138691.3; Refseq protein accession number NP_619636.2
  3. HGVS: Human Genome Variation Society (https://www.hgvs.org/); Sequence Variant Nomenclature (http://varnomen.hgvs.org/); CADD: Combined Annotation Dependent Depletion (https://cadd.gs.washington.edu/); REVEL: Rare Exome Variant Ensemble Learner (https://sites.google.com/site/revelgenomics/); KRGDB: Korean Reference Genome Database (http://coda.nih.go.kr/coda/KRGDB/index.jsp); gnomAD: The Genome Aggregation Database (https://gnomad.broadinstitute.org/); ACMG/AMP 2018 guideline (http://wintervar.wglab.org/); Clinvar (https://www.ncbi.nlm.nih.gov/clinvar/)
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BMC Medical Genomics

ISSN: 1755-8794

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